Contacts of the strand formed by residues 99 - 105 (chain B) in PDB entry 3QG2
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B THR 5.7 0.2 - - - -
65B VAL* 4.0 7.2 - - - -
97B LYS* 3.4 18.4 + - + +
98B LEU* 1.3 81.0 - - - +
100B ASN* 1.3 63.3 + - - +
121B ASN* 3.5 34.6 - - + +
122B ARG 3.9 9.1 + - - -
123B ILE* 3.3 28.9 - - + +
157B ASN 4.1 3.2 + - - -
158B TYR* 3.1 7.3 - - - -
159B TYR* 2.7 32.4 + - - +
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Residues in contact with ASN 100 (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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62B THR 3.2 29.3 + - - +
63B THR 3.4 4.0 + - - -
64B TYR 2.6 30.9 + - - +
65B VAL* 3.1 13.6 - - - +
99B GLN* 1.3 74.9 - - - +
101B VAL* 1.3 64.6 + - - +
121B ASN 4.7 3.2 + - - -
122B ARG* 3.7 5.1 - - + +
123B ILE* 2.8 28.2 + - - +
159B TYR* 3.4 6.8 - - - +
160B LYS* 2.8 41.5 + - - +
162B PHE* 4.0 12.6 - - + -
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Residues in contact with VAL 101 (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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100B ASN* 1.3 75.0 - - - +
102B VAL* 1.3 62.8 + - - +
103B VAL* 4.3 3.8 - - + -
123B ILE* 3.5 29.2 - - + +
125B VAL* 3.7 21.5 - - + -
149B LEU* 5.1 1.1 - - + -
153B LEU* 4.3 11.9 - - + -
156B LEU* 4.7 5.8 - - + -
158B TYR* 3.4 31.9 - - + -
160B LYS 2.9 10.6 + - - +
161B CYS* 3.3 22.1 - - + -
162B PHE* 2.6 34.7 + - - +
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Residues in contact with VAL 102 (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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62B THR* 4.3 15.3 - - - +
101B VAL* 1.3 78.1 - - - +
103B VAL* 1.3 62.2 + - - +
104B MET* 4.3 3.3 + - + +
119B LEU* 4.1 14.1 - - + -
122B ARG* 3.9 29.4 - - + -
123B ILE 3.0 5.2 + - - +
124B ASN* 3.7 33.9 - - + +
125B VAL* 2.9 30.3 + - - +
162B PHE* 3.2 7.6 - - + +
164B LEU* 3.9 23.1 - - + -
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Residues in contact with VAL 103 (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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101B VAL* 4.3 1.8 - - + -
102B VAL* 1.3 77.5 - - - +
104B MET* 1.3 64.4 + - - +
125B VAL* 3.6 18.8 - - + +
127B LEU* 4.4 20.4 - - + -
143B ILE* 4.5 3.8 - - + -
149B LEU* 3.8 33.7 - - + -
161B CYS* 4.0 9.4 - - - -
162B PHE 2.8 9.3 + - - -
163B ILE* 3.5 23.5 - - + +
164B LEU* 2.7 32.5 + - - -
165B GLY 3.8 2.0 - - - +
169B VAL* 4.9 1.8 - - + -
173B PHE* 4.4 13.9 - - + -
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Residues in contact with MET 104 (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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102B VAL* 4.6 9.6 - - + -
103B VAL* 1.3 79.0 - - - +
105B GLY* 1.3 66.9 + - - +
108B ASN* 3.6 21.8 - - - +
109B TRP* 3.5 46.2 - - + -
112B ILE* 3.5 31.4 - - + -
119B LEU* 3.8 22.2 - - + -
124B ASN* 4.7 1.8 - - + +
125B VAL 3.3 11.3 + - - +
126B ILE* 3.5 3.5 - - + -
127B LEU* 3.1 23.4 + - - -
164B LEU* 4.1 10.8 - - + -
165B GLY 3.0 7.6 - - - -
169B VAL* 4.4 2.7 - - - -
709B CP6 4.8 0.4 - - - -
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Residues in contact with GLY 105 (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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104B MET* 1.3 77.2 - - - +
106B ARG* 1.3 61.0 + - - -
107B THR 3.4 2.0 - - - -
108B ASN* 3.1 4.2 + - - +
109B TRP* 2.9 26.2 + - - +
126B ILE* 4.4 1.3 - - - -
127B LEU 3.9 4.9 - - - -
165B GLY 2.9 13.9 + - - -
169B VAL* 3.6 12.7 - - - +
710B NDP 3.5 21.3 - - - -
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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