Contacts of the helix formed by residues 664 - 673 (chain A) in PDB entry 4OSI
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 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A CYS* 4.2 2.5 - - - -
662A GLY 5.5 0.7 - - - +
663A LEU* 1.3 77.5 - - - +
665A PRO* 1.3 64.2 - - - +
666A GLN* 3.3 23.0 + - - +
667A GLN* 2.7 63.2 + - + +
668A VAL* 3.2 5.2 + - - +
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Residues in contact with PRO 665 (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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627A HIS 5.7 3.8 - - - +
628A GLY 5.4 4.9 - - - +
629A LEU* 4.4 20.2 - - + -
633A GLN* 5.0 0.2 - - - -
654A LEU* 5.1 8.1 - - + -
658A CYS* 3.7 23.9 - - - -
663A LEU 4.2 0.7 - - - +
664A THR* 1.3 85.4 - - - +
666A GLN* 1.3 76.6 + - - +
668A VAL* 3.3 7.0 + - + +
669A VAL* 2.9 31.1 + - + +
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Residues in contact with GLN 666 (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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633A GLN* 4.3 21.1 + - - +
664A THR* 3.2 20.5 + - - +
665A PRO* 1.3 87.8 - - - +
667A GLN* 1.3 58.3 + - + +
669A VAL* 3.8 2.1 - - - +
670A ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 667 (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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662A GLY 4.8 1.2 - - - +
663A LEU* 3.8 18.4 - - + +
664A THR* 2.7 52.0 + - + +
666A GLN* 1.3 67.7 - - + +
668A VAL* 1.3 69.0 + - - +
670A ALA* 2.7 20.3 + - - +
671A ILE* 3.0 15.8 + - - +
701A ASP* 3.5 31.4 + - - +
704A VAL* 4.0 32.9 - - + +
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Residues in contact with VAL 668 (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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650A VAL* 4.1 30.3 - - + -
653A LEU 6.0 0.2 - - - -
654A LEU* 4.9 16.6 - - + -
657A LEU* 4.1 32.3 - - + -
658A CYS* 4.6 14.1 - - - -
663A LEU* 4.5 8.7 - - + +
664A THR 3.2 8.6 + - - +
665A PRO* 3.7 8.5 - - + +
667A GLN* 1.3 78.2 - - - +
669A VAL* 1.3 66.4 + - + +
671A ILE* 3.0 12.3 + - - +
672A ALA* 2.9 21.9 + - - +
681A LEU* 4.2 12.2 - - + +
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Residues in contact with VAL 669 (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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629A LEU* 4.0 22.7 - - + -
633A GLN* 3.9 44.0 - - + +
636A ALA* 5.1 2.5 - - + -
637A ILE* 4.4 16.8 - - + -
650A VAL* 5.8 0.9 - - + -
654A LEU* 6.1 0.9 - - + -
665A PRO* 2.9 23.1 + - + +
666A GLN 3.8 3.4 - - - +
668A VAL* 1.3 71.8 - - + +
670A ALA* 1.3 66.7 + - - +
672A ALA* 4.6 5.4 - - - +
673A SER* 2.7 42.9 + - - +
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Residues in contact with ALA 670 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666A GLN 2.9 14.7 + - - +
667A GLN* 2.7 18.7 + - - +
669A VAL* 1.3 74.7 - - - +
671A ILE* 1.3 62.7 - - - +
673A SER* 3.2 9.8 + - - +
674A ASN* 3.0 15.2 + - - -
704A VAL* 5.4 0.7 - - + -
708A CYS* 3.2 23.2 - - - -
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Residues in contact with ILE 671 (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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657A LEU* 6.0 0.7 - - + -
663A LEU* 5.3 4.3 - - + -
667A GLN 3.0 14.3 + - - +
668A VAL* 3.0 8.0 + - - +
670A ALA* 1.3 74.3 - - - +
672A ALA* 1.3 58.8 + - - +
674A ASN* 2.6 28.7 + - - +
676A GLY 5.6 0.2 - - - -
677A GLY* 4.5 3.6 - - - -
680A ALA* 3.7 27.9 - - + +
681A LEU* 3.4 26.9 - - + +
684A ILE* 4.6 9.2 - - + -
704A VAL* 3.8 33.2 - - + +
707A ALA* 3.7 26.9 - - + +
708A CYS* 3.7 18.2 - - - +
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Residues in contact with ALA 672 (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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637A ILE* 3.9 21.3 - - + +
640A HIS* 4.6 0.2 - - - -
646A ALA* 4.0 13.7 - - + +
650A VAL* 3.5 32.1 - - + -
668A VAL 2.9 15.2 + - - +
669A VAL 4.2 2.2 - - - +
671A ILE* 1.3 75.7 - - - +
673A SER* 1.3 52.2 + - - +
674A ASN 2.8 22.5 + - - +
677A GLY* 3.9 15.1 - - - -
681A LEU* 4.4 6.5 - - + -
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Residues in contact with SER 673 (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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636A ALA* 3.4 37.0 + - - +
637A ILE* 3.7 4.2 + - - +
640A HIS* 2.8 26.2 + - - -
669A VAL* 2.7 29.9 + - - +
670A ALA* 3.6 6.2 - - - +
671A ILE 3.1 1.6 + - - -
672A ALA* 1.3 72.7 - - - +
674A ASN* 1.3 63.6 + - - +
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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