Contacts of the helix formed by residues 164 - 177 (chain B) in PDB entry 4GZM
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 GLY 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TYR* 5.7 7.0 - - - -
148A GLU* 2.9 36.1 + - - +
155B LEU* 5.6 1.2 - - - +
156B GLU 4.3 8.6 - - - +
157B CYS* 3.8 4.5 - - - +
162B GLN 3.3 2.6 + - - -
163B ARG* 1.3 71.9 - - - +
165B LEU* 1.3 62.3 + - - +
167B THR* 3.5 11.8 + - - -
168B VAL* 3.4 15.9 - - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.5 0.4 + - - -
19B LEU* 3.8 35.9 - - + +
22B SER* 3.4 32.5 - - - +
23B TYR* 4.1 20.9 - - + +
157B CYS* 4.1 14.1 - - + -
158B SER 4.6 1.6 - - - +
159B ALA* 4.3 10.5 - - - -
162B GLN* 3.5 34.3 + - + +
163B ARG 3.2 0.8 - - - +
164B GLY* 1.3 77.0 - - - +
166B LYS* 1.3 66.6 + - + +
168B VAL* 3.4 10.7 + - + +
169B PHE* 3.2 27.9 - - + -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 5.1 1.3 - - - +
144A ALA* 4.1 28.0 - - + +
148A GLU* 3.4 18.3 + - + +
23B TYR* 4.0 22.7 + - + +
162B GLN 6.0 0.2 - - - +
165B LEU* 1.3 79.5 - - + +
167B THR* 1.3 57.2 + - - +
169B PHE* 3.1 8.1 + - - +
170B ASP* 2.9 38.4 + - - +
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 3.0 31.8 - - + +
148A GLU* 2.4 25.1 + - - -
155B LEU* 4.1 16.4 - - + -
164B GLY* 3.6 8.5 + - - -
165B LEU 3.3 0.2 - - - -
166B LYS* 1.3 74.0 - - - +
168B VAL* 1.3 59.4 + - - +
170B ASP* 3.5 10.0 + - - -
171B GLU* 2.7 59.4 + - + +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.6 3.6 - - + -
79B LEU* 4.1 22.7 - - + +
111B ILE* 5.1 0.9 - - - +
113B VAL* 3.9 28.0 - - + -
155B LEU* 3.7 22.8 - - + +
157B CYS* 3.6 26.7 - - + -
164B GLY 3.4 17.3 - - - +
165B LEU* 3.4 11.7 - - + +
166B LYS 3.2 0.2 - - - -
167B THR* 1.3 76.3 - - - +
169B PHE* 1.3 67.5 + - + +
171B GLU* 4.0 2.6 - - - +
172B ALA* 3.1 25.0 + - - +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 5.5 0.4 - - - -
19B LEU* 3.3 34.1 - - + -
20B LEU* 4.0 11.4 - - + -
23B TYR* 3.4 58.8 - + + +
53B LEU* 4.4 9.9 - - + -
55B LEU* 3.9 29.6 - - + -
79B LEU* 4.2 14.4 - - + -
165B LEU* 3.2 30.1 - - + -
166B LYS 3.1 2.5 + - - +
168B VAL* 1.3 78.5 - - + +
170B ASP* 1.3 64.9 + - - +
171B GLU 3.3 0.4 - - - -
172B ALA* 3.7 8.9 - - + +
173B ILE* 3.1 31.9 + - - +
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 2.7 30.2 + - - +
23B TYR* 5.1 2.6 + - - -
44B VAL* 5.0 4.0 - - - +
46B VAL* 3.4 32.5 - - + +
166B LYS* 2.9 28.4 + - - +
167B THR* 2.9 8.5 + - - +
169B PHE* 1.3 80.2 - - - +
171B GLU* 1.3 61.6 + - - +
173B ILE* 3.9 5.5 - - - +
174B ARG* 3.0 44.0 + - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 5.5 0.9 - - - +
94A ARG* 5.4 1.7 + - - -
111B ILE* 4.7 6.6 - - + +
153B LYS* 3.9 34.7 - - + +
155B LEU* 3.7 28.7 - - + -
167B THR* 2.7 39.0 + - + +
168B VAL 4.0 0.2 - - - +
170B ASP* 1.3 71.5 - - - +
172B ALA* 1.3 60.1 + - - +
174B ARG* 3.3 35.3 + - - +
175B ALA* 2.8 31.9 + - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 4.8 8.1 - - + -
53B LEU* 5.7 4.0 - - + -
77B VAL* 3.8 26.0 - - + +
79B LEU* 4.6 14.8 - - + -
111B ILE* 4.6 5.1 - - - +
168B VAL 3.1 18.8 + - - +
169B PHE* 3.7 14.1 - - + +
170B ASP 3.4 0.2 - - - -
171B GLU* 1.3 78.7 - - - +
173B ILE* 1.3 63.2 + - + +
175B ALA* 3.4 13.5 + - - +
176B VAL* 3.6 12.1 - - - +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 10.1 - - + -
23B TYR* 5.5 0.4 - - - +
44B VAL* 4.6 17.3 - - + -
46B VAL* 4.7 18.4 - - + -
51B VAL* 3.9 34.3 - - + -
53B LEU* 4.1 31.6 - - + -
169B PHE* 3.1 20.7 + - + +
170B ASP* 3.9 3.4 - - - +
172B ALA* 1.3 75.4 - - - +
174B ARG* 1.3 64.3 + - + +
176B VAL* 3.0 16.1 + - - +
177B LEU* 3.1 36.5 + - + +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 4.3 21.6 + - - -
94A ARG* 4.6 9.1 - - - +
46B VAL* 4.2 20.2 - - + +
47B ASP* 3.6 32.0 + - - +
170B ASP* 3.0 31.4 + - - +
171B GLU* 3.1 37.7 + - - +
173B ILE* 1.3 76.8 - - + +
175B ALA* 1.3 60.9 + - - +
177B LEU* 3.5 22.4 + - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 4.3 16.6 - - + -
109B PRO* 4.5 19.3 - - + +
111B ILE* 4.5 12.6 - - + -
152B VAL* 5.1 11.2 - - + -
171B GLU 2.8 12.3 + - - +
172B ALA 3.4 11.7 - - - +
173B ILE 3.1 0.2 - - - -
174B ARG* 1.3 79.2 - - - +
176B VAL* 1.3 60.5 + - - +
177B LEU 3.6 2.1 + - - -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 20.2 - - + -
76B ASP* 3.7 49.4 - - + +
77B VAL* 3.9 12.1 - - + -
109B PRO* 5.3 1.6 - - + -
172B ALA 3.6 15.5 - - - +
173B ILE 3.0 5.7 + - - +
175B ALA* 1.3 76.0 - - + +
177B LEU* 1.3 64.7 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.8 12.6 - - + -
46B VAL 5.1 0.4 - - - +
47B ASP* 4.3 19.9 - - + +
49B LYS* 4.1 39.5 + - + +
51B VAL* 4.7 10.1 - - + -
173B ILE* 3.1 37.8 + - + +
174B ARG* 3.6 16.8 - - - +
175B ALA 3.3 2.8 - - - -
176B VAL* 1.3 85.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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