Contacts of the helix formed by residues 129 - 136 (chain B) in PDB entry 4CGS
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B THR* 4.0 0.9 - - - -
108B PRO* 3.3 25.1 - - - +
110B ASP* 2.6 28.2 + - - -
121B ARG* 3.0 24.2 + - - +
128B MET* 1.3 75.5 - - - +
130B PRO* 1.3 71.5 - - - +
132B THR* 2.7 26.2 + - - -
133B ARG* 2.9 20.8 + - - +
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Residues in contact with PRO 130 (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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107B THR* 4.4 4.5 - - + -
108B PRO 4.0 7.4 - - - +
109B THR* 5.7 0.4 - - - -
110B ASP* 3.3 14.6 - - - +
129B SER* 1.3 83.9 - - - +
131B ILE* 1.3 61.1 + - + +
133B ARG* 3.4 36.7 + - - +
134B GLU* 3.2 38.8 + - - +
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Residues in contact with ILE 131 (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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110B ASP* 2.9 41.3 + - + +
118B ILE* 5.0 15.0 - - + -
119B PHE 4.7 11.0 - - - +
130B PRO* 1.3 72.8 - - + +
132B THR* 1.3 58.0 + - - +
134B GLU* 3.3 19.0 + - + +
135B TYR* 2.9 33.1 + - + +
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Residues in contact with THR 132 (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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118B ILE* 6.1 0.4 - - - -
119B PHE 3.6 3.6 + - - -
120B VAL* 3.6 25.5 - - + +
121B ARG 2.9 22.4 + - - +
122B VAL* 4.1 1.6 - - + -
128B MET* 4.0 16.4 - - + -
129B SER* 2.7 31.7 + - - -
131B ILE* 1.3 79.4 - - - +
133B ARG* 1.3 61.5 + - - +
135B TYR* 3.2 5.0 + - - +
136B LEU* 3.0 48.1 + - + +
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Residues in contact with ARG 133 (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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107B THR* 4.1 10.9 - - - +
128B MET* 2.9 51.1 + - + +
129B SER 2.9 16.5 + - - +
130B PRO* 3.4 38.3 - - - +
132B THR* 1.3 78.0 - - - +
134B GLU* 1.3 58.9 + - + +
136B LEU 3.2 19.2 - - - +
141B ARG* 3.3 25.7 + - - +
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Residues in contact with GLU 134 (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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130B PRO* 3.2 29.5 + - - +
131B ILE* 3.7 18.5 - - + +
132B THR 3.2 0.6 - - - -
133B ARG* 1.3 77.5 - - + +
135B TYR* 1.3 65.1 + - - +
136B LEU 3.9 2.9 - - - +
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Residues in contact with TYR 135 (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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46B ILE* 5.2 1.6 - - + -
57B ARG* 4.0 12.2 + - - -
58B TYR* 2.8 28.1 + + - -
90B ASP* 2.5 31.3 + - + -
93B GLU* 4.6 9.6 - - + -
95B LYS* 5.4 1.1 - - + -
97B VAL* 3.5 15.2 - - + +
118B ILE* 3.8 48.5 - - + -
120B VAL* 4.0 11.9 - - + -
131B ILE* 2.9 18.2 + - + +
132B THR* 3.8 2.9 - - - +
134B GLU* 1.3 79.9 - - - +
136B LEU* 1.3 85.1 - - + +
137B ASP* 3.7 1.6 + - - +
140B GLN* 4.4 1.9 - - - +
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Residues in contact with LEU 136 (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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46B ILE* 4.0 20.9 - - + -
120B VAL* 4.5 7.9 - - + -
128B MET* 4.6 4.7 - - + -
132B THR* 3.0 38.2 + - + +
133B ARG 3.2 6.9 - - - +
134B GLU 3.9 2.6 - - - +
135B TYR* 1.3 101.4 - - + +
137B ASP* 1.3 60.7 + - - +
140B GLN* 3.4 23.1 - - + +
141B ARG* 2.8 48.3 + - + +
144B VAL* 4.6 18.4 - - + -
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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