Contacts of the strand formed by residues 434 - 440 (chain B) in PDB entry 3VI4
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 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.3 34.8 - - + -
96B PRO* 3.4 24.2 - - + +
97B GLN 3.8 4.9 - - - -
98B GLN 4.7 0.9 - - - +
99B LEU* 5.0 2.0 - - + +
111B PHE* 4.9 5.6 - - + -
113B LEU* 3.5 24.2 - - + -
424B LYS* 3.3 7.0 - - - -
425B ILE* 3.0 39.7 + - + +
433B GLU* 1.3 74.6 - - - +
435B GLU* 1.3 73.5 + - - +
436B VAL* 3.6 13.2 + - + +
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Residues in contact with GLU 435 (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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97B GLN 3.0 8.7 + - - +
98B GLN* 3.5 37.9 + - + +
99B LEU* 3.2 23.6 + - - +
422B SER* 3.8 11.3 + - - -
423B PHE 3.9 4.3 - - - -
424B LYS* 3.4 34.7 + - + +
433B GLU* 4.1 1.2 - - + -
434B VAL* 1.3 73.9 - - - +
436B VAL* 1.3 62.0 + - - +
437B ILE* 3.4 27.5 - - + +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.6 24.9 - - + -
101B LEU* 4.7 5.6 - - + -
111B PHE* 4.5 13.5 - - + -
410B ILE* 3.8 28.5 - - + -
421B ASP 3.5 11.2 - - - +
422B SER 5.1 0.2 - - - -
423B PHE* 3.0 39.9 + - + +
425B ILE* 4.4 8.1 - - + -
434B VAL* 3.6 22.4 - - + +
435B GLU* 1.3 79.2 + - - +
437B ILE* 1.3 64.1 + - - +
438B LEU* 3.2 6.0 + - + +
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Residues in contact with ILE 437 (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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98B GLN* 3.5 20.9 - - - +
99B LEU 3.3 7.3 + - - +
100B VAL* 3.4 31.0 - - + +
101B LEU 2.8 26.0 + - - -
420B SER* 4.2 20.0 - - - +
422B SER* 3.8 17.9 - - - +
435B GLU* 3.4 27.4 - - + +
436B VAL* 1.3 67.8 - - - +
438B LEU* 1.3 61.5 + - - +
439B GLN* 5.1 7.9 - - + +
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Residues in contact with LEU 438 (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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101B LEU* 3.4 31.6 - - + +
103B LEU* 3.9 28.7 - - + -
369B LEU* 5.6 0.2 - - + -
373B VAL* 4.6 10.8 - - + -
410B ILE* 4.5 13.9 - - + -
419B ASP 3.8 0.5 - - - +
420B SER* 3.1 30.3 - - - -
421B ASP* 3.9 14.1 + - + +
423B PHE* 3.8 29.2 - - + -
436B VAL* 3.2 10.8 + - + +
437B ILE* 1.3 73.1 - - - +
439B GLN* 1.3 60.2 - - - +
440B TYR* 4.2 27.6 - - + +
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Residues in contact with GLN 439 (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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100B VAL* 4.2 16.0 - - + +
101B LEU 3.0 10.7 + - - +
102B ARG* 2.7 45.4 + - + +
103B LEU* 3.1 27.9 + - - +
419B ASP 4.4 6.1 - - - +
420B SER* 5.3 2.5 - - - -
437B ILE* 4.0 8.9 + - + +
438B LEU* 1.3 77.2 - - - +
440B TYR* 1.3 63.5 + - - +
441B ILE* 4.0 1.9 + - + +
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Residues in contact with TYR 440 (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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103B LEU* 4.0 11.0 - - + +
370B SER* 4.6 1.9 + - - -
373B VAL* 4.4 14.2 - - + +
412B SER* 4.8 11.9 - - - -
415B CYS* 5.3 0.7 - - - -
416B PRO* 3.7 35.0 - - + -
417B LYS* 4.4 13.0 - - + +
418B LYS* 5.0 2.4 - - - -
419B ASP 3.4 30.7 + - - -
420B SER* 4.1 5.4 - - - -
421B ASP* 2.7 45.1 + - - +
438B LEU* 4.2 22.6 - - + +
439B GLN* 1.3 77.1 - - - +
441B ILE* 1.3 64.2 + - - +
442B CYS* 3.8 20.8 + - - -
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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