Contacts of the strand formed by residues 603 - 609 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ASN 3.8 15.0 - - - +
602B GLU* 1.3 81.7 - - - +
604B PHE* 1.3 67.6 + - - +
632B VAL* 4.4 20.6 - - + -
671B VAL* 3.6 28.3 - - + -
672B ALA 3.7 10.1 - - - +
673B ASP* 4.5 10.1 - - + +
819B THR* 4.1 16.2 - - + +
821B HIS* 3.8 32.3 - - + +
822B PRO 2.9 8.4 + - - +
823B VAL* 3.4 5.0 - - + -
824B ARG* 3.1 22.9 + - - -
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Residues in contact with PHE 604 (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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32B ARG* 5.9 2.7 - - - -
598B ARG* 3.9 28.0 - - + -
602B GLU* 4.1 5.2 - - + -
603B LEU* 1.3 75.9 - - - +
605B LEU* 1.3 61.8 + - - +
670B VAL 3.6 0.7 - - - +
671B VAL* 3.1 6.4 - - - +
672B ALA 3.0 33.4 + - - +
673B ASP 3.4 26.5 - - - -
674B THR* 3.5 11.7 - - + +
675B PRO* 3.7 37.7 - - + -
678B ALA* 3.9 3.8 - - + +
823B VAL* 4.3 2.5 - - - -
824B ARG* 3.6 21.1 - - + +
5013B GOL 3.7 13.7 - - - -
5014B GOL 3.6 39.3 - - - +
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Residues in contact with LEU 605 (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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604B PHE* 1.3 76.7 - - - +
606B ARG* 1.3 74.3 + - - +
607B LEU* 3.9 21.5 - - + +
635B LEU* 4.7 1.6 - - + -
669B ALA* 3.7 22.0 - - + -
670B VAL 3.3 6.3 - - - +
671B VAL* 4.6 4.3 - - + -
678B ALA* 4.6 1.6 - - - -
808B VAL* 6.0 0.2 - - + -
811B ALA* 3.5 30.3 - - + +
812B VAL* 4.0 6.7 - - + -
815B ALA* 3.8 17.3 - - + -
823B VAL* 3.9 13.7 - - + +
824B ARG 3.0 11.1 + - - +
825B CYS* 3.4 37.1 - - + +
5014B GOL 4.6 6.1 + - - -
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Residues in contact with ARG 606 (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 LEU* 1.3 78.4 - - - +
607B LEU* 1.3 65.9 + - - +
608B VAL* 4.1 1.9 - - - +
669B ALA* 3.3 0.7 - - - -
670B VAL* 2.9 31.5 + - - +
675B PRO 5.4 0.7 - - - -
678B ALA* 3.6 24.5 - - + +
679B GLU* 3.7 42.5 + - - +
682B ALA* 3.6 21.7 - - + +
825B CYS* 5.1 1.6 - - - -
826B MET 5.8 0.2 + - - -
828B ASP* 2.7 27.9 + - - -
830B ASN* 4.8 7.5 + - - +
831B GLU* 3.1 43.4 + - - +
5014B GOL 6.0 0.4 + - - -
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Residues in contact with LEU 607 (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 LEU* 3.9 13.0 - - + +
606B ARG* 1.3 87.4 + - - +
608B VAL* 1.3 60.1 + - - +
609B THR* 3.9 15.0 + - + +
666B ILE* 3.9 38.6 - - + -
668B GLY 3.7 5.8 - - - +
669B ALA* 4.3 1.1 - - + -
682B ALA* 4.3 2.9 - - - +
807B LEU 4.9 0.4 - - - +
808B VAL* 4.3 12.6 - - + -
811B ALA* 3.8 28.0 - - + -
825B CYS* 5.1 2.8 - - - -
827B LEU* 3.9 27.8 - - + -
831B GLU* 4.4 11.6 + - - +
835B ILE* 4.1 13.5 - - + -
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Residues in contact with VAL 608 (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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607B LEU* 1.3 73.2 - - - +
609B THR* 1.3 65.4 + - - +
634B PHE* 3.6 24.9 - - + -
666B ILE* 3.8 0.5 - - - -
667B ILE* 2.9 33.5 + - + +
668B GLY 2.8 17.5 + - - +
669B ALA* 3.9 11.0 - - - -
670B VAL* 4.0 7.2 - - + +
682B ALA* 4.0 26.5 - - + +
685B VAL* 4.2 24.9 - - + +
687B VAL* 5.0 9.4 - - + -
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Residues in contact with THR 609 (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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607B LEU* 3.9 16.0 + - + +
608B VAL* 1.3 83.4 - - - +
610B SER* 1.3 68.4 + - - +
611B THR* 3.7 8.8 + - - +
664B GLY* 3.5 30.3 - - - +
665B HIS 3.4 3.4 - - - -
666B ILE* 4.2 6.5 - - + -
667B ILE* 4.1 5.6 - - - +
687B VAL* 6.0 0.3 - - - +
689B TYR* 4.1 4.0 + - - -
834B LEU* 4.5 8.7 - - - +
835B ILE* 3.6 24.0 - - + +
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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