Contacts of the strand formed by residues 603 - 609 (chain A) in PDB entry 1VDV
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 LEU 603 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ARG* 5.9 0.2 - - - +
601A ASN 3.9 12.3 - - - +
602A GLU* 1.3 81.5 - - - +
604A PHE* 1.3 68.1 + - - +
632A VAL* 4.3 18.2 - - + -
671A VAL* 3.7 25.8 - - + -
672A ALA 3.7 13.0 - - - +
673A ASP* 4.4 13.0 - - + +
819A THR* 4.2 15.3 - - + +
821A HIS* 3.9 31.2 - - + +
822A PRO 3.0 8.9 + - - +
823A VAL* 3.3 6.3 - - + -
824A ARG* 3.1 23.7 + - - +
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Residues in contact with PHE 604 (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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32A ARG* 5.9 4.7 - - + -
598A ARG* 3.7 36.6 - - + -
602A GLU* 3.9 6.1 - - + -
603A LEU* 1.3 76.1 - - - +
605A LEU* 1.3 61.7 + - - +
670A VAL 3.7 0.5 - - - +
671A VAL* 3.2 5.7 - - - +
672A ALA 2.9 34.4 + - - +
673A ASP 3.4 26.2 - - - -
674A THR* 3.7 17.9 - - - +
675A PRO* 3.4 32.1 - - + -
678A ALA* 4.0 4.3 - - + +
823A VAL* 4.3 2.2 - - - -
824A ARG* 3.6 17.9 - - + +
5006A GOL 3.4 39.5 - - - -
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Residues in contact with LEU 605 (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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604A PHE* 1.3 76.7 - - - +
606A ARG* 1.3 74.4 + - - +
607A LEU* 3.9 19.3 - - + +
635A LEU* 5.2 0.7 - - + -
669A ALA* 3.8 21.5 - - + -
670A VAL 3.3 5.4 - - - +
671A VAL* 4.7 3.4 - - + -
678A ALA* 4.6 1.8 - - - -
808A VAL* 5.9 0.7 - - + -
811A ALA* 3.5 31.6 - - + +
812A VAL* 3.9 7.2 - - + -
815A ALA* 3.7 17.5 - - + -
823A VAL* 3.9 13.2 - - + -
824A ARG 3.0 11.1 + - - +
825A CYS* 3.4 35.8 - - + +
5006A GOL 4.8 4.2 + - - -
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Residues in contact with ARG 606 (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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605A LEU* 1.3 78.0 - - - +
607A LEU* 1.3 64.6 + - - +
608A VAL* 3.7 1.0 + - - +
669A ALA* 3.3 0.5 - - - -
670A VAL* 2.8 36.9 + - - +
675A PRO 5.5 0.4 - - - -
678A ALA* 3.6 25.4 - - + +
679A GLU* 3.5 38.2 + - - +
682A ALA* 3.6 21.5 - - + -
825A CYS* 5.2 0.9 - - - -
828A ASP* 3.0 27.7 + - - -
830A ASN* 4.9 6.9 + - - +
831A GLU* 3.0 39.9 + - - +
5019A GOL 3.4 31.5 + - - -
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Residues in contact with LEU 607 (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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605A LEU* 3.9 13.6 - - + +
606A ARG* 1.3 81.5 + - - +
608A VAL* 1.3 60.1 + - - +
609A THR* 3.9 13.1 + - + +
655A PHE* 4.9 0.2 - - + -
666A ILE* 3.8 38.1 - - + -
668A GLY 3.7 5.8 - - - +
669A ALA* 4.3 2.0 - - + +
807A LEU* 4.8 0.9 - - + +
808A VAL* 4.4 13.7 - - + -
811A ALA* 3.9 28.3 - - + -
825A CYS* 5.1 2.5 - - - -
827A LEU* 3.9 26.9 - - + -
831A GLU* 4.4 8.2 + - - +
835A ILE* 4.2 14.1 - - + -
5019A GOL 3.6 21.7 + - - -
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Residues in contact with VAL 608 (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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606A ARG 4.2 0.2 - - - +
607A LEU* 1.3 74.7 - - - +
609A THR* 1.3 66.1 + - - +
634A PHE* 3.9 21.8 - - + -
666A ILE* 3.8 1.2 - - - -
667A ILE* 2.8 33.6 + - + +
668A GLY 2.9 18.6 + - - +
669A ALA* 4.1 5.4 - - - -
670A VAL* 4.0 12.1 - - + -
682A ALA* 3.9 25.6 - - + +
685A VAL* 4.2 25.4 - - + +
687A VAL* 4.9 10.1 - - + -
5019A GOL 3.6 7.6 - - - +
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Residues in contact with THR 609 (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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607A LEU* 4.2 10.8 - - + +
608A VAL* 1.3 82.1 - - - +
610A SER* 1.3 66.0 + - - +
611A THR* 3.6 8.8 + - - +
664A GLY* 3.5 32.3 - - - +
665A HIS 3.3 3.6 - - - -
666A ILE* 4.1 11.0 - - + -
667A ILE* 4.0 5.6 - - - +
687A VAL* 6.0 0.3 - - - +
689A TYR* 4.1 3.6 + - - -
834A LEU* 4.5 9.0 - - - +
835A ILE* 3.6 24.2 - - + +
5019A GOL 3.0 20.3 + - - +
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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