Contacts of the helix formed by residues 128 - 146 (chain B) in PDB entry 2YZ5
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 ASP 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 1.3 72.5 - - - +
129B LEU* 1.3 66.3 + - - +
130B LYS* 3.4 13.5 + - - +
131B GLU* 2.9 66.0 + - - +
132B VAL* 3.0 12.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124B TYR* 4.2 22.8 + - + -
127B ARG* 3.7 5.2 + - - -
128B ASP* 1.3 72.3 + - - +
130B LYS* 1.3 61.5 + - - +
132B VAL* 3.3 6.8 + - + -
133B PHE* 3.1 44.7 + - + -
163B HIS* 3.5 47.6 - - + +
164B ARG 4.1 10.5 - - - +
165B LEU* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 3.1 13.1 + - - +
129B LEU* 1.3 78.2 - - - +
131B GLU* 1.3 58.2 + - - +
133B PHE* 3.3 2.6 + - - +
134B ARG* 2.9 54.8 + - - +
165B LEU* 4.4 17.2 - - + +
169B ALA* 4.3 19.5 - - + +
172B GLU* 4.2 15.2 + - - -
173B LEU* 3.8 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 2.9 38.3 + - - +
130B LYS* 1.3 74.5 - - - +
132B VAL* 1.3 61.7 + - + +
134B ARG* 3.7 19.3 - - - +
135B ALA* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 22.7 - - + +
113B TRP* 4.3 8.5 - - + -
115B LEU* 4.1 11.0 - - + -
124B TYR* 4.1 24.2 - - + -
127B ARG* 3.5 32.8 - - + +
128B ASP 3.0 15.5 + - - +
129B LEU* 3.5 12.1 - - + +
131B GLU* 1.3 77.5 - - + +
133B PHE* 1.3 57.8 + - - +
135B ALA* 3.7 2.2 - - - +
136B TYR* 2.9 28.1 + - - +
158B PRO* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.1 37.4 + - + +
130B LYS 3.7 6.3 - - - +
132B VAL* 1.3 78.4 - - - +
134B ARG* 1.3 62.8 + - - +
136B TYR* 3.2 4.7 + - - +
137B PHE* 2.9 51.0 + + + -
156B ASP* 4.1 10.5 - - + -
158B PRO* 3.5 35.0 - - + -
159B LYS* 3.6 11.7 - - + -
163B HIS 3.2 27.1 - - - -
164B ARG* 4.9 2.0 - - - -
165B LEU* 3.5 32.3 - - + -
170B LEU* 4.3 16.2 - - + -
173B LEU* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 2.9 50.3 + - - +
131B GLU* 3.7 21.2 - - - +
133B PHE* 1.3 77.1 - - - +
135B ALA* 1.3 62.1 + - - +
137B PHE* 3.3 5.8 + - - +
138B GLN* 3.0 53.6 + - + +
173B LEU* 3.7 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.0 18.6 - - + -
131B GLU 2.8 17.9 + - - +
132B VAL* 3.7 4.3 - - - +
134B ARG* 1.3 75.9 - - - +
136B TYR* 1.3 63.1 + - - +
138B GLN* 3.3 14.8 + - - +
139B GLU* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 2.7 54.4 + - + +
110B LEU* 3.9 10.7 - - + +
115B LEU* 3.9 16.8 - - + -
132B VAL 2.9 17.2 + - - +
133B PHE 3.5 4.5 - - - +
134B ARG 3.2 0.2 - - - -
135B ALA* 1.3 77.4 - - - +
137B PHE* 1.3 67.2 + + - +
139B GLU* 3.1 7.4 + - - +
140B VAL* 3.0 36.7 + - + +
153B GLY 4.5 1.7 + - - -
154B HIS* 3.5 12.8 + - - -
155B LEU* 3.3 26.9 - - - -
157B LEU* 3.4 25.0 - - + +
158B PRO* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 2.9 43.4 + + + +
134B ARG 4.0 2.5 - - - +
136B TYR* 1.3 77.1 - + - +
138B GLN* 1.3 62.4 + - + +
140B VAL* 2.9 6.0 + - + +
141B GLU* 2.8 30.3 + - - +
155B LEU* 3.2 44.6 - - + -
156B ASP* 4.2 6.3 - - + -
170B LEU* 3.7 26.9 - - + -
