Contacts of the strand formed by residues 633 - 641 (chain B) in PDB entry 4V1M
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 633 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401B PHE* 3.9 17.7 - - + +
404B LYS 5.3 4.3 + - - +
406B LEU* 3.2 36.3 - - + -
521B LEU* 3.5 40.6 - - + +
539B LEU* 3.9 23.1 - - + -
543B SER* 4.0 6.3 - - - -
544B CYS 3.4 11.9 - - - +
545B ILE* 3.8 4.9 - - + -
631B GLY 4.2 1.3 - - - +
632B ARG* 1.3 70.6 - - - +
634B TYR* 1.3 61.7 + - - +
694B ASP* 3.4 18.9 - - - +
695B ALA 3.9 1.0 + - - -
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Residues in contact with TYR 634 (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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41B LYS* 4.1 9.0 + - - -
521B LEU* 3.6 4.2 - - - +
542B MET 3.8 0.7 - - - +
543B SER* 3.3 6.1 - - - -
544B CYS* 2.9 56.0 + - + +
545B ILE 3.7 5.7 + - - -
546B SER* 3.2 30.1 - - - -
612B GLU* 4.0 27.7 + - + +
632B ARG* 3.6 13.7 - - - +
633B VAL* 1.3 72.6 - - - +
635B ARG* 1.3 60.6 + - - +
692B TYR* 3.4 53.9 - + + -
693B ILE 3.7 20.6 - - - +
694B ASP* 3.9 6.3 - - + +
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Residues in contact with ARG 635 (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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519B TRP* 3.0 32.7 + - - +
520B GLY* 3.7 37.5 + - - +
521B LEU* 3.8 13.5 - - + -
542B MET* 4.0 6.1 - - + +
634B TYR* 1.3 75.8 - - - +
636B PRO* 1.4 72.2 + - + +
637B LEU* 3.8 14.0 + - + +
691B GLU 3.7 0.3 - - - +
692B TYR* 4.4 4.3 - - - -
693B ILE* 3.0 32.5 + - - +
698B GLU* 2.7 26.3 + - - +
703B ILE* 3.7 21.2 - - - +
742B GLU* 2.5 34.9 + - - -
748B ILE* 5.1 1.2 - - - +
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Residues in contact with PRO 636 (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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37B PHE* 3.9 14.6 - - + -
542B MET* 3.3 44.4 - - + +
635B ARG* 1.4 87.0 + - + +
637B LEU* 1.3 65.8 + - - +
681B TRP* 3.5 37.0 - - + -
690B VAL* 4.3 1.8 - - + -
691B GLU 3.2 8.5 - - - +
692B TYR* 3.7 13.9 - - + -
742B GLU* 5.5 0.3 - - - +
743B ILE* 3.3 16.4 - - + +
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Residues in contact with LEU 637 (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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635B ARG* 3.8 17.7 + - + +
636B PRO* 1.3 77.9 - - - +
638B PHE* 1.3 66.2 + - - +
639B ILE* 4.3 0.5 - - - +
690B VAL* 3.2 6.6 - - - +
691B GLU* 2.9 32.5 + - - +
693B ILE* 3.7 32.1 - - + -
701B ILE* 3.8 22.7 - - + -
703B ILE* 3.8 18.8 - - + -
740B HIS* 4.2 4.9 - - + -
741B CYS 3.3 17.0 - - - +
742B GLU* 3.6 34.8 - - - +
743B ILE* 4.0 2.2 - - - +
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Residues in contact with PHE 638 (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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25B ILE* 5.3 11.2 - - + -
30B SER* 4.2 11.7 - - - -
33B VAL* 3.5 44.0 - - + -
637B LEU* 1.3 73.6 - - - +
639B ILE* 1.4 60.0 + - - +
651B LEU* 3.6 31.6 - - + -
653B VAL* 3.5 29.4 - - + -
684B LEU* 6.3 0.2 - - + -
689B LEU 3.8 3.6 - - - -
690B VAL* 4.4 7.0 - - + -
707B PRO* 5.4 3.4 - - + -
740B HIS* 3.2 7.1 - - - +
741B CYS* 2.8 37.0 + - + +
742B GLU 4.0 7.2 - - - -
743B ILE* 3.6 44.5 - - + +
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Residues in contact with ILE 639 (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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605B ARG* 3.4 40.8 - - + +
638B PHE* 1.4 74.0 - - - +
640B VAL* 1.3 63.8 + - - +
641B GLU* 3.7 19.1 - - + +
651B LEU* 3.5 5.0 - - - +
652B LYS* 3.0 29.5 + - + +
653B VAL* 4.8 0.5 + - - +
688B GLY 3.4 25.6 - - - +
689B LEU 2.9 13.7 + - - +
690B VAL 3.7 13.9 - - - +
691B GLU* 3.6 39.3 - - + +
739B THR 4.0 6.1 - - - +
740B HIS* 3.9 6.1 - - + -
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Residues in contact with VAL 640 (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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639B ILE* 1.3 75.0 - - - +
641B GLU* 1.3 75.3 + - - +
649B LYS* 3.8 15.1 - - + -
650B GLU 3.9 1.3 - - - -
651B LEU* 3.7 31.9 - - + +
704B ALA* 5.8 0.9 - - + -
711B GLU* 3.2 25.8 - - - +
738B PHE* 3.7 27.0 - - + +
739B THR* 3.0 20.0 + - - +
740B HIS 3.5 28.3 - - - +
741B CYS* 3.7 4.5 - - + +
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Residues in contact with GLU 641 (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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598B GLU* 5.6 2.6 - - - +
605B ARG* 3.4 26.6 + - - -
639B ILE* 3.7 5.7 + - + +
640B VAL* 1.3 88.5 - - - +
642B ASP* 1.4 60.4 + - - +
643B ASP* 2.8 47.2 + - + +
649B LYS* 3.6 5.6 - - - +
650B GLU 2.8 36.0 + - - +
652B LYS* 4.1 31.4 - - + +
739B THR 5.0 0.2 - - - +
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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