Contacts of the helix formed by residues 116 - 135 (chain B) in PDB entry 3NUI
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 SER 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN* 3.6 14.8 - - - -
119A GLU* 2.5 29.3 + - - -
114B THR* 2.8 19.6 + - - -
115B ASN* 1.3 80.0 - - - +
117B GLY* 1.3 64.2 + - - +
118B SER* 3.5 4.7 + - - -
119B GLU* 3.2 14.8 + - - +
120B ALA* 3.0 8.8 + - - +
294B MET 4.0 3.1 - - - -
295B GLY* 3.5 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER* 1.3 72.8 - - - +
118B SER* 1.3 56.5 + - - +
120B ALA* 3.2 3.3 + - - +
121B ASN* 3.0 28.4 + - - +
258B VAL* 3.8 17.0 - - - +
282B ILE* 3.9 4.0 - - - +
283B SER 4.2 4.5 - - - -
284B SER* 3.2 34.2 - - - -
285B LYS* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 4.0 9.2 + - - +
116B SER* 3.1 9.8 + - - -
117B GLY* 1.3 75.0 - - - +
119B GLU* 1.3 65.3 + - - +
121B ASN* 3.3 7.7 + - - +
122B ASP* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 2.6 35.4 + - - -
118A SER* 4.6 3.8 - - - -
119A GLU* 3.4 16.7 + - + +
153A VAL* 5.4 7.0 - - + +
154A THR* 4.0 19.8 - - + +
114B THR* 3.6 15.5 - - + +
115B ASN* 2.9 36.7 + - - +
116B SER* 3.2 13.1 + - - +
118B SER* 1.3 78.2 - - - +
120B ALA* 1.3 57.4 + - - +
122B ASP* 3.4 7.8 + - - +
123B THR* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.5 22.8 + - + +
116B SER 3.0 8.4 + - - +
117B GLY 3.2 4.7 + - - +
119B GLU* 1.3 73.0 - - - +
121B ASN* 1.3 57.8 + - - +
123B THR* 3.3 0.6 + - - -
124B MET* 2.8 35.7 + - - +
282B ILE* 3.6 21.8 - - + -
283B SER 4.3 1.8 - - - +
296B ALA 3.7 22.2 - - - +
297B VAL* 3.6 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY 3.0 13.6 + - - +
118B SER* 3.4 12.3 - - - +
119B GLU 3.2 0.2 - - - -
120B ALA* 1.3 75.7 - - - +
122B ASP* 1.3 63.8 + - - +
124B MET* 3.1 5.4 + - - +
125B VAL* 3.0 29.5 + - - +
173B LEU* 6.1 0.8 - - - +
221B PHE* 3.7 22.7 - - - -
256B ASP* 3.8 17.3 - - - +
282B ILE* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 4.8 2.3 - - - +
154A THR* 3.3 20.0 - - + -
155A ALA* 2.9 39.7 + - - +
156A VAL 4.9 0.3 + - - -
118B SER 3.1 9.3 + - - +
119B GLU* 3.4 12.6 - - - +
121B ASN* 1.3 82.8 - - - +
123B THR* 1.3 55.8 + - - +
125B VAL* 3.4 8.5 + - - +
126B LYS* 3.0 34.7 + - - +
173B LEU* 4.0 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 5.6 4.5 + - - +
112B PHE* 5.1 7.6 - - + -
114B THR* 3.6 15.4 - - + +
119B GLU* 2.9 22.8 + - - +
120B ALA* 3.6 8.5 - - - -
122B ASP* 1.3 68.6 + - - +
124B MET* 1.3 69.0 + - - +
126B LYS* 3.3 10.4 + - - +
127B MET* 2.9 32.2 + - + +
297B VAL* 4.1 13.0 - - + -
320B GLY 4.9 7.0 + - - +
321B PHE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA 2.8 17.5 + - - +
121B ASN 3.5 7.9 - - - +
123B THR* 1.3 74.0 - - - +
125B VAL* 1.3 62.5 + - - +
127B MET* 3.2 12.2 + - - +
128B LEU* 3.0 26.6 + - + +
221B PHE* 3.7 18.4 - - + -
254B ILE* 4.0 23.6 - - + -
280B ALA* 3.0 35.0 - - + -
281B ILE 4.1 7.6 - - - +
282B ILE* 4.1 7.4 - - + -
297B VAL* 3.0 36.8 - - + +
299B LEU* 3.8 12.8 - - + -
303B LEU* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 3.0 27.6 + - - +
122B ASP 3.6 6.1 - - - +
124B MET* 1.3 77.6 - - - +
126B LYS* 1.3 63.3 + - - +
128B LEU* 3.1 9.6 + - - +
129B TRP* 3.0 57.8 + - + +
143B ILE* 4.1 19.3 - - + -
173B LEU* 4.1 20.4 - - + -
221B PHE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 2.8 38.0 + - - +
155A ALA* 4.5 5.2 - - + +
158A ALA* 4.3 6.5 - - - +
166A ASN* 4.6 1.6 + - - -
169A PHE* 3.4 51.2 - - + -
171A LEU* 3.9 14.8 - - + -
122B ASP* 3.0 28.7 + - - +
123B THR* 3.3 11.9 + - - +
125B VAL* 1.3 75.2 - - - +
127B MET* 1.3 57.1 + - - +
129B TRP* 3.3 25.3 + - + +
