Contacts of the strand formed by residues 1109 - 1113 (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 PHE1109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714C ILE* 4.2 2.0 - - - -
715C PRO 3.7 5.2 - - - -
716C THR 3.3 31.6 - - - -
717C ASN* 4.4 3.1 - - - -
718C PHE* 3.9 25.4 - + - -
911C VAL* 4.7 8.3 - - + -
915C VAL* 4.1 30.5 - - + -
919C ASN* 4.9 5.4 - - - -
1067C TYR* 4.2 14.6 - - - +
1105C THR* 3.3 1.9 + - - -
1106C GLN* 2.9 47.2 + - - +
1107C ARG 3.5 1.0 + - - -
1108C ASN* 1.3 79.0 - - - +
1110C TYR* 1.3 81.2 + - - +
1111C GLU* 4.7 10.8 - - + -
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Residues in contact with TYR1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C ILE* 4.1 10.5 - - + -
715C PRO 3.2 18.3 + - - +
716C THR* 4.1 20.1 - - + +
1073C LYS* 4.8 10.7 + - - -
1075C PHE* 3.6 44.6 - + - -
1096C VAL* 4.4 14.8 - - + +
1098C ASN* 5.2 5.2 - - - +
1103C PHE* 4.7 9.7 - - - -
1105C THR* 3.8 9.6 - - + -
1109C PHE* 1.3 86.2 - - - +
1111C GLU* 1.3 61.7 + - - +
1112C PRO* 3.8 38.5 - - + +
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Residues in contact with GLU1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123B SER* 4.9 2.9 + - - -
912C THR* 4.6 1.0 + - - +
914C ASN* 3.0 32.4 + - - +
915C VAL* 4.6 5.0 - - - +
918C GLU* 5.2 0.9 - - - +
1104C VAL 3.9 3.8 - - - +
1105C THR* 3.1 19.7 + - - +
1106C GLN* 3.7 26.8 + - + +
1109C PHE* 3.5 9.8 + - + +
1110C TYR* 1.3 74.5 - - - +
1112C PRO* 1.3 71.0 - - + +
1113C GLN* 3.6 30.8 + - + +
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Residues in contact with PRO1112 (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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1103C PHE* 3.9 27.8 - - + -
1104C VAL 3.9 5.2 - - - +
1105C THR* 4.3 4.7 - - - -
1110C TYR* 3.8 40.8 - - + +
1111C GLU* 1.3 89.9 - - + +
1113C GLN* 1.3 66.1 + - - +
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Residues in contact with GLN1113 (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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1122B VAL 5.6 4.4 + - - -
1103C PHE* 3.3 13.6 - - - +
1104C VAL* 3.1 38.4 + - + +
1111C GLU* 3.6 30.5 + - + +
1112C PRO* 1.3 81.7 - - - +
1114C ILE* 1.3 69.7 + - - +
1119C ASN* 4.2 14.4 + - - +
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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