Contacts of the strand formed by residues 311 - 314 (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 GLY 311 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C GLU 3.4 2.4 + - - -
310C LYS* 1.3 78.1 - - - +
312C ILE* 1.3 61.3 + - - -
313C TYR* 3.9 9.9 - - - -
597C VAL 3.9 0.2 - - - +
598C ILE* 3.5 3.3 - - - +
599C THR* 2.9 36.3 + - - +
664C ILE* 4.1 16.2 - - - -
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Residues in contact with ILE 312 (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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311C GLY* 1.3 74.9 - - - -
313C TYR* 1.3 70.9 + - - +
314C GLN* 4.8 5.6 - - - +
596C SER* 3.7 29.6 - - - +
597C VAL 3.4 6.1 - - - +
598C ILE* 3.5 28.5 - - + +
611C LEU* 5.0 7.2 - - + -
664C ILE* 4.1 12.8 - - + -
665C PRO* 3.7 27.4 - - + +
666C ILE* 4.5 9.4 - - + +
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Residues in contact with TYR 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 3.8 25.6 - - + -
303C LEU* 4.3 25.6 - - + +
308C VAL* 3.6 14.6 - - + +
309C GLU* 2.7 30.3 + - - +
310C LYS 4.2 2.9 + - - -
311C GLY* 3.9 12.1 - - - -
312C ILE* 1.3 78.0 - - - +
314C GLN* 1.3 65.4 + - - +
315C THR 3.6 0.3 + - - -
596C SER* 3.3 6.6 - - - -
597C VAL* 2.9 41.2 + - + +
599C THR* 3.6 30.7 - - + -
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Residues in contact with GLN 314 (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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735A SER* 4.3 21.8 + - - +
768A THR* 5.3 13.2 - - + -
859A THR* 5.4 1.2 + - - -
861A LEU* 4.1 26.5 - - + +
299C THR* 5.0 1.9 - - - +
312C ILE* 4.8 6.9 - - - +
313C TYR* 1.3 76.4 - - - +
315C THR* 1.3 64.0 + - - +
594C GLY* 6.0 0.2 - - - -
595C VAL 3.9 6.8 + - - +
596C SER* 3.0 16.3 + - - -
613C GLN* 3.3 24.3 + - - +
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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
------------------------------------------------------------
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