Contacts of the helix formed by residues 154 - 161 (chain A) in PDB entry 3K8G
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 ARG 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.0 0.7 - - - +
152A ARG 3.5 1.5 + - - +
153A GLU* 1.3 80.4 - - - +
155A MET* 1.3 65.9 + - - +
156A SER* 3.4 5.6 + - - +
157A LYS* 3.0 20.1 + - + +
158A MET 3.2 9.0 + - - -
35B ASP* 2.9 35.7 + - + +
37B LEU* 3.6 22.2 - - - +
38B GLY* 4.5 4.3 - - - +
165B PRO* 6.5 0.7 - - + -
166B ASP 3.9 6.1 - - - +
167B ARG* 3.7 30.3 - - + +
168B PRO* 3.0 51.0 + - - +
170B LEU* 4.2 5.5 - - - +
175B GLU* 2.7 43.0 + - - -
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Residues in contact with MET 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.8 31.4 - - + -
129A GLU* 5.6 4.4 + - + +
134A ASP* 3.5 43.6 + - + +
135A VAL 3.8 3.1 - - - +
136A SER* 3.8 18.8 - - - +
144A CYS* 3.7 25.4 - - - +
146A ILE* 3.7 28.7 - - + +
153A GLU 3.6 2.8 + - - -
154A ARG* 1.3 71.4 - - - +
156A SER* 1.3 57.1 + - - +
158A MET* 3.1 4.9 + - - +
159A LEU* 2.8 45.2 + - + +
167B ARG* 4.7 2.2 - - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.0 33.2 - - - -
154A ARG* 3.2 8.2 + - - +
155A MET* 1.3 78.9 - - - +
157A LYS* 1.3 56.6 + - - +
159A LEU* 3.9 3.2 - - - +
160A SER* 3.0 27.2 + - - -
168B PRO 4.5 0.6 + - - -
169B GLN* 3.6 5.1 - - - -
170B LEU 3.0 30.3 + - - +
172B PRO* 5.6 0.2 - - - +
175B GLU* 2.4 33.1 + - - +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.6 27.8 + - + +
154A ARG* 3.0 22.5 + - + +
156A SER* 1.3 78.1 + - - +
158A MET* 1.3 63.2 + - - +
160A SER* 2.6 25.5 + - - +
161A ARG* 3.7 13.4 + - - +
35B ASP* 3.9 24.9 + - - +
175B GLU* 3.7 21.8 - - + +
179B THR* 3.6 31.7 - - - +
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Residues in contact with MET 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.7 42.1 - - + +
40A VAL* 4.2 10.8 - - + -
94A ARG* 4.3 8.7 - - + -
95A LEU 3.5 33.2 - - - +
96A PHE* 4.5 1.1 - - + -
144A CYS* 3.9 21.5 - - + -
145A VAL 4.6 0.2 - - - +
146A ILE* 3.6 34.5 - - + -
153A GLU* 3.4 16.8 + - - +
154A ARG 3.2 4.8 + - - -
155A MET* 3.1 9.7 + - - +
157A LYS* 1.3 76.6 - - - +
159A LEU* 1.3 62.7 + - - +
161A ARG* 3.0 27.2 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 4.1 16.4 - - + -
127A TYR* 3.4 39.5 - - + +
136A SER* 3.8 13.9 - - - +
138A PRO* 3.7 28.9 - - + -
144A CYS* 3.8 18.2 - - - -
155A MET* 2.8 29.7 + - + +
156A SER* 4.0 5.4 - - - +
158A MET* 1.3 73.0 - - - +
160A SER* 1.3 56.7 + - - +
161A ARG 3.0 0.4 - - - -
162A LEU* 2.9 41.1 + - + +
163A VAL* 4.2 2.6 + - - +
172B PRO* 5.2 3.5 - - + +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A SER 3.0 11.2 + - - -
157A LYS* 2.6 22.5 + - - +
159A LEU* 1.3 75.6 - - - +
161A ARG* 1.3 60.7 + - - +
162A LEU 3.2 0.4 - - - -
163A VAL* 3.1 9.4 + - - +
164A ASN* 2.9 26.1 + - - +
172B PRO* 3.7 28.0 - - - +
175B GLU* 3.5 31.0 - - - +
176B LYS* 4.8 2.7 + - - -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 3.4 20.2 + - - +
39A VAL* 2.9 40.4 + - - +
40A VAL 3.5 4.6 + - - -
41A GLY* 3.8 5.9 - - - -
94A ARG* 3.4 18.9 - - - +
153A GLU* 2.6 44.0 + - - -
157A LYS* 3.9 19.0 + - - +
158A MET* 3.0 20.2 + - - +
160A SER* 1.3 77.1 - - - +
162A LEU* 1.3 63.2 + - - +
163A VAL 3.1 1.3 - - - -
164A ASN 3.5 15.7 - - - +
165A PRO* 3.3 23.0 - - - +
166A ASP* 3.5 29.2 + - - +
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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