Contacts of the helix formed by residues 516 - 527 (chain B) in PDB entry 2OBF
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 SER 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514B PRO 4.0 2.4 + - - -
515B ASP* 1.3 74.1 + - - +
517B ALA* 1.3 69.1 + - - +
518B PRO* 3.3 3.0 - - - -
519B GLY* 3.5 3.8 + - - -
520B GLN* 3.1 40.5 + - - +
689B PRO* 5.8 1.2 - - - +
696B ARG* 3.5 31.6 - - - +
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Residues in contact with ALA 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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515B ASP* 3.4 7.5 + - - +
516B SER* 1.3 82.6 + - - +
518B PRO* 1.3 61.1 - - + +
520B GLN* 3.0 10.8 + - - +
521B ALA* 2.7 37.3 + - - +
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Residues in contact with PRO 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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515B ASP* 3.1 35.4 - - + +
516B SER 3.4 4.3 - - - -
517B ALA* 1.3 92.9 - - + +
519B GLY* 1.3 64.9 + - - +
521B ALA* 3.1 13.3 + - + +
522B ALA* 3.1 11.6 + - - +
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Residues in contact with GLY 519 (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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515B ASP 5.3 1.0 + - - -
516B SER 3.5 5.5 + - - -
518B PRO* 1.3 79.8 - - - +
520B GLN* 1.3 61.6 + - - +
522B ALA* 3.1 10.7 + - - +
523B VAL* 3.0 27.8 + - - +
689B PRO* 4.5 22.7 - - - +
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Residues in contact with GLN 520 (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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516B SER* 3.1 42.1 + - - +
517B ALA* 3.0 12.9 + - - +
519B GLY* 1.3 77.9 - - - +
521B ALA* 1.3 56.8 + - - +
523B VAL* 3.2 9.9 + - - +
524B ALA* 3.0 28.5 + - - +
658B ASP* 5.1 0.5 - - - +
660B HIS* 3.5 55.2 + - + +
661B GLN* 4.1 11.4 + - - -
689B PRO* 5.1 2.4 - - + +
693B SER* 5.4 2.9 + - - +
696B ARG* 5.0 4.2 - - - +
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Residues in contact with ALA 521 (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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517B ALA* 2.7 19.7 + - + +
518B PRO* 3.5 6.7 - - + +
520B GLN* 1.3 73.6 - - - +
522B ALA* 1.3 57.5 + - - +
524B ALA* 3.8 6.7 - - - +
525B SER* 3.0 29.8 + - - -
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Residues in contact with ALA 522 (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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518B PRO 3.1 11.9 + - - +
519B GLY* 3.1 14.3 + - - +
521B ALA* 1.3 75.9 - - - +
523B VAL* 1.3 64.9 + - + +
525B SER* 3.5 5.1 - - - -
526B ALA* 3.0 26.0 + - - +
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Residues in contact with VAL 523 (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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519B GLY 3.0 17.8 + - - +
520B GLN* 3.2 10.5 + - - +
522B ALA* 1.3 73.5 - - + +
524B ALA* 1.3 68.5 + - - +
526B ALA* 3.2 6.1 + - - +
527B TYR* 3.0 45.3 + - + -
660B HIS* 4.4 6.7 - - + -
687B VAL* 3.3 43.5 - - + +
689B PRO* 4.3 13.2 - - + -
730B THR 6.1 0.4 - - - +
3002B SAH 4.4 6.5 - - - +
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Residues in contact with ALA 524 (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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520B GLN 3.0 15.6 + - - +
521B ALA* 3.8 8.5 - - - +
523B VAL* 1.3 78.4 - - - +
525B SER* 1.3 65.3 + - - +
527B TYR* 3.2 8.0 + - - +
528B GLN* 3.3 21.8 + - - +
602B PHE* 4.1 28.9 - - + -
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Residues in contact with SER 525 (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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521B ALA 3.0 18.8 + - - -
522B ALA* 3.5 7.2 - - - -
524B ALA* 1.3 74.7 - - - +
526B ALA* 1.3 61.9 + - - +
528B GLN* 2.8 17.5 + - - +
529B ARG* 2.4 37.4 + - - +
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Residues in contact with ALA 526 (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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522B ALA 3.0 15.6 + - - +
523B VAL* 3.6 6.1 - - - +
525B SER* 1.3 79.2 + - - +
527B TYR* 1.3 62.4 + - + +
528B GLN 3.2 1.2 + - - -
529B ARG* 3.3 23.3 + - - +
530B PHE 4.2 1.0 + - - -
727B ALA* 4.3 3.5 - - - +
729B LEU* 3.8 30.1 - - + +
730B THR 5.7 1.1 - - - +
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Residues in contact with TYR 527 (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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523B VAL* 3.0 39.2 + - + +
524B ALA* 3.7 6.7 - - - +
525B SER 3.1 0.6 + - - -
526B ALA* 1.3 74.8 - - + +
528B GLN* 1.3 63.2 + - - +
529B ARG 3.2 0.9 - - - -
530B PHE* 3.3 28.8 - + - +
602B PHE* 4.5 6.7 - - + -
603B LEU* 3.2 40.0 - - + +
686B ALA* 2.8 36.0 + - - +
687B VAL* 4.0 0.7 - - + -
722B TYR* 2.5 32.9 + - - -
729B LEU* 3.6 14.8 - - + +
730B THR 6.0 0.2 - - - -
3002B SAH 3.6 45.9 - + - +
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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