Contacts of the strand formed by residues 716 - 722 (chain A) in PDB entry 2V3V
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 CYS 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603A GLU* 3.5 26.9 - - + +
612A TYR* 3.4 8.8 - - - -
613A LEU* 2.9 50.9 + - - -
665A THR* 4.1 5.6 - - - -
667A ARG* 3.8 19.5 - - - +
699A LEU 4.1 3.1 - - - -
700A PHE* 3.7 26.5 - - + -
701A LEU* 4.6 8.1 - - + +
712A GLU 5.6 0.2 - - - +
715A ILE* 1.3 77.9 - - - +
717A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 717 (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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603A GLU* 3.1 17.5 + - + +
604A GLU 3.9 19.3 - - - +
605A PRO 4.0 5.6 - - - -
609A TYR* 3.8 29.3 - - + +
611A LEU 3.4 4.5 - - - -
665A THR* 3.4 25.2 - - - -
666A ARG* 3.9 9.0 + - - +
716A CYS* 1.3 77.2 - - - +
718A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 3.9 6.0 - - - +
610A PRO 3.2 8.1 - - - -
611A LEU* 2.9 35.6 + - + +
613A LEU* 3.8 26.0 - - + -
663A VAL* 4.6 1.6 - - + -
664A GLU 3.3 12.1 - - - +
665A THR* 4.1 6.5 - - + -
685A ILE* 3.9 19.1 - - + -
717A ALA* 1.3 74.7 - - - +
719A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 719 (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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608A GLU* 3.4 43.0 + - - +
609A TYR* 3.7 23.0 + - + -
610A PRO* 3.8 15.9 - - + -
611A LEU* 4.3 3.6 - - - -
662A ILE 3.7 0.7 - - - +
663A VAL* 3.6 0.3 - - - -
664A GLU* 2.8 76.5 + - + +
718A ALA* 1.3 76.0 - - - +
720A VAL* 1.3 70.1 + - - +
721A ARG* 4.7 5.9 - - - +
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Residues in contact with VAL 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 3.5 25.9 - - + +
645A ILE* 4.3 9.6 - - + -
653A THR* 5.4 3.3 + - - -
655A ILE* 3.8 26.7 - - + +
661A VAL* 3.9 24.2 - - + -
662A ILE 3.3 3.8 - - - +
663A VAL* 4.4 8.3 - - + -
685A ILE* 3.6 25.1 - - + -
719A ARG* 1.3 84.1 - - - +
721A ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 721 (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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655A ILE* 4.7 2.7 - - - -
661A VAL* 3.3 7.6 - - - +
662A ILE* 2.7 76.4 + - + +
664A GLU* 2.9 35.2 + - - +
719A ARG* 4.7 7.5 - - - +
720A VAL* 1.3 77.3 - - - +
722A LYS* 1.3 66.5 + - - +
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Residues in contact with LYS 722 (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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654A GLY 4.3 14.5 + - - +
655A ILE* 4.5 12.9 - - + +
656A LYS* 6.1 1.4 - - - +
659A ASP* 3.3 33.3 + - + +
660A SER 4.0 10.5 - - - +
661A VAL* 4.3 4.0 - - - -
662A ILE* 4.6 1.0 - - - +
721A ARG* 1.3 83.0 - - - +
723A ALA* 1.3 72.0 + - - +
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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