Contacts of the strand formed by residues 639 - 645 (chain A) in PDB entry 2VZ9
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 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637A GLY* 3.7 2.1 - - - -
638A ILE* 1.3 73.8 - - - +
640A PRO* 1.3 90.3 - - + +
641A ALA* 3.9 7.4 - - + +
651A ILE* 3.3 7.0 - - - +
652A SER 3.1 32.2 + - - +
683A HIS 4.2 12.1 - - - +
684A SER* 4.3 9.9 - - - -
685A TYR* 3.7 33.9 - - + +
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Residues in contact with PRO 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A TRP* 2.8 44.7 - - + -
630A CYS* 4.0 23.8 - - + -
631A LYS* 3.9 36.8 - - + +
634A CYS* 5.4 1.1 - - + -
638A ILE 4.2 3.4 - - - +
639A VAL* 1.3 96.5 - - + +
641A ALA* 1.3 57.8 + - - +
649A VAL* 4.4 2.9 - - + -
651A ILE* 4.2 9.0 - - + -
742A PRO* 4.9 3.1 - - - +
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Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A MET* 4.3 5.4 - - + -
627A TRP* 3.8 3.6 - - - -
639A VAL* 3.7 1.3 + - + -
640A PRO* 1.3 73.7 - - - +
642A CYS* 1.3 62.0 + - - +
650A THR 3.1 15.4 + - - +
652A SER* 3.6 23.3 - - - -
682A PHE 4.1 0.7 - - - +
683A HIS* 3.4 32.3 - - + +
742A PRO* 3.4 10.5 - - - +
743A VAL* 3.2 25.6 + - - +
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Residues in contact with CYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A HIS* 4.2 11.2 - - - -
581A SER* 5.8 0.2 - - - -
620A MET* 4.7 4.0 - - - -
627A TRP* 4.1 2.2 - - - -
641A ALA* 1.3 81.6 - - - +
643A HIS* 1.3 60.3 + - - +
644A ASN* 3.6 12.3 - - - +
649A VAL* 3.1 15.0 - - - +
650A THR* 3.0 57.8 + - - +
683A HIS* 4.4 12.1 - - - -
743A VAL* 3.0 28.9 - - + -
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Residues in contact with HIS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A TRP* 3.1 52.3 + + + +
641A ALA 4.3 0.2 - - - -
642A CYS* 1.3 70.8 - - - +
644A ASN* 1.3 62.3 + - - +
645A SER 3.9 8.1 + - - -
646A LYS* 5.2 3.2 + - - -
649A VAL* 3.8 7.4 - - + -
743A VAL 3.1 12.7 + - - +
744A LEU* 4.5 4.3 - - + -
745A PHE* 2.8 10.8 + - - +
746A GLN* 2.7 69.3 + - + +
747A GLU* 3.1 34.1 + - - +
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Residues in contact with ASN 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A HIS* 2.8 36.9 + - - -
622A ALA* 4.9 3.5 - - - +
642A CYS* 3.5 10.3 + - - +
643A HIS* 1.3 76.2 - - - +
645A SER* 1.3 62.4 + - - +
648A THR* 3.1 27.3 + - + +
650A THR* 3.2 20.4 + - - -
745A PHE* 3.9 7.6 - - + -
746A GLN* 3.1 24.0 + - - +
749A LEU* 4.1 4.0 - - - +
767A LEU* 5.0 3.9 - - - +
770A VAL* 3.4 34.9 - - + +
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Residues in contact with SER 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A HIS* 3.9 11.1 + - - -
644A ASN* 1.3 79.7 + - - +
646A LYS* 1.3 62.1 + - - +
647A ASP* 2.8 10.8 + - - -
648A THR* 2.5 50.2 + - - +
649A VAL* 5.3 0.5 - - - +
746A GLN* 3.3 14.9 - - - +
770A VAL* 3.9 10.3 - - - -
773A ARG* 4.8 7.4 - - - -
774A SER* 3.4 23.3 - - - -
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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