Contacts of the strand formed by residues 106 - 110 (chain B) in PDB entry 3COG
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 GLN 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.5 0.2 - - - +
105B ASP* 1.3 75.0 - - - +
107B ILE* 1.3 73.8 + - - +
108B ILE* 4.1 7.3 - - - +
131B LYS* 3.1 30.5 - - + +
133B SER* 2.5 33.5 + - - +
146B ALA 3.9 10.6 + - - +
148B THR* 3.1 20.7 + - - +
150B GLU* 2.7 24.6 + - + +
151B THR* 2.6 28.8 + - - +
152B LYS* 3.0 25.6 + - - +
153B LEU 3.6 5.4 + - - +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 4.0 22.0 - - + -
101B LEU* 3.4 31.9 - - + -
105B ASP 4.4 0.2 + - - -
106B GLN* 1.3 77.7 - - - +
108B ILE* 1.3 72.8 + - - +
109B CYS* 4.2 4.0 - - + +
121B PHE* 4.2 26.7 - - + -
125B ALA* 4.9 0.2 - - + -
130B LEU* 4.4 8.5 - - + -
131B LYS 2.7 8.2 + - - +
132B ILE* 3.3 32.3 - - + -
133B SER 2.8 27.0 + - - -
153B LEU* 3.4 24.5 - - + +
155B TRP* 5.1 0.9 - - + -
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Residues in contact with ILE 108 (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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106B GLN* 4.1 13.7 - - - +
107B ILE* 1.3 75.7 - - - +
109B CYS* 1.3 65.0 + - - +
133B SER* 3.2 5.2 - - - +
135B VAL* 3.6 26.5 - - + -
137B CYS* 4.8 2.0 - - - -
143B LEU* 3.9 27.4 - - + -
146B ALA* 3.7 38.4 - - + +
147B ILE* 3.9 11.0 - - + +
151B THR* 4.1 18.8 - - + -
153B LEU 2.9 10.4 + - - +
154B VAL* 3.3 11.5 - - + +
155B TRP 2.9 24.6 + - - -
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Residues in contact with CYS 109 (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 ILE* 3.9 5.2 - - + -
108B ILE* 1.3 76.0 - - - +
110B MET* 1.3 78.0 + - - +
113B VAL* 4.0 20.6 - - - -
121B PHE* 3.6 37.9 - - + -
132B ILE* 4.6 2.2 - - + -
133B SER 2.8 8.0 + - - +
134B PHE* 3.1 27.3 - - + -
135B VAL 2.9 24.6 + - - -
137B CYS* 4.9 0.2 - - - -
155B TRP* 3.8 9.6 - - - -
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Residues in contact with MET 110 (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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108B ILE 4.3 0.2 - - - -
109B CYS* 1.3 87.4 - - - +
111B ASP* 1.3 63.3 + - - +
112B ASP* 3.7 22.0 - - + +
113B VAL* 3.6 12.4 - - + +
134B PHE* 3.5 4.2 - - - -
135B VAL 3.4 6.3 - - - -
137B CYS* 3.6 30.9 - - + +
138B SER 6.2 0.2 - - - +
155B TRP 3.1 13.6 + - - +
156B ILE* 3.6 13.0 - - + -
157B GLU* 3.4 35.0 - - + +
160B THR* 3.3 34.5 - - + -
165B LYS* 5.7 2.5 - - - +
167B ILE* 3.9 15.5 - - + -
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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