Contacts of the helix formed by residues 127 - 151 (chain B) in PDB entry 3NA1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU 3.4 16.8 + - - -
124B ALA* 3.1 20.4 + - - +
125B THR 3.0 1.0 - - - -
126B LYS* 1.3 88.2 - - - +
128B PHE* 1.3 63.4 + - - +
129B LEU 3.3 1.0 + - - -
130B PRO* 3.6 15.7 - - - +
131B LEU* 4.0 12.8 - - - +
259B TYR* 3.5 49.3 - - + +
265B ARG* 3.9 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU 3.4 21.5 - - - -
119B VAL* 3.9 4.0 - - - -
124B ALA 4.0 7.4 - - - -
125B THR* 2.8 43.4 + - + +
127B ASN* 1.3 79.8 - - - +
129B LEU* 1.3 64.8 + - - +
130B PRO 3.5 0.4 - - - -
131B LEU* 3.1 5.7 + - - +
132B LEU* 2.9 37.0 + - + +
174B VAL* 3.2 27.4 - - + -
259B TYR* 3.2 27.4 - + - -
262B ILE* 3.9 15.7 - - + -
428B ILE* 3.6 31.2 - - + -
431B LEU* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR 4.2 4.3 - - - +
126B LYS* 3.4 17.9 - - + +
128B PHE* 1.3 75.7 - - - +
130B PRO* 1.4 65.5 - - + +
132B LEU* 3.8 1.0 - - - +
133B ASP* 2.9 33.5 + - - +
328B MET* 4.6 7.2 - - + -
329B ALA* 3.6 41.1 - - + +
332B LEU* 3.8 15.5 - - + -
431B LEU* 3.7 39.3 - - + -
435B ILE* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS 4.2 3.1 - - - +
127B ASN* 3.6 16.4 - - - +
129B LEU* 1.4 96.3 - - + +
131B LEU* 1.3 61.8 + - + +
133B ASP* 4.0 5.3 - - + +
134B ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN 4.0 9.9 - - - +
128B PHE* 3.1 7.9 + - - +
130B PRO* 1.3 82.6 - - + +
132B LEU* 1.3 63.0 + - - +
134B ALA* 3.8 1.6 + - - +
135B VAL* 3.4 14.0 + - - +
173B ASN* 2.8 60.2 + - + +
174B VAL* 4.1 17.7 - - + +
177B GLY* 4.7 11.9 - - - +
259B TYR* 3.8 35.7 - - + +
260B ARG 5.6 0.4 - - - -
261B GLY* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 2.9 34.6 + - + +
129B LEU 4.0 2.5 - - - +
131B LEU* 1.3 74.6 - - - +
133B ASP* 1.3 64.8 + - - +
135B VAL* 3.1 7.9 + - - +
136B SER* 3.1 24.5 + - - +
166B PHE* 5.1 1.0 - - - -
170B SER* 4.0 37.7 + - - +
174B VAL* 4.6 10.1 - - + -
428B ILE* 4.1 10.5 - - + +
431B LEU* 3.7 17.7 - - + -
432B GLU* 3.7 39.0 - - + +
435B ILE* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU 2.9 19.5 + - - +
130B PRO* 4.0 5.6 - - + +
132B LEU* 1.3 74.8 - - - +
134B ALA* 1.3 59.6 + - - +
136B SER 3.3 0.3 + - - -
137B ARG* 2.9 58.2 + - - +
321B ARG* 5.3 1.2 + - - -
328B MET* 3.8 30.4 - - + +
435B ILE* 3.5 13.0 - - + +
439B ASN* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PRO 3.0 20.2 + - - +
131B LEU* 3.9 7.2 - - + +
132B LEU 3.3 0.2 - - - -
133B ASP* 1.3 75.2 - - - +
135B VAL* 1.3 61.7 + - - +
137B ARG* 3.6 8.9 + - - +
138B ASP* 3.2 28.4 + - - +
173B ASN* 4.8 3.4 - - - +
179B ARG* 3.9 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 3.4 16.4 - - - +
132B LEU* 3.1 7.8 + - - +
134B ALA* 1.3 73.0 - - - +
136B SER* 1.3 60.2 + - - +
138B ASP* 3.1 5.7 + - - +
139B PHE* 2.9 24.1 + - - +
166B PHE* 3.7 14.8 - - + -
169B GLU* 3.7 37.0 - - + +
170B SER* 3.6 22.4 - - - +
173B ASN* 3.8 14.8 - - + +
179B ARG* 3.9 19.5 - - - +
183B LEU* 3.5 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.1 14.0 + - - +
133B ASP 3.8 1.6 - - - -
135B VAL* 1.3 74.6 - - - +
137B ARG* 1.3 64.9 + - - +
139B PHE* 3.2 5.3 + - - +
140B VAL* 3.1 25.8 + - - +
166B PHE* 3.4 21.9 - - - -
432B GLU 4.4 1.2 + - - -
435B ILE* 4.0 3.7 - - - +
436B PHE* 3.3 29.2 + - - -
439B ASN* 3.5 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASP* 2.9 48.5 + - - +
134B ALA* 3.8 8.3 - - - +
135B VAL 3.3 0.2 - - - -
136B SER* 1.3 74.1 - - - +
138B ASP* 1.3 66.5 + - - +
140B VAL* 3.3 9.2 + - - +
141B SER* 3.1 23.4 + - - -
321B ARG* 4.6 19.8 - - - +
439B ASN* 3.8 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA 3.2 7.4 + - - +
135B VAL 3.1 10.1 + - - +
137B ARG* 1.3 77.5 - - - +
139B PHE* 1.3 64.8 + - - +
141B SER* 3.1 12.1 + - - -
142B VAL* 3.0 25.5 + - - +
145B ARG* 5.0 0.5 + - - -