130B PHE* 2.8 30.0 + - - +
319B HIS* 4.2 10.3 + - - -
320B GLY* 5.4 1.2 + - - -
321B PHE* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.2 17.5 - - - -
123B THR* 2.9 23.7 + - - +
124B MET* 3.3 13.2 - - - +
126B LYS* 1.3 76.6 - - - +
128B LEU* 1.3 61.2 + - + +
130B PHE* 3.3 4.2 + - - +
131B LEU* 2.9 33.4 + - + +
297B VAL* 4.2 9.9 - - - -
299B LEU* 3.4 46.4 - - + -
303B LEU* 5.5 4.3 - - + +
307B LEU* 3.9 20.8 - - + +
321B PHE* 3.0 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 3.0 19.3 + - + +
125B VAL* 3.1 5.8 + - - +
127B MET* 1.3 77.0 - - + +
129B TRP* 1.3 66.3 + - - +
131B LEU* 3.3 8.0 + - + -
132B HIS* 2.9 37.6 + - + +
143B ILE* 4.1 9.9 - - + -
218B ALA* 3.7 31.4 - - + +
219B GLY* 4.5 3.4 - - - -
221B PHE* 3.9 26.9 - - + -
252B PRO* 3.9 24.0 - - + -
254B ILE* 4.6 8.7 - - + -
303B LEU* 4.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 4.4 10.1 - - + -
168A VAL 4.5 1.8 - - - -
169A PHE* 3.6 21.5 - - + +
171A LEU* 3.9 18.4 - - + -
173A LEU* 4.3 14.1 - - + -
125B VAL* 3.0 36.3 + - + +
126B LYS* 3.5 26.0 - - + +
128B LEU* 1.3 76.1 - - - +
130B PHE* 1.3 64.1 + - - +
132B HIS* 4.4 0.3 - - - +
133B ALA* 3.1 26.9 + - - +
140B LYS 4.2 5.5 - - - +
141B ARG* 2.9 81.3 + - + +
143B ILE* 5.7 0.4 - - + -
173B LEU* 4.2 16.4 - - + -
174B PRO 4.5 13.0 - - - -
218B ALA* 4.4 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 3.5 49.4 - - + +
169A PHE* 4.0 8.7 - + + -
126B LYS 2.8 18.1 + - - +
127B MET* 3.4 6.1 - - - +
128B LEU 3.1 0.2 - - - -
129B TRP* 1.3 76.5 - - - +
131B LEU* 1.3 63.7 + - - +
133B ALA* 3.8 1.9 - - - +
134B ALA* 2.9 31.3 + - + +
307B LEU* 4.0 21.3 - - + -
310B ALA* 4.6 7.2 - - + -
311B ILE* 4.2 12.3 - - + -
314B ILE* 4.1 21.4 - - + +
316B GLU* 3.6 21.5 - - + -
317B PHE 5.0 0.2 - - - -
318B PRO* 3.5 38.8 - - + -
321B PHE* 5.0 0.2 - + - -
----------------------------------------------------------
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 MET* 2.9 19.4 + - + +
128B LEU* 3.8 9.6 - - + +
130B PHE* 1.3 80.4 - - + +
132B HIS* 1.3 66.5 + - + +
134B ALA* 3.2 4.4 + - - +
135B GLU* 2.9 55.2 + - - +
303B LEU* 4.0 23.6 - - + +
306B ARG* 3.3 58.6 - - + +
307B LEU* 3.9 9.4 - - + +
310B ALA* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 2.9 30.4 + - - +
129B TRP 4.4 0.7 - - - +
131B LEU* 1.3 78.1 - - + +
133B ALA* 1.3 62.6 + - - +
135B GLU* 3.2 9.1 + - - +
136B GLY 3.2 5.2 + - - -
137B LYS* 2.8 27.7 + - + +
140B LYS* 3.6 55.9 - - + +
218B ALA* 2.8 46.1 + - + -
250B ASP 4.9 0.7 - - - -
252B PRO* 4.1 15.5 - - + +
306B ARG* 3.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A SER 6.0 0.7 - - - +
168A VAL* 4.3 12.1 - - - +
169A PHE 6.1 0.2 - - - -
170A GLY* 6.0 2.2 - - - +
129B TRP 3.1 19.0 + - - +
130B PHE 3.9 2.9 - - - +
132B HIS* 1.3 76.8 - - - +
134B ALA* 1.3 57.8 + - - +
136B GLY* 2.9 21.3 + - - -
137B LYS 3.7 1.0 + - - -
138B PRO* 3.9 30.8 - - + +
141B ARG* 6.4 0.2 - - - +
314B ILE* 5.6 0.9 - - + -
----------------------------------------------------------
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 PHE* 2.9 21.8 + - + +
131B LEU 3.2 4.2 + - - +
133B ALA* 1.3 75.0 - - - +
135B GLU* 1.3 58.3 + - - +
136B GLY 3.2 2.0 + - - -
310B ALA* 3.7 28.7 - - + +
313B ALA* 5.6 6.1 - - + +
314B ILE* 3.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 2.9 36.0 + - + +
132B HIS* 3.2 8.6 + - - +
134B ALA* 1.3 76.3 - - - +
136B GLY* 1.3 60.1 + - - +
137B LYS* 3.5 8.8 + - + +
306B ARG* 2.7 52.0 + - - +
309B THR* 5.6 0.9 + - - -
310B ALA* 4.9 5.3 - - + +
----------------------------------------------------------
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