Contacts of the helix formed by residues 528 - 537 (chain B) in PDB entry 4OSV
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 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522B CYS* 3.6 2.7 - - - -
526B GLY 5.0 3.1 - - - +
527B LEU* 1.3 78.2 - - - +
529B PRO* 1.3 75.2 - - + +
530B GLN* 3.8 9.6 + - - +
531B GLN* 2.8 46.9 + - - +
532B VAL* 3.1 12.5 + - - +
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Residues in contact with PRO 529 (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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493B LEU* 5.4 6.7 - - + -
497B GLN* 6.1 0.2 - - - -
518B LEU* 4.1 27.0 - - + +
522B CYS* 3.7 19.3 - - + -
527B LEU 4.6 0.2 - - - +
528B THR* 1.3 89.5 - - + +
530B GLN* 1.3 56.1 + - - +
532B VAL* 3.1 4.2 + - + +
533B VAL* 2.9 33.9 + - - +
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Residues in contact with GLN 530 (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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497B GLN* 5.3 12.7 - - - +
528B THR* 3.1 9.2 - - - +
529B PRO* 1.3 81.7 - - - +
531B GLN* 1.3 57.3 + - + +
533B VAL* 3.4 8.8 + - + +
534B ALA* 3.0 27.6 + - + +
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Residues in contact with GLN 531 (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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526B GLY 4.4 1.6 - - - +
527B LEU* 3.2 17.0 - - + +
528B THR* 2.8 42.9 + - - +
530B GLN* 1.3 76.4 - - + +
532B VAL* 1.3 63.9 + - - +
534B ALA* 3.1 8.4 + - - +
535B ILE* 3.0 30.0 + - - +
563B PRO* 5.1 1.2 - - - +
564B GLN* 4.3 23.6 - - - +
567B VAL* 3.8 38.6 - - + +
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Residues in contact with VAL 532 (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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514B VAL* 4.7 11.9 - - + -
518B LEU* 3.8 34.8 - - + +
521B LEU* 3.9 31.2 - - + -
522B CYS* 4.3 12.6 - - - -
527B LEU* 4.3 8.3 - - + -
528B THR 3.1 12.8 + - - +
529B PRO 3.1 6.9 + - - +
531B GLN* 1.3 75.5 - - - +
533B VAL* 1.3 61.6 + - - +
535B ILE* 3.4 9.6 + - - +
536B ALA* 3.0 22.3 + - - +
545B LEU* 3.7 15.6 - - + +
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU* 3.8 35.7 - - + -
497B GLN* 4.1 37.2 - - + +
500B ALA* 5.7 0.7 - - + -
501B ILE* 4.2 9.4 - - + -
514B VAL* 5.5 0.9 - - + -
518B LEU* 4.9 4.3 - - + -
529B PRO 2.9 19.6 + - - +
530B GLN* 3.7 7.2 - - - +
531B GLN 3.3 0.2 - - - -
532B VAL* 1.3 75.8 - - - +
534B ALA* 1.3 59.8 + - - +
536B ALA* 3.2 6.4 + - - +
537B SER* 2.7 43.9 + - - +
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Residues in contact with ALA 534 (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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530B GLN 3.0 14.3 + - - +
531B GLN* 3.1 13.2 + - - +
533B VAL* 1.3 79.0 - - - +
535B ILE* 1.3 63.2 + - - +
537B SER* 3.4 10.1 + - - -
538B ASN* 3.3 15.8 - - - +
567B VAL* 5.0 2.9 - - + -
571B SER* 4.0 17.4 - - - +
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Residues in contact with ILE 535 (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 LEU* 5.5 0.2 - - + -
527B LEU* 4.1 24.7 - - + -
531B GLN 3.0 15.6 + - - +
532B VAL* 3.7 7.6 - - - +
534B ALA* 1.3 76.6 - - - +
536B ALA* 1.3 62.9 + - - +
537B SER 3.4 0.5 + - - -
538B ASN* 3.7 12.5 + - - +
541B GLY* 4.1 8.3 - - - -
544B ALA* 3.6 30.7 - - + +
545B LEU* 3.6 24.7 - - + +
548B VAL* 4.1 15.9 - - + -
567B VAL* 4.1 15.0 - - + -
570B ALA* 4.1 12.3 - - + +
571B SER* 3.6 20.4 - - - +
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Residues in contact with ALA 536 (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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501B ILE* 3.9 14.6 - - + +
504B ASN* 4.3 1.9 + - - -
510B ALA* 3.7 16.0 - - + +
514B VAL* 3.4 30.1 - - + -
532B VAL 3.0 17.8 + - - +
533B VAL 3.2 4.7 + - - +
535B ILE* 1.3 73.2 - - - +
537B SER* 1.3 57.0 + - - +
538B ASN 3.0 19.9 + - - +
541B GLY* 3.9 4.2 - - - -
545B LEU* 3.9 15.0 - - + -
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Residues in contact with SER 537 (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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500B ALA* 4.0 19.6 - - - +
501B ILE* 3.6 17.9 - - - +
504B ASN* 2.9 19.5 + - - +
533B VAL* 2.7 27.7 + - - +
534B ALA* 3.4 7.8 + - - -
535B ILE 3.3 1.8 - - - -
536B ALA* 1.3 74.3 - - - +
538B ASN* 1.3 65.2 + - - +
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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