Contacts of the strand formed by residues 636 - 641 (chain B) in PDB entry 5ZE3
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 THR 636 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B ILE* 5.1 2.2 - - + -
634B VAL* 3.7 2.0 - - - +
635B PHE* 1.3 95.5 - - + +
637B HIS* 1.3 76.2 + - - +
638B TYR* 3.1 34.6 - - + +
653B LYS* 3.4 17.3 - - - -
654B ALA* 3.3 14.9 + - - +
656B PHE* 3.6 27.4 - - + -
712B VAL* 4.6 0.9 - - + -
713B VAL 3.0 13.2 - - - +
714B ILE* 4.6 10.1 - - + -
716B PRO* 4.0 1.8 - - - +
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Residues in contact with HIS 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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634B VAL* 3.4 9.6 - - + -
636B THR* 1.3 90.6 + - - +
638B TYR* 1.3 62.6 + - - +
639B ASP* 3.2 17.6 - - - +
647B LYS* 5.6 2.7 - - - -
652B HIS 3.8 4.3 - - - -
653B LYS* 3.4 40.7 + - + +
711B GLN* 3.2 15.6 - - - +
712B VAL* 3.4 0.7 - - - -
713B VAL* 2.9 37.1 + - + +
716B PRO* 3.3 29.3 - - + +
717B ASN* 4.7 9.4 + - - -
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Residues in contact with TYR 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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599B PHE* 3.5 33.0 - + + -
601B SER* 2.9 10.3 + - - -
636B THR* 3.1 29.7 - - + +
637B HIS* 1.3 70.4 - - - +
639B ASP* 1.3 64.1 + - - +
651B GLY* 3.3 3.3 - - - -
652B HIS* 2.9 45.2 + - + -
654B ALA* 4.0 14.4 - - + -
656B PHE* 3.3 18.2 - - - -
695B CYS 4.1 10.8 - - - -
696B GLN* 2.7 26.0 + - - -
697B TRP 3.7 14.6 - - - +
698B VAL* 3.5 20.7 - - + +
710B PHE* 5.6 0.2 - - - -
711B GLN 3.9 2.7 - - - -
712B VAL* 3.6 22.2 - - + -
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Residues in contact with ASP 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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637B HIS* 3.2 32.3 - - - +
638B TYR* 1.3 84.1 - - - +
640B LEU* 1.3 59.5 + - - +
641B LEU* 3.8 14.9 + - + +
647B LYS* 3.4 39.9 + - + +
651B GLY* 4.0 8.7 - - - -
652B HIS 4.0 7.6 - - - +
653B LYS* 4.8 3.1 - - - -
698B VAL* 4.3 3.6 - - - +
710B PHE* 3.7 8.4 - - - -
711B GLN* 3.2 45.5 + - + +
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Residues in contact with LEU 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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597B LEU* 3.8 20.4 - - + -
639B ASP* 1.3 75.1 - - - +
641B LEU* 1.3 60.4 + - - +
647B LYS* 4.1 2.3 - - - +
648B VAL* 3.3 4.2 + - + +
649B ALA* 2.9 44.2 + - + +
698B VAL* 4.6 7.4 - - + +
700B ILE* 4.3 14.1 - - + -
703B VAL* 4.2 18.2 - - + -
708B TYR* 4.0 29.8 - - + -
709B LEU 3.5 4.9 - - - +
710B PHE* 3.6 26.2 - - + -
734B SER* 3.9 16.4 - - - +
736B TYR* 5.9 0.7 - - + -
741B ILE* 5.6 4.5 - - + -
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Residues in contact with LEU 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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639B ASP* 3.8 28.3 - - + +
640B LEU* 1.3 73.7 - - - +
642B ASN* 1.3 65.9 + - - +
645B GLY* 3.5 22.7 - - - +
646B THR 2.5 26.2 - - - +
647B LYS* 3.8 13.2 - - + -
648B VAL* 3.6 6.3 - - - -
708B TYR* 3.3 4.0 - - - +
709B LEU* 2.3 57.8 + - + +
711B GLN* 4.7 21.3 - - + +
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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