Contacts of the helix formed by residues 761 - 767 (chain B) in PDB entry 5IYB
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 761 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B SER 2.8 24.4 + - - +
711B ILE 3.4 29.8 - - - +
712B PRO* 4.0 3.8 - - + -
759B VAL 4.3 0.2 + - - -
760B THR* 1.3 89.1 + - - +
762B ARG* 1.3 66.3 + - - +
763B SER* 3.0 13.8 + - - -
764B MET* 3.0 24.8 + - + +
765B GLU 4.3 0.9 + - - -
999B ALA 3.7 22.2 - - - +
1000B THR 4.9 0.2 - - - -
1001B PRO* 4.9 9.4 - - + -
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Residues in contact with ARG 762 (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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24B GLU* 4.4 14.8 + - - -
27B TRP* 3.1 62.5 - - + +
760B THR* 5.3 3.1 - - - -
761B THR* 1.3 71.1 - - - +
763B SER* 1.3 63.7 + - - +
764B MET 3.1 1.2 + - - -
765B GLU* 3.2 27.6 + - - +
766B TYR* 3.8 9.7 - - - +
998B ASP* 3.8 31.6 + - - +
1000B THR* 3.8 11.4 + - + +
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Residues in contact with SER 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 4.8 1.6 - - - -
528B LEU* 4.4 9.2 - - - +
701B SER* 4.0 9.4 + - - -
702B MET* 3.3 28.4 - - - +
709B SER* 4.2 22.7 + - - -
761B THR* 3.0 13.4 + - - -
762B ARG* 1.3 78.1 - - - +
764B MET* 1.3 56.2 + - - +
765B GLU 3.2 0.2 - - - -
766B TYR* 3.0 38.0 + - - +
767B LEU* 3.7 7.7 + - - +
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Residues in contact with MET 764 (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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709B SER 4.2 6.7 - - - +
710B ILE* 3.3 31.9 - - - +
757B PRO* 4.3 5.8 - - - -
760B THR* 3.3 13.7 - - - +
761B THR* 3.0 52.6 + - + +
763B SER* 1.3 72.3 - - - +
765B GLU* 1.3 61.2 + - - +
766B TYR 3.0 7.1 + - - -
767B LEU* 3.2 19.1 + - + +
768B ARG* 3.6 0.3 + - - -
769B PHE* 3.5 58.8 + - + +
770B ARG* 4.3 9.1 + - + +
938B ARG* 3.8 9.4 - - - +
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Residues in contact with GLU 765 (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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760B THR* 5.3 0.4 + - - -
761B THR 4.3 0.8 + - - -
762B ARG* 3.2 22.5 + - - +
763B SER 3.2 0.2 - - - -
764B MET* 1.3 78.0 - - - +
766B TYR* 1.3 79.0 + - + +
768B ARG* 3.8 18.2 + - - -
770B ARG* 2.3 56.2 + - - +
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Residues in contact with TYR 766 (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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27B TRP* 3.5 32.5 + + - +
30B ILE* 4.2 15.5 - - + -
31B SER* 3.2 33.0 + - - -
34B PHE* 3.5 42.2 - + + +
39B LEU* 3.2 21.9 - - + +
528B LEU* 5.6 1.8 - - + -
702B MET* 5.7 0.9 - - + -
762B ARG* 3.8 20.4 - - - +
763B SER* 3.0 23.9 + - - +
764B MET 3.0 0.6 - - - -
765B GLU* 1.3 99.1 - - + +
767B LEU* 1.3 57.4 + - + +
768B ARG* 3.2 14.1 + - - +
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Residues in contact with LEU 767 (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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39B LEU* 3.9 22.0 - - + -
475B PHE* 3.5 20.7 - - - -
479B LEU* 3.9 8.5 - - + -
528B LEU* 4.9 9.4 - - + -
706B VAL* 3.8 41.5 - - + +
709B SER* 4.4 9.2 - - - -
710B ILE* 3.7 33.9 - - + -
763B SER 4.1 8.7 - - - +
764B MET* 3.2 16.5 + - + +
766B TYR* 1.3 80.1 - - + +
768B ARG* 1.3 63.8 + - - +
769B PHE* 2.7 19.5 + - + +
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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