Contacts of the strand formed by residues 712 - 715 (chain C) in PDB entry 6ZGI
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 ILE 712 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895A GLN* 3.5 15.4 + - - +
896A ILE* 4.0 28.0 - - + -
897A PRO* 4.8 0.9 - - + -
900A MET* 4.9 2.9 - - + -
904A TYR* 4.7 2.2 - - - +
711C SER* 1.3 73.7 + - - +
713C ALA* 1.3 69.0 + - - +
714C ILE* 3.9 26.7 - - + -
1073C LYS 3.8 0.2 - - - +
1074C ASN* 3.5 5.4 - - - +
1075C PHE* 2.9 52.7 + - + +
1077C THR* 4.1 16.8 - - + +
1094C VAL* 4.0 24.7 - - + -
1096C VAL* 4.1 10.5 - - + -
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Residues in contact with ALA 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.7 31.0 - - + +
895A GLN* 3.4 26.4 + - - +
712C ILE* 1.3 79.7 - - - +
714C ILE* 1.3 65.0 + - - +
715C PRO* 4.1 0.4 - - - +
1072C GLU* 3.9 23.1 - - + +
1073C LYS 3.2 9.6 - - - +
1074C ASN* 4.1 6.1 - - - +
1321C NAG 6.3 0.4 - - + +
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Residues in contact with ILE 714 (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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712C ILE* 3.9 29.8 - - + -
713C ALA* 1.3 79.8 - - - +
715C PRO* 1.3 81.3 - - + +
716C THR* 3.7 4.0 + - - +
1072C GLU* 4.1 1.8 - - - -
1073C LYS* 2.9 28.6 + - - +
1075C PHE* 3.6 28.9 - - + -
1094C VAL* 4.5 14.6 - - + -
1096C VAL* 4.6 6.1 - - + -
1105C THR* 5.0 2.0 - - + -
1106C GLN 4.3 4.5 - - - +
1107C ARG* 3.9 18.8 - - - +
1109C PHE 4.2 3.1 - - - -
1110C TYR* 4.1 23.3 - - + +
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Residues in contact with PRO 715 (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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894A LEU* 3.7 24.2 - - + -
713C ALA 4.1 0.4 - - - +
714C ILE* 1.3 92.0 - - + +
716C THR* 1.3 58.6 + - - +
717C ASN 4.3 9.0 - - - +
1069C PRO* 3.7 30.1 - - + -
1070C ALA 4.5 2.9 - - - +
1071C GLN 3.2 10.1 - - - +
1072C GLU* 4.0 2.9 - - + -
1107C ARG 4.2 7.0 - - - +
1108C ASN* 3.3 29.4 - - - +
1109C PHE* 3.7 3.4 - - + -
1110C TYR* 3.2 24.8 + - - +
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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