Contacts of the helix formed by residues 699 - 707 (chain C) in PDB entry 5IA0
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 ALA 699 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697C ASN 3.8 0.4 + - - +
698C GLY* 1.3 71.2 - - - -
700C LEU* 1.3 65.4 + - - +
701C ASP* 3.3 16.1 + - - +
702C LYS* 3.4 12.6 + - + +
703C PHE* 3.0 23.4 + - - +
743C ARG* 3.9 18.6 - - - +
745C ILE 3.4 6.1 - - - -
746C LEU* 3.8 9.8 - - + +
1001C A5B 4.8 11.5 + - - -
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Residues in contact with LEU 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698C GLY 3.6 0.4 + - - -
699C ALA* 1.3 72.2 - - - +
701C ASP* 1.3 63.2 + - - +
703C PHE* 3.3 2.9 + - + +
704C LEU* 3.0 49.1 + - + +
719C MET* 4.4 7.6 - - - -
723C ILE* 3.7 31.0 - - + -
742C ALA* 3.5 18.3 + - + +
745C ILE* 2.7 33.7 + - + +
747C VAL* 3.7 24.0 - - + -
753C CYS* 4.2 10.1 - - - -
806C VAL* 4.9 0.7 - - + -
810C VAL* 3.7 16.6 - - + -
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Residues in contact with ASP 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699C ALA* 3.6 10.0 - - - +
700C LEU* 1.3 75.4 - - - +
702C LYS* 1.3 74.3 + - - +
704C LEU* 3.5 2.0 + - - -
705C ARG* 3.1 58.0 + - - +
742C ALA* 3.7 22.5 + - + -
743C ARG* 3.5 31.1 - - - +
809C GLU* 4.5 7.0 - - - +
814C GLY* 4.1 11.1 - - - -
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Residues in contact with LYS 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699C ALA* 3.4 13.9 + - + +
700C LEU 3.4 0.4 - - - -
701C ASP* 1.3 86.5 + - - +
703C PHE* 1.3 62.6 + - - +
705C ARG* 3.4 19.4 + - - +
706C GLU* 3.0 30.4 + - + +
1001C A5B 3.3 28.9 - - - +
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Residues in contact with PHE 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697C ASN* 3.5 48.2 - - + +
699C ALA 3.0 18.0 + - - +
700C LEU* 3.6 6.7 - - + +
702C LYS* 1.3 78.4 - - - +
704C LEU* 1.3 68.5 + - + +
706C GLU* 3.2 6.9 + - + +
707C LYS* 2.9 58.7 + - + +
711C PHE* 3.6 33.4 - + - -
719C MET* 4.9 3.8 - - + -
747C VAL* 4.1 25.8 - - + -
751C LEU* 4.0 11.9 - - + -
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Residues in contact with LEU 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C LEU* 3.0 38.4 + - + +
701C ASP* 4.1 3.1 - - - +
703C PHE* 1.3 75.3 - - + +
705C ARG* 1.3 67.5 + - - +
707C LYS* 3.1 3.8 + - - +
708C ASP* 2.9 24.3 + - - -
711C PHE* 3.9 32.1 - - + -
716C LEU* 4.2 8.1 - - + -
719C MET* 4.4 9.2 - - - -
809C GLU 4.3 3.8 - - - +
810C VAL* 3.7 43.3 - - + +
813C TYR* 3.5 28.5 - - + +
814C GLY* 4.2 1.3 - - - +
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Residues in contact with ARG 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LYS* 5.3 0.9 - - - -
701C ASP* 3.1 50.2 + - - +
702C LYS* 3.7 17.9 - - + +
703C PHE 3.3 0.2 - - - -
704C LEU* 1.3 75.9 - - - +
706C GLU* 1.3 63.7 + - - +
707C LYS 3.4 0.2 + - - -
708C ASP* 3.4 15.4 + - - +
813C TYR 3.3 18.2 - - - +
814C GLY 2.7 35.2 + - - +
815C GLU 5.2 0.6 - - - -
816C ARG* 5.5 1.6 - - - +
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Residues in contact with GLU 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LYS* 3.9 8.5 + - - +
795A THR* 3.9 16.2 - - - +
858A ARG* 2.9 43.6 + - - -
702C LYS* 3.0 21.4 + - + +
703C PHE* 3.6 10.5 - - + +
704C LEU 3.2 0.2 - - - -
705C ARG* 1.3 78.0 - - - +
707C LYS* 1.3 75.6 + - + +
708C ASP 3.3 2.8 + - - -
710C GLU* 3.8 0.2 - - - +
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Residues in contact with LYS 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LYS* 3.7 2.9 - - - -
858A ARG* 4.0 22.6 - - - +
859A ALA* 5.3 11.3 - - - +
703C PHE* 2.9 54.0 + - + +
704C LEU* 3.1 5.1 + - - +
706C GLU* 1.3 92.7 + - - +
708C ASP* 1.3 64.5 + - - -
709C GLY 3.1 0.7 + - - -
710C GLU* 3.0 38.8 + - + +
711C PHE* 3.9 21.7 - - + -
813C TYR* 3.4 5.9 - - - -
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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