179B ARG* 2.7 41.3 + - - +
183B LEU* 4.0 11.9 - - + -
184B GLU* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL 2.9 12.6 + - - +
136B SER* 3.2 10.0 + - - +
138B ASP* 1.3 75.1 - - - +
140B VAL* 1.3 62.7 + - + +
142B VAL* 3.3 11.4 + - + +
143B LEU* 3.2 43.4 + - + +
159B ILE* 4.3 13.2 - - + -
162B ASP* 3.6 40.4 - - + -
163B LEU* 4.0 15.5 - - + -
166B PHE* 3.8 25.6 - - + -
183B LEU* 3.6 18.5 - - + +
436B PHE* 3.5 29.8 - + + -
440B MET* 4.1 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER 3.1 15.8 + - - +
137B ARG* 3.5 10.3 - - - +
139B PHE* 1.3 76.8 - - + +
141B SER* 1.3 57.4 + - - +
143B LEU 3.2 2.9 + - - -
144B HIS* 3.0 39.5 + - + +
439B ASN* 3.7 38.4 - - + +
440B MET* 4.3 7.4 - - - +
443B ASN* 3.5 29.4 - - + +
444B PHE* 3.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG 3.1 14.6 + - - -
138B ASP* 3.1 16.2 + - - -
140B VAL* 1.3 75.2 - - - +
142B VAL* 1.3 64.5 + - - +
144B HIS* 3.3 10.1 + - - +
145B ARG* 3.0 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP* 3.0 20.3 + - + +
139B PHE* 3.4 15.3 - - + +
141B SER* 1.3 77.0 - - - +
143B LEU* 1.3 66.2 + - + +
145B ARG* 3.2 20.1 + - - +
146B ARG* 3.0 52.9 + - + +
162B ASP* 5.3 3.1 - - + +
183B LEU* 3.3 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.2 24.6 + - + +
140B VAL 3.2 3.2 + - - +
142B VAL* 1.3 81.7 - - + +
144B HIS* 1.3 57.8 + - - +
146B ARG* 3.2 12.0 + - - +
147B ILE* 2.9 36.0 + - + +
155B TYR* 4.2 28.4 - - + +
159B ILE* 4.5 8.7 - - + -
162B ASP* 6.5 0.4 - - + -
440B MET* 3.6 35.4 - - + -
444B PHE* 3.5 26.9 - - + -
472B PHE* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.0 33.2 + - + +
141B SER* 3.7 10.8 - - - +
143B LEU* 1.3 75.6 - - - +
145B ARG* 1.3 62.3 + - + +
147B ILE* 3.5 11.2 + - - +
148B LYS* 3.1 23.2 + - - +
443B ASN* 3.1 33.6 + - - -
444B PHE* 3.6 20.1 - + - -
474B PRO* 4.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP 5.0 0.4 + - - -
141B SER* 3.0 40.2 + - - +
142B VAL* 3.5 31.8 - - - +
144B HIS* 1.3 74.8 - - + +
146B ARG* 1.3 60.4 + - + +
148B LYS* 3.1 9.5 + - - +
149B LYS* 2.9 31.2 + - - +
183B LEU 4.2 7.7 + - - -
184B GLU* 4.9 10.3 + - - +
185B GLU* 5.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.0 36.8 + - + +
143B LEU* 3.2 12.0 + - - +
145B ARG* 1.3 75.9 - - + +
147B ILE* 1.3 56.8 + - - +
149B LYS* 3.9 8.1 - - + +
150B ALA* 3.0 31.0 + - - +
155B TYR* 3.2 59.5 + - + -
158B ASP 5.6 0.2 + - - -
159B ILE* 4.3 4.0 - - - +
162B ASP* 2.7 45.7 + - - -
165B ARG* 4.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 2.9 16.0 + - + +
144B HIS* 3.6 10.8 - - - +
145B ARG 3.2 0.2 - - - -
146B ARG* 1.3 75.3 - - - +
148B LYS* 1.3 65.2 + - - +
150B ALA* 3.3 3.6 + - - +
151B GLY* 3.2 18.4 + - - -
153B GLY* 3.9 13.4 + - - -
154B ASN 3.9 23.6 - - - +
155B TYR* 3.7 21.8 - - + +
444B PHE* 3.6 37.0 - - + -
472B PHE* 3.9 15.7 - - + +
474B PRO* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B HIS 3.1 14.5 + - - +
145B ARG* 3.1 11.9 + - + +
147B ILE* 1.3 77.9 - - - +
149B LYS* 1.3 60.9 + - - +
151B GLY* 3.4 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 5.2 7.5 + - - -
467A PRO* 3.4 18.9 - - - +
145B ARG 2.9 17.0 + - - +
146B ARG* 3.9 9.2 - - + +
148B LYS* 1.3 76.5 - - - +
150B ALA* 1.3 64.9 + - - +
151B GLY* 3.1 1.4 + - - -
185B GLU* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PRO* 3.8 24.7 - - - +
469A SER* 6.5 1.3 - - - -
146B ARG 3.0 19.4 + - - +
147B ILE 3.7 0.7 - - - +
149B LYS* 1.3 77.3 - - - +
151B GLY* 1.3 57.7 + - - +
152B SER* 3.3 9.8 + - - +
154B ASN* 3.4 23.3 - - - +
155B TYR* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS* 4.0 16.6 + - - +
467A PRO* 4.2 11.0 - - - -
147B ILE 3.2 9.2 + - - -
148B LYS 3.4 11.9 + - - -
149B LYS 3.1 4.4 - - - -
150B ALA* 1.3 75.8 - - - +
152B SER* 1.3 59.1 + - - +
153B GLY 3.6 3.4 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il