Contacts of the helix formed by residues 706 - 711 (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 VAL 706 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.3 2.2 - - + -
476B ALA* 4.4 18.6 - - + +
479B LEU* 4.2 20.6 - - + +
480B SER* 4.7 8.3 - - - +
483B ARG* 3.9 29.4 - - - +
513B GLU* 4.2 2.8 + - - +
525B ASN* 5.8 1.2 - - - +
526B LEU 4.4 3.2 + - - -
528B LEU* 3.5 10.1 - - + +
705B GLY* 1.3 69.3 - - - +
707B CYS* 1.3 67.3 + - - +
709B SER* 2.9 25.3 + - - -
710B ILE* 3.6 9.4 + - + +
767B LEU* 3.8 35.8 - - + +
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Residues in contact with CYS 707 (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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476B ALA* 4.9 9.4 - - - -
480B SER* 4.1 11.7 - - - -
513B GLU* 3.1 21.7 + - - +
706B VAL* 1.3 78.7 - - - +
708B ALA* 1.3 56.6 + - - +
709B SER 2.8 11.4 + - - -
710B ILE* 3.1 20.9 + - - +
711B ILE* 3.6 8.0 - - - +
725B GLN* 5.3 2.9 + - - +
726B SER* 3.5 24.7 + - - +
729B GLY* 5.1 4.9 - - - -
730B LYS* 2.9 39.9 - - - -
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Residues in contact with ALA 708 (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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510B CYS* 3.8 18.2 - - - -
512B ALA* 3.9 14.1 - - + +
513B GLU* 3.7 2.0 + - - -
704B LEU* 3.3 43.3 - - + +
705B GLY 3.6 1.5 + - - +
706B VAL 3.4 0.6 - - - -
707B CYS* 1.3 75.2 - - - +
709B SER* 1.3 59.6 + - - +
711B ILE* 3.3 25.5 - - + +
714B PRO* 4.8 3.1 - - + +
722B ASN* 5.4 4.9 - - + +
726B SER* 3.6 6.5 + - - +
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Residues in contact with SER 709 (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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528B LEU* 3.7 8.8 - - - +
701B SER 5.3 0.3 + - - -
702B MET* 5.9 0.5 - - - +
704B LEU* 3.4 19.5 + - - +
705B GLY 2.5 22.2 + - - -
706B VAL* 2.9 13.0 + - - -
707B CYS 2.8 0.8 - - - -
708B ALA* 1.3 80.6 - - - +
710B ILE* 1.3 62.3 + - - +
711B ILE 3.2 1.8 - - - -
761B THR* 2.8 31.8 + - - +
763B SER* 4.2 19.6 + - - -
764B MET* 4.1 2.7 - - - +
767B LEU* 4.4 8.3 - - - -
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Residues in contact with ILE 710 (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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476B ALA* 3.5 26.5 - - + -
706B VAL* 4.2 7.0 - - + +
707B CYS* 3.1 14.8 + - + +
709B SER* 1.3 78.8 - - - +
711B ILE* 1.3 56.9 + - - +
725B GLN* 4.9 11.4 - - - +
729B GLY* 6.4 2.2 - - - -
764B MET* 3.3 14.3 - - + +
767B LEU* 3.7 23.6 - - + -
769B PHE* 3.5 49.8 - - + -
938B ARG* 3.1 33.0 + - + -
1047B TYR* 6.2 0.2 - - + -
1049B GLN* 5.6 3.4 - - - +
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Residues in contact with ILE 711 (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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707B CYS 3.6 7.9 - - - +
708B ALA* 3.3 36.9 - - - +
710B ILE* 1.3 73.2 - - + +
712B PRO* 1.4 71.4 - - + +
714B PRO* 3.7 16.6 - - + +
717B ASN* 3.4 28.5 - - - +
722B ASN* 3.5 19.5 - - + +
725B GLN* 4.0 22.7 - - + +
726B SER* 5.5 0.9 - - - +
761B THR* 3.4 12.4 - - - +
938B ARG* 3.2 27.8 - - + +
939B HIS* 4.5 1.6 - - - +
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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