Contacts of the strand formed by residues 641 - 646 (chain D) in PDB entry 3A98
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 ALA 641 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618D THR* 3.7 3.8 + - - -
619D GLY 3.4 13.4 + - - +
622D CYS* 3.2 13.1 - - - -
624D HIS* 3.4 27.8 - - + -
625D MSE 3.9 14.4 - - + -
637D VAL 2.6 18.3 + - - +
638D LEU* 4.1 4.3 - - - +
639D GLU 3.5 0.4 - - - -
640D LEU* 1.3 73.7 - - - +
642D PHE* 1.3 62.6 + - - +
654D PHE 3.6 3.8 - - - +
655D ILE* 3.5 12.6 - - + -
662D TYR* 4.2 2.3 - - - -
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Residues in contact with PHE 642 (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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562D PHE* 3.6 35.7 - + - -
616D VAL* 4.6 7.6 - - + -
617D VAL 3.0 14.4 - - - +
618D THR* 4.5 2.7 - - - -
622D CYS* 3.5 2.5 - - - -
624D HIS* 3.9 0.2 + - - -
640D LEU 3.5 16.4 - - - -
641D ALA* 1.3 74.3 - - - +
643D SER* 1.3 70.4 + - - +
654D PHE* 2.9 68.4 + + - +
656D ALA* 4.0 11.0 - - + -
662D TYR* 4.1 20.6 - + + -
665D TRP* 3.8 24.9 - - + -
666D THR* 5.0 6.7 - - - +
669D LEU* 4.0 14.4 - - + -
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Residues in contact with SER 643 (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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616D VAL* 3.3 3.5 - - - -
617D VAL* 2.6 60.6 + - - +
623D PRO* 4.5 1.6 - - - -
624D HIS* 2.7 33.9 - - - -
642D PHE* 1.3 78.3 + - - +
644D ILE* 1.3 62.9 + - - +
645D LEU* 3.5 4.2 - - - +
652D LEU 3.0 13.0 - - - -
653D ASN* 2.7 14.0 + - - -
654D PHE* 3.7 2.5 - - - -
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Residues in contact with ILE 644 (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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586D LEU* 3.6 28.3 - - + -
608D LEU* 4.3 9.6 - - + -
613D ILE* 3.2 47.3 - - + -
615D ALA 4.2 1.8 - - - -
616D VAL* 4.4 4.5 - - + +
643D SER* 1.3 71.2 - - - +
645D LEU* 1.3 60.7 + - - +
646D TYR* 3.7 2.4 - - + -
651D GLN* 3.1 4.9 - - - -
652D LEU* 2.7 45.2 + - + -
654D PHE* 3.4 30.1 - - + -
665D TRP* 5.7 0.7 - - + -
669D LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 645 (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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613D ILE* 3.4 4.3 - - - +
614D LYS* 2.5 38.1 + - + +
615D ALA* 2.9 26.7 + - + +
617D VAL* 3.4 50.3 - - + -
623D PRO* 4.6 8.3 - - + -
643D SER* 3.5 5.4 - - - +
644D ILE* 1.3 80.5 - - - +
646D TYR* 1.3 57.2 + - - +
650D CYS 3.6 8.1 - - - +
651D GLN* 4.4 9.2 - - + -
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Residues in contact with TYR 646 (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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588D TYR* 4.0 15.8 + - - -
607D LYS 6.1 0.2 - - - -
608D LEU* 3.6 31.0 - - + -
612D ASP* 3.3 19.3 - - + +
613D ILE* 3.9 7.9 - - + -
614D LYS* 3.5 9.1 - - - +
644D ILE* 3.7 11.4 - - + -
645D LEU* 1.3 78.9 - - - +
647D ASP* 1.3 96.8 + - - +
648D SER 4.0 0.3 - - - +
650D CYS* 2.9 50.6 + - + +
651D GLN 3.6 31.9 + - - -
652D LEU* 3.8 10.3 - - + +
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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