Contacts of the strand formed by residues 625 - 628 (chain B) in PDB entry 4AY6
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 ILE 625 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B LEU* 3.9 15.3 - - + -
547B ARG 3.4 3.0 + - - -
548B VAL* 3.3 11.3 - - + +
549B GLY 2.8 25.5 + - - -
623B ILE* 3.3 3.0 - - - +
624B HIS* 1.3 87.0 - - + +
626B LEU* 1.3 67.2 + - - +
627B VAL* 4.3 12.1 - - + -
648B ILE* 3.4 31.2 - - + +
650B ALA* 4.8 8.1 - - + -
1010B TYR* 3.7 55.2 - - + +
1013B MET* 4.5 9.6 - - + -
1014B TRP* 5.0 0.4 - - + -
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Residues in contact with LEU 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLY* 3.5 17.7 - - - +
551B VAL* 3.7 15.9 - - + -
581B TYR* 4.6 4.3 - - + -
618B ILE* 4.0 31.4 - - + -
623B ILE* 3.8 16.1 - - + +
625B ILE* 1.3 73.3 - - - +
627B VAL* 1.3 59.6 + - - +
640B LEU* 5.4 1.8 - - + +
641B PHE* 3.5 34.6 - - + +
645B PRO* 4.4 8.7 - - + -
646B ALA* 3.8 14.8 - - + +
648B ILE 2.9 6.5 + - - -
649B GLN* 3.3 20.4 - - + +
650B ALA 2.9 24.3 + - - +
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Residues in contact with VAL 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B VAL* 3.8 20.6 - - + -
549B GLY 2.8 12.4 + - - +
550B TYR* 3.8 12.7 - - + -
551B VAL* 3.0 28.8 + - - +
625B ILE* 4.3 8.7 - - + -
626B LEU* 1.3 75.0 - - - +
628B ASN* 1.3 64.0 + - - +
629B MET* 3.6 1.8 + - + +
641B PHE* 3.8 2.5 - - - -
650B ALA* 3.3 12.3 - - + +
652B TRP* 3.3 45.3 - - + +
668B ILE* 5.0 0.9 - - + -
1010B TYR* 3.5 24.2 - - + +
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Residues in contact with ASN 628 (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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551B VAL 4.1 1.1 - - - +
627B VAL* 1.3 70.9 - - - +
629B MET* 1.3 61.0 + - - +
630B ASN* 2.9 20.8 + - - +
631B GLY* 3.0 13.3 + - - +
638B ASN* 3.2 25.3 + - - +
641B PHE* 3.2 41.2 - - + +
650B ALA 2.7 13.9 + - - +
651B MET* 3.6 12.8 - - - +
652B TRP 3.1 23.3 + - - +
655B TYR 5.8 0.3 + - - -
663B PHE* 5.5 0.6 - - - -
664B MET* 4.0 17.2 - - + -
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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