Contacts of the strand formed by residues 735 - 740 (chain B) in PDB entry 3ZHT
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 735 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671B THR 3.1 6.0 + - - +
672B ILE* 3.8 9.7 - - + +
673B HIS* 2.9 28.2 + - - +
705B PRO* 3.8 10.1 - - + +
707B PHE* 3.8 28.5 - - + -
724B ALA* 3.4 47.1 - - + +
727B PHE* 3.5 27.6 - - + -
728B ARG 4.2 1.1 - - - +
733B LYS 3.9 4.7 - - - +
734B ASP* 1.3 75.7 - - - +
736B VAL* 1.3 68.1 + - - +
737B ILE* 4.2 0.9 - - - -
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Residues in contact with VAL 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 4.5 6.5 - - + -
658B LEU* 5.5 0.7 - - + -
673B HIS* 3.6 27.8 - - + -
675B VAL* 4.4 5.2 - - + -
696B THR* 3.6 35.0 - - + -
699B ALA* 3.5 28.3 - - + -
704B ALA* 4.5 8.3 - - + -
705B PRO 3.1 11.5 + - - +
706B ILE* 3.4 10.1 - - + +
707B PHE* 2.9 28.2 + - - -
734B ASP* 5.4 0.4 - - + -
735B VAL* 1.3 78.2 - - - +
737B ILE* 1.3 68.7 + - - +
738B ASP 4.0 0.2 - - - -
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Residues in contact with ILE 737 (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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517B MET* 3.7 31.0 - - + -
521B VAL* 5.0 0.2 - - + -
672B ILE* 4.3 15.7 - - + -
673B HIS 2.8 12.8 + - - +
674B ILE* 3.4 14.3 - - + +
675B VAL* 2.8 32.9 + - - +
707B PHE* 3.5 4.3 - - + +
709B VAL* 3.8 14.4 - - + -
720B VAL* 3.8 21.1 - - + -
721B ALA* 3.8 22.4 - - + +
724B ALA* 3.7 29.2 - - + -
735B VAL* 4.9 1.6 - - + -
736B VAL* 1.3 78.7 - - - +
738B ASP* 1.3 57.7 + - - +
739B MET 3.6 1.6 + - - +
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Residues in contact with ASP 738 (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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675B VAL* 4.1 5.0 - - - +
677B ASN* 2.8 42.8 + - - +
694B TYR* 4.1 7.6 - - - +
695B CYS* 3.6 8.3 + - - -
696B THR* 3.7 21.2 + - + +
706B ILE* 4.6 1.1 - - + -
707B PHE 2.8 10.0 + - - +
708B HIS* 2.7 35.2 + - + +
709B VAL* 2.8 28.5 + - - -
736B VAL 4.0 0.6 - - - -
737B ILE* 1.3 70.8 - - - +
739B MET* 1.3 57.8 + - - +
740B LEU* 3.4 11.1 + - - +
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Residues in contact with MET 739 (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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511B ALA* 3.7 26.7 - - + +
513B THR* 3.9 13.5 - - - -
514B VAL* 3.6 30.5 - - + +
517B MET* 3.7 34.5 - - + +
674B ILE* 4.9 3.1 - - + -
675B VAL 2.9 17.8 + - - +
676B VAL* 4.4 5.4 - - + -
677B ASN* 3.0 25.8 + - - +
709B VAL* 3.6 7.6 - - + -
711B GLY* 4.0 15.3 - - - -
717B CYS* 4.2 0.4 - - - -
737B ILE* 3.6 1.8 + - + -
738B ASP* 1.3 70.9 - - - +
740B LEU* 1.3 60.8 + - - +
741B CYS* 3.4 33.6 + - + -
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Residues in contact with LEU 740 (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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387B ILE* 3.2 56.8 - - + +
388B ASP* 3.9 16.6 - - + -
389B PRO* 3.6 8.7 - - + +
677B ASN* 3.5 20.2 - - - +
679B GLN* 4.2 15.0 - - + +
694B TYR* 5.9 0.7 - - + -
708B HIS* 4.3 4.0 - - + -
709B VAL 2.8 12.0 + - - +
711B GLY* 2.7 32.1 + - - -
738B ASP* 3.4 31.9 + - - +
739B MET* 1.3 67.9 - - - +
741B CYS* 1.3 58.5 + - - +
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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