Contacts of the strand formed by residues 4122 - 4127 (chain B) in PDB entry 4O2W
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 GLN4122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4105B SER 4.2 1.8 - - - +
4106B TRP* 3.3 12.5 - - - +
4107B GLY* 2.8 35.2 + - - +
4114B LEU* 3.7 20.8 - - + +
4116B HIS* 3.9 22.8 - - + +
4118B ASN* 4.6 7.9 + - - +
4120B ASP* 3.8 14.1 + - - +
4121B ARG* 1.3 82.9 + - - +
4123B ARG* 1.3 60.4 + - - +
4124B ARG 3.3 16.2 + - - +
4126B ARG* 3.8 30.9 - - + +
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Residues in contact with ARG4123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4056B TYR 4.0 5.2 - - - +
4057B GLY* 3.6 23.6 - - - +
4060B GLY* 3.0 16.3 - - - -
4061B GLN 3.2 1.0 + - - -
4062B GLY* 2.9 43.2 + - - -
4063B ASN* 3.5 10.5 - - - +
4064B SER* 3.1 43.2 + - - +
4121B ARG* 4.0 20.9 - - + +
4122B GLN* 1.3 73.9 + - - +
4124B ARG* 1.3 60.3 + - - +
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Residues in contact with ARG4124 (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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4060B GLY 3.8 5.4 - - - +
4061B GLN 4.4 5.6 + - - -
4062B GLY* 3.6 33.0 + - - +
4075B ALA* 4.2 16.8 - - + +
4106B TRP* 3.6 9.9 - - - +
4122B GLN* 3.8 12.2 - - - +
4123B ARG* 1.3 84.4 - - - +
4125B PRO* 1.3 79.9 - - + +
4126B ARG* 3.3 4.2 + - - +
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Residues in contact with PRO4125 (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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4060B GLY* 3.4 23.1 - - - +
4073B ILE* 3.7 21.5 - - + -
4075B ALA* 4.0 14.7 - - + +
4076B LEU* 3.8 24.0 - - + -
4104B PHE* 4.0 16.5 - - + -
4105B SER 3.7 7.9 - - - +
4106B TRP* 3.7 25.1 - - + -
4124B ARG* 1.3 91.0 - - + +
4126B ARG* 1.3 58.5 + - - +
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Residues in contact with ARG4126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4104B PHE* 3.5 5.1 - - - -
4105B SER 2.9 29.8 + - - +
4116B HIS* 3.3 35.7 + - + +
4122B GLN* 3.8 31.7 - - - +
4124B ARG 4.1 5.2 - - - +
4125B PRO* 1.3 74.9 - - - +
4127B GLN* 1.3 70.1 + - - +
4129B GLU* 5.8 4.6 - - - +
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Residues in contact with GLN4127 (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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4102B GLU* 3.5 39.5 + - + +
4103B VAL 3.4 14.3 - - - +
4104B PHE* 3.2 32.0 - - + -
4116B HIS* 3.3 11.8 + - - -
4126B ARG* 1.3 78.4 + - - +
4128B ILE* 1.3 68.2 + - - +
4129B GLU* 3.1 24.7 + - - +
4131B LEU 5.7 0.6 - - - -
4132B GLN* 3.5 43.4 + - - +
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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