Contacts of the strand formed by residues 625 - 628 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546D LEU* 3.9 20.0 - - + -
547D ARG 3.4 3.4 + - - -
548D VAL* 3.3 11.9 - - + +
549D GLY 2.9 24.9 + - - -
623D ILE* 3.3 4.2 - - - +
624D HIS* 1.3 86.5 - - + +
626D LEU* 1.3 69.5 + - - +
627D VAL* 4.4 10.1 - - + -
648D ILE* 3.3 35.7 - - + +
650D ALA* 4.7 9.2 - - + -
1010D TYR* 3.7 50.9 - - + +
1013D MET* 4.7 5.6 - - - -
1014D TRP* 5.0 0.4 - - + -
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Residues in contact with LEU 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D GLY* 3.5 15.0 - - - +
551D VAL* 3.8 17.5 - - + -
581D TYR* 4.5 3.6 - - + -
618D ILE* 3.9 33.2 - - + -
623D ILE* 3.8 19.4 - - + +
625D ILE* 1.3 71.9 - - - +
627D VAL* 1.3 60.7 + - - +
640D LEU* 5.3 1.6 - - + +
641D PHE* 3.7 33.4 - - + +
645D PRO* 4.4 9.4 - - + -
646D ALA* 3.8 13.8 - - + +
648D ILE 2.9 6.1 + - - -
649D GLN* 3.2 19.3 - - + +
650D ALA 2.8 25.6 + - - +
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Residues in contact with VAL 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D VAL* 3.8 16.4 - - + -
549D GLY 2.7 18.5 + - - +
550D TYR* 3.7 11.7 - - + -
551D VAL* 3.0 28.8 + - - +
625D ILE* 4.4 6.7 - - + +
626D LEU* 1.3 76.1 - - - +
628D ASN* 1.3 63.0 + - - +
629D MET* 3.7 1.6 + - + +
641D PHE* 3.7 2.2 - - - -
650D ALA* 3.2 11.0 - - + +
652D TRP* 3.4 45.5 - - + +
668D ILE* 5.1 1.6 - - + -
1010D TYR* 3.6 24.0 - - + +
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Residues in contact with ASN 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D VAL 4.2 1.5 - - - +
627D VAL* 1.3 69.2 - - - +
629D MET* 1.3 60.9 + - - +
630D ASN* 2.9 22.0 + - - +
631D GLY* 3.0 12.8 + - - +
638D ASN* 3.1 25.4 + - - +
641D PHE* 3.2 38.6 - - + +
650D ALA 2.7 14.1 + - - +
651D MET* 3.6 13.3 - - - +
652D TRP 3.0 23.3 + - - +
655D TYR 5.7 0.5 + - - -
663D PHE* 5.6 0.6 - - - -
664D 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