173B LEU* 3.5 41.1 - - + +
174B ALA* 3.8 26.7 - - + -
176B PRO* 6.5 0.4 - - + -
177B ALA* 3.9 11.4 - - + +
208B LEU* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 3.0 47.4 + - + +
135B ALA* 3.6 16.1 - - - +
136B TYR 3.2 0.2 - - - -
137B PHE* 1.3 76.6 - - + +
139B GLU* 1.3 65.4 + - - +
141B GLU* 3.4 17.4 + - - +
142B LYS* 3.3 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.5 13.5 - - - +
85B PRO* 3.4 30.2 - - - +
107B VAL* 3.9 26.2 - - + -
109B TYR 4.8 2.9 - - - +
110B LEU* 4.5 12.3 - - + -
135B ALA 3.1 16.3 + - - +
136B TYR 3.1 9.7 + - - +
138B GLN* 1.3 77.8 - - - +
140B VAL* 1.3 64.8 + - - +
142B LYS* 2.5 37.6 + - - +
143B ALA 3.0 17.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
107B VAL* 4.2 14.1 - - + +
136B TYR* 3.0 40.8 + - + +
137B PHE* 2.9 12.0 + - - +
139B GLU* 1.3 74.5 - - - +
141B GLU* 1.3 59.6 + - - +
143B ALA* 3.0 5.4 + - - +
144B ALA* 2.8 27.2 + - - +
152B ILE* 3.6 35.2 - - + -
153B GLY 5.9 0.4 - - - +
155B LEU* 3.8 21.8 - - + +
177B ALA* 4.1 8.7 - - + -
181B VAL* 5.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE 2.8 12.3 + - - +
138B GLN* 3.5 20.7 - - - +
140B VAL* 1.3 78.2 - - - +
142B LYS* 1.3 62.1 + - + +
144B ALA* 3.2 6.7 + - - +
145B ARG* 3.1 44.9 + - + +
176B PRO* 3.8 30.6 - - - +
177B ALA* 4.2 15.4 - - - +
180B ALA* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.3 21.7 - - + -
85B PRO* 4.2 13.2 - - + +
138B GLN* 3.3 17.5 + - - +
139B GLU* 2.5 39.8 + - - +
140B VAL 3.1 0.4 - - - -
141B GLU* 1.3 77.1 - - + +
143B ALA* 1.3 64.6 + - - +
145B ARG* 3.0 9.4 + - - +
146B SER* 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.4 40.6 - - + -
105B GLY 5.4 2.5 - - - +
107B VAL* 4.7 3.8 - - + -
139B GLU 3.0 8.3 + - - +
140B VAL* 3.0 11.9 + - - +
142B LYS* 1.3 75.8 - - - +
144B ALA* 1.3 60.9 + - - +
146B SER* 2.7 20.4 + - - -
147B GLY 4.3 1.4 + - - -
149B PHE* 3.4 19.4 + - + -
152B ILE* 4.2 11.2 - - + -
186B LEU* 4.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL 2.8 12.2 + - - +
141B GLU* 3.4 10.1 - - - +
142B LYS 3.1 0.2 - - - -
143B ALA* 1.3 79.0 - - - +
145B ARG* 1.3 59.2 + - - +
146B SER 3.4 0.2 - - - -
147B GLY* 4.4 3.8 + - - -
152B ILE* 4.1 3.8 - - + +
180B ALA* 3.7 20.6 - - + -
181B VAL* 3.9 27.4 - - + +
184B ALA* 3.1 26.5 - - - +
186B LEU* 4.0 16.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
141B GLU* 3.1 32.8 + - + +
142B LYS* 3.0 9.2 + - - +
144B ALA* 1.3 73.5 - - - +
146B SER* 1.3 62.9 + - - +
147B GLY* 3.3 4.5 + - - -
176B PRO 4.8 0.8 + - - -
179B ARG* 4.5 2.8 - - - +
180B ALA* 3.3 30.2 + - - +
183B GLU* 2.5 42.8 + - - +
184B ALA* 5.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.9 13.9 - - - -
88B GLU* 4.8 4.0 - - - -
142B LYS 2.9 11.3 + - - -
143B ALA 2.7 20.0 + - - -
145B ARG* 1.3 78.6 - - - +
147B GLY* 1.3 61.5 + - - +
148B LEU* 3.2 32.1 + - - +
149B PHE* 3.4 12.5 - - - -
----------------------------------------------------------
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