Contacts of the helix formed by residues 508 - 518 (chain B) in PDB entry 3VS5
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 THR 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378B GLU* 3.2 18.6 - - - +
442B LYS* 4.0 15.7 - - - +
445B VAL* 5.2 0.7 - - - -
507B PRO* 1.3 75.5 - - - +
509B PHE* 1.3 58.9 + - - +
510B GLU* 3.6 15.1 + - - +
511B TYR* 3.0 26.8 + - - +
512B ILE* 3.0 30.8 + - - +
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Residues in contact with PHE 509 (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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371B ALA* 4.0 8.0 - - - +
374B MET* 3.4 52.5 - - + -
375B ALA* 3.7 23.0 - - + +
378B GLU* 3.1 11.0 + - - +
387B LEU* 4.5 0.7 - - + -
441B ILE* 3.6 33.7 - - + -
444B ASP* 3.6 7.0 - - + -
445B VAL* 3.5 29.6 - - + -
448B PHE* 3.6 31.0 - + + -
507B PRO 4.2 0.2 + - - -
508B THR* 1.3 70.5 - - - +
510B GLU* 1.3 60.7 + - - +
512B ILE* 3.8 14.5 - - + +
513B GLN* 2.8 32.6 + - - +
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Residues in contact with GLU 510 (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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497A ARG* 5.5 6.7 + - - -
375B ALA* 4.0 11.0 - - + +
378B GLU* 3.2 17.1 + - - +
379B GLN* 4.7 11.5 - - - +
508B THR* 3.7 11.8 + - - +
509B PHE* 1.3 77.3 - - - +
511B TYR* 1.3 56.0 + - - +
513B GLN* 3.9 6.2 - - - +
514B SER* 3.1 25.6 + - - -
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Residues in contact with TYR 511 (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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511A TYR* 4.0 34.8 - + + -
514A SER* 4.4 19.4 + - - -
494B ILE* 5.4 8.3 - - + -
497B ARG* 3.8 28.7 + - - -
507B PRO* 4.1 16.8 - - + -
508B THR* 3.0 25.0 + - - +
510B GLU* 1.3 75.4 + - - +
512B ILE* 1.3 69.2 + - + +
514B SER* 3.1 7.0 + - - -
515B VAL* 2.9 49.6 + - + +
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Residues in contact with ILE 512 (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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371B ALA* 3.9 6.1 - - + -
445B VAL* 4.2 9.0 - - + -
448B PHE* 3.6 28.3 - - + -
494B ILE* 4.5 15.3 - - + -
498B CYS* 4.0 25.4 - - - -
507B PRO* 4.1 19.5 - - + -
508B THR 3.0 21.9 + - - +
509B PHE* 3.8 22.7 - - + +
511B TYR* 1.3 78.1 - - + +
513B GLN* 1.3 58.3 + - - +
515B VAL* 3.3 3.9 + - - +
516B LEU* 2.9 41.6 + - + +
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Residues in contact with GLN 513 (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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368B ALA 4.3 2.9 - - - +
371B ALA* 3.8 17.0 - - + +
372B GLU* 3.6 40.9 - - + +
375B ALA* 3.5 19.8 - - - +
509B PHE 2.8 19.7 + - - +
510B GLU* 3.9 6.9 - - - +
512B ILE* 1.3 73.0 - - - +
514B SER* 1.3 59.1 + - - +
516B LEU* 4.6 1.3 - - - +
517B ASP* 2.9 56.8 + - - +
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Residues in contact with SER 514 (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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511A TYR* 3.9 28.3 + - - -
510B GLU 3.1 12.2 + - - -
511B TYR* 3.2 14.1 + - - -
513B GLN* 1.3 81.7 - - - +
515B VAL* 1.3 64.1 + - - +
517B ASP* 4.0 5.2 - - - +
518B ASP* 3.7 21.8 + - - +
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Residues in contact with VAL 515 (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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523A THR* 3.9 30.3 + - + +
494B ILE* 3.9 24.9 - - + -
511B TYR* 2.9 53.6 + - + +
512B ILE* 3.9 4.0 - - - +
514B SER* 1.3 77.9 - - - +
516B LEU* 1.3 68.0 + - + +
517B ASP 3.4 0.2 + - - -
518B ASP* 3.4 2.5 + - - -
519B PHE* 3.0 28.0 + - + -
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Residues in contact with LEU 516 (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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157B LYS* 5.1 1.7 + - - -
364B ILE* 4.0 17.4 - - + +
365B ASP* 6.0 0.2 - - - -
367B SER* 3.6 38.8 - - - +
368B ALA* 3.9 18.6 - - + +
371B ALA* 4.3 0.9 - - + -
448B PHE* 4.0 8.5 - - + -
452B LEU* 4.2 2.7 - - + -
491B LEU* 4.1 25.6 - - + -
494B ILE* 4.7 12.1 - - + -
512B ILE* 2.9 38.0 + - + +
513B GLN 4.2 0.9 - - - +
515B VAL* 1.3 79.0 - - + +
517B ASP* 1.3 63.0 + - - +
519B PHE* 3.3 28.2 - - + +
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Residues in contact with ASP 517 (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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156B ARG* 5.9 0.9 - - - +
157B LYS* 3.0 60.6 + - + +
160B GLU* 4.9 1.0 - - - +
161B ARG* 3.9 3.8 + - - -
368B ALA* 3.4 19.9 - - - +
372B GLU* 5.4 2.4 - - - +
513B GLN* 2.9 44.7 + - - +
514B SER* 4.0 6.1 - - - +
516B LEU* 1.3 77.3 - - - +
518B ASP* 1.3 66.9 + - - +
519B PHE 3.6 1.2 + - - -
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Residues in contact with ASP 518 (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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522A ALA* 4.8 0.2 - - - +
523A THR* 4.7 4.6 + - - -
156B ARG* 2.8 43.4 + - - -
157B LYS* 5.3 1.7 - - - +
160B GLU* 5.2 3.1 - - - +
514B SER 3.7 13.3 + - - +
515B VAL* 3.4 5.7 + - - +
517B ASP* 1.3 85.1 - - - +
519B PHE* 1.3 59.5 + - - +
520B TYR 3.1 3.4 - - - -
521B THR* 2.8 47.1 + - - +
523B THR 6.2 0.2 - - - +
526B GLN* 3.3 19.7 + - - +
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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