Contacts of the strand formed by residues 641 - 648 (chain B) in PDB entry 5IA0
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 VAL 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631B MET* 3.4 5.3 - - - -
632B LEU* 2.9 43.9 + - + +
634B THR* 4.7 14.1 - - + +
639B LYS* 3.9 13.5 - - + +
640B GLU* 1.3 80.1 - - - +
642B PRO* 1.3 70.4 - - + +
643B VAL* 3.9 16.7 - - + +
677B ARG* 6.0 1.8 - - - +
679B GLU* 4.7 13.2 - - - +
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Residues in contact with PRO 642 (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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629B LYS* 4.1 13.9 - - - +
630B GLY 3.4 7.0 - - - +
631B MET* 3.7 17.3 - - + -
640B GLU 4.4 1.6 - - - +
641B VAL* 1.3 90.7 - - + +
643B VAL* 1.3 66.5 + - - +
693B GLU* 4.5 1.7 - - - -
694B TYR* 3.6 27.1 + - + -
696B GLU* 5.0 10.8 - - - +
1005B EDO 5.7 5.4 - - - -
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Residues in contact with VAL 643 (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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613B VAL* 5.3 1.1 - - + -
629B LYS* 3.4 6.4 - - - +
630B GLY 2.8 49.6 + - - +
631B MET 3.9 12.8 - - - -
632B LEU* 3.7 21.3 - - + -
641B VAL* 3.9 10.3 - - + +
642B PRO* 1.3 79.2 - - - +
644B ALA* 1.3 59.4 + - - +
645B ILE* 3.8 18.2 - - + -
679B GLU* 4.1 9.4 - - + -
691B ILE* 3.7 19.3 - - + -
692B THR 3.3 14.8 - - - +
693B GLU* 5.0 0.7 - - - -
694B TYR* 3.7 7.6 - - - +
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Residues in contact with ALA 644 (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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619B ILE* 4.7 2.0 - - + -
627B VAL* 4.9 2.2 - - + -
628B TYR 3.3 8.5 - - - +
643B VAL* 1.3 74.0 - - - +
645B ILE* 1.3 60.3 + - - +
646B LYS* 4.1 1.6 - - + -
690B ILE 3.7 0.6 - - - +
691B ILE* 3.4 4.5 - - - -
692B THR* 2.9 44.5 + - - +
693B GLU 4.2 1.6 - - - +
694B TYR* 3.8 7.6 - - + +
1001B A5B 3.4 44.0 - - + +
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Residues in contact with ILE 645 (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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613B VAL* 3.4 27.6 - - + -
614B THR 4.1 0.7 - - - +
615B ARG* 3.8 20.2 - - + -
627B VAL* 3.3 4.2 - - - +
628B TYR* 2.8 44.2 + - + +
630B GLY* 4.0 25.6 - - - +
643B VAL* 3.8 14.4 - - + +
644B ALA* 1.3 77.6 - - - +
646B LYS* 1.3 60.9 + - - +
647B THR* 4.2 8.5 - - + -
689B MET* 3.5 38.4 - - + -
690B ILE 3.6 3.1 - - - -
691B ILE* 4.4 7.0 - - + -
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Residues in contact with LYS 646 (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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622B GLY* 5.4 7.4 - - - -
623B GLU* 5.8 4.1 - - - +
624B PHE* 5.6 8.8 - - - +
626B GLU 4.0 3.6 - - - -
627B VAL* 3.9 28.3 - - + -
644B ALA 5.6 0.9 - - - -
645B ILE* 1.3 73.7 - - - +
647B THR* 1.3 62.3 + - - +
660B PHE* 3.5 11.4 - - + -
663B GLU* 3.2 30.1 + - - +
689B MET* 3.1 6.2 - - - +
690B ILE* 2.8 47.9 + - + +
692B THR* 5.8 5.2 - - + +
1001B A5B 3.1 47.1 + - - +
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Residues in contact with THR 647 (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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615B ARG* 4.4 5.4 - - - +
624B PHE* 3.4 15.1 - - - +
625B GLY* 3.5 8.9 + - - -
626B GLU* 2.8 38.2 + - - -
628B TYR* 3.6 29.0 - - + -
645B ILE* 4.2 4.7 - - + -
646B LYS* 1.3 78.0 - - - +
648B LEU* 1.3 62.2 + - - +
649B LYS* 5.2 0.6 - - - +
660B PHE* 3.8 7.8 - - - -
687B PRO* 4.4 11.2 - - + -
688B MET 3.4 5.6 - - - -
689B MET* 4.0 25.6 - - + -
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Residues in contact with LEU 648 (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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624B PHE* 3.7 33.4 - - + +
647B THR* 1.3 71.8 - - - +
649B LYS* 1.3 62.6 + - - +
650B ALA 3.9 0.2 + - - -
652B TYR* 3.6 42.3 - - + -
656B GLN* 4.4 4.0 - - + +
657B ARG* 4.0 11.7 - - - -
660B PHE* 3.7 28.5 - - + -
687B PRO* 3.4 21.5 - - - +
688B MET* 3.0 49.5 + - + +
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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