Contacts of the strand formed by residues 6922 - 6927 (chain A) in PDB entry 6W4H
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 TRP6922 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6864A ARG* 3.5 32.8 - - + +
6865A VAL 3.5 30.7 - - - -
6866A ILE* 3.7 24.5 - - + -
6892A LEU* 4.6 3.8 - - + -
6894A VAL* 3.6 28.5 - - + -
6918A THR* 3.1 36.2 + - + +
6920A ASN* 3.2 28.4 + - - -
6921A LYS* 1.3 75.4 - - - +
6923A ASP* 1.3 65.4 + - - +
6924A LEU 3.5 5.2 - - - +
6925A ILE* 4.4 8.1 - - + -
6954A PHE* 3.7 16.5 - + - -
6958A LYS* 2.7 18.0 + - + +
6959A LEU* 3.4 6.1 - - - +
6960A ALA* 2.8 26.3 + - - +
7086A VAL* 3.8 13.0 - - + -
7088A ILE* 3.9 5.8 - - + -
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Residues in contact with ASP6923 (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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6858A ALA 5.1 3.0 - - - +
6860A PRO* 3.5 11.4 - - + +
6863A MET* 3.5 23.6 - - + +
6864A ARG* 2.8 29.1 + - - +
6922A TRP* 1.3 75.1 - - - +
6924A LEU* 1.3 62.0 + - - +
6959A LEU* 4.3 1.1 - - - -
6963A GLY* 3.2 13.0 - - - -
6964A SER 3.0 21.5 + - - -
7079A ILE* 3.5 22.1 - - + +
7081A ARG* 2.8 46.1 + - - -
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Residues in contact with LEU6924 (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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6852A LEU* 5.1 5.2 - - + -
6857A LEU* 4.9 10.3 - - + -
6863A MET* 3.9 23.3 - - + -
6864A ARG 3.2 3.5 + - - +
6865A VAL* 3.4 22.9 - - + +
6866A ILE* 3.1 24.6 + - - +
6883A LEU* 5.7 0.2 - - + -
6886A TRP* 3.7 32.3 - - + -
6922A TRP* 3.5 1.5 - - - +
6923A ASP* 1.3 80.7 - - - +
6925A ILE* 1.3 65.6 - - - +
6926A ILE* 3.9 27.1 - - + -
6964A SER* 3.2 34.1 - - - +
6965A VAL* 4.3 3.6 - - - +
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Residues in contact with ILE6925 (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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6866A ILE* 3.4 15.9 - - + +
6868A PHE* 4.1 28.0 - - + -
6922A TRP* 4.4 3.6 - - + -
6924A LEU* 1.3 77.8 - - - +
6926A ILE* 1.3 64.0 + - - +
6951A ILE* 4.7 4.7 - - + -
6954A PHE* 3.5 26.9 - - + -
6955A ILE* 4.1 17.3 - - + -
6959A LEU* 3.9 35.0 - - + -
6964A SER 3.0 5.9 + - - -
6965A VAL* 3.1 10.1 - - + +
6966A ALA 2.9 25.6 + - - +
6967A ILE* 4.3 15.9 - - + +
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Residues in contact with ILE6926 (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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6845A TYR* 4.2 17.5 - - + +
6848A LEU* 4.6 12.3 - - + -
6852A LEU* 4.4 10.1 - - + -
6865A VAL* 4.6 3.4 - - + -
6866A ILE 2.9 11.4 + - - +
6867A HIS* 3.3 23.5 - - + -
6868A PHE* 2.8 27.0 + - - +
6883A LEU* 4.2 22.9 - - + -
6924A LEU* 3.9 29.8 - - + -
6925A ILE* 1.3 82.0 - - - +
6927A SER* 1.3 67.8 + - - +
6966A ALA* 3.3 24.0 - - + +
7003A PHE* 5.4 1.8 - - + -
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Residues in contact with SER6927 (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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6868A PHE* 3.4 13.2 - - - -
6926A ILE* 1.3 77.4 - - - +
6928A ASP* 1.3 57.4 + - - +
6929A MET* 3.2 31.2 + - - +
6947A PHE* 5.1 1.7 - - - -
6951A ILE* 4.3 8.5 - - - +
6966A ALA 2.9 11.1 + - - +
6967A ILE* 3.7 29.5 - - - +
6968A LYS* 2.8 30.5 + - - +
7003A PHE* 4.1 4.0 - - - -
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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