Contacts of the strand formed by residues 699 - 704 (chain C) in PDB entry 1RHM
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 GLU 699 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662C GLU* 4.5 7.9 - - - +
663C GLY 3.0 13.4 + - - +
664C LEU* 3.6 15.1 - - + +
665C CYS 3.0 22.0 + - - -
697C LYS 3.9 1.8 + - - -
698C TYR* 1.3 69.8 - - - +
700C VAL* 1.3 65.5 + - - +
701C ARG* 3.1 36.5 + - + +
727C ARG* 4.0 12.5 + - - -
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Residues in contact with VAL 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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665C CYS* 3.5 15.9 - - + +
667C ILE* 3.8 20.4 - - + -
690C ARG* 3.7 42.8 + - + +
693C PHE* 4.2 9.6 - - + -
694C ARG* 4.0 15.3 - - + +
698C TYR 3.2 14.1 + - - +
699C GLU* 1.3 77.2 - - - +
701C ARG* 1.3 72.3 + - - +
702C ASN* 3.8 17.3 - - - +
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Residues in contact with ARG 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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664C LEU* 3.9 19.1 - - - +
665C CYS 3.0 7.1 + - - +
666C ILE* 3.6 27.1 - - + +
667C ILE* 3.0 24.8 + - - +
690C ARG* 4.7 0.9 - - - +
699C GLU* 3.1 31.3 + - + +
700C VAL* 1.3 81.3 - - - +
702C ASN* 1.3 66.1 + - - +
703C LYS* 5.0 8.5 - - + +
714C LEU* 5.9 2.4 - - - +
718C VAL* 4.5 6.5 - - - +
721C GLU* 3.2 37.4 + - - -
727C ARG* 4.2 2.8 - - - +
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Residues in contact with ASN 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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667C ILE* 3.7 23.6 - - - +
669C ASN* 5.6 1.0 - - + +
686C ALA* 3.6 30.9 + - - +
690C ARG* 2.3 42.3 + - - +
700C VAL* 3.8 6.8 - - - +
701C ARG* 1.3 76.5 - - - +
703C LYS* 1.3 74.8 + - - +
704C ASN* 4.6 12.8 - - - +
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Residues in contact with LYS 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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666C ILE* 4.9 7.0 - - + -
667C ILE 3.1 10.2 + - - +
668C ILE* 3.7 6.9 - - + -
669C ASN* 2.7 31.0 + - - +
701C ARG* 5.0 9.4 - - + +
702C ASN* 1.3 83.8 - - - +
704C ASN* 1.3 64.6 + - - +
706C LEU* 3.5 30.3 - - + -
714C LEU* 3.8 36.0 - - + +
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Residues in contact with ASN 704 (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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669C ASN* 3.1 33.4 + - - +
671C LYS* 6.2 0.6 - - - +
683C ASP* 4.4 6.5 + - - -
686C ALA* 5.5 2.2 - - - +
702C ASN* 4.6 9.8 - - - +
703C LYS* 1.3 81.3 + - - +
705C ASP* 1.3 79.7 + - - +
706C LEU* 3.3 12.7 + - - +
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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