Contacts of the helix formed by residues 266 - 275 (chain V) in PDB entry 5GJQ
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 THR 266 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262V GLU* 4.0 7.5 - - - +
265V MET* 1.4 85.4 - - - +
267V PRO* 1.4 73.7 - - - +
268V GLU* 3.5 6.0 + - - +
269V GLN* 3.5 27.2 + - - +
270V LEU* 3.0 25.5 + - - +
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Residues in contact with PRO 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266V THR* 1.4 86.5 - - - +
268V GLU* 1.3 97.8 + - - +
270V LEU* 2.9 31.9 + - + +
271V ALA* 2.9 16.3 + - - +
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Residues in contact with GLU 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ASP* 5.6 6.9 - - + +
266V THR* 3.6 6.2 + - - +
267V PRO* 1.3 114.9 - - - +
269V GLN* 1.3 62.3 + - + +
271V ALA* 3.6 13.9 + - - +
272V ILE* 3.8 15.1 + - - +
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Residues in contact with GLN 269 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265V MET* 2.6 56.9 - - + +
266V THR* 3.5 25.9 + - - +
267V PRO 3.3 0.4 - - - -
268V GLU* 1.3 77.8 - - + +
270V LEU* 1.3 61.6 + - - +
272V ILE* 3.2 31.2 - - + +
273V LYS* 3.4 12.4 + - - +
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Residues in contact with LEU 270 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K GLN* 5.4 7.9 - - - +
262V GLU* 3.6 29.6 - - - +
265V MET* 5.2 0.2 - - - +
266V THR 3.0 17.8 + - - +
267V PRO* 2.9 22.8 + - + +
269V GLN* 1.3 77.2 - - - +
271V ALA* 1.3 61.0 + - + +
273V LYS* 2.9 15.9 + - - +
274V ASN* 2.9 48.4 + - + +
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Residues in contact with ALA 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ASP* 4.3 10.4 - - + -
98K GLN* 3.9 32.5 - - + +
267V PRO 2.9 11.2 + - - +
268V GLU* 3.8 11.4 - - - +
269V GLN 3.4 0.2 - - - -
270V LEU* 1.3 79.2 - - + +
272V ILE* 1.3 63.0 + - + +
274V ASN* 5.6 0.2 - - - -
275V VAL* 3.0 43.0 + - + +
276V GLY 4.2 0.2 + - - -
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Residues in contact with ILE 272 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ASP* 6.6 0.4 - - - -
268V GLU 3.9 15.0 - - - +
269V GLN* 3.2 18.6 - - + +
270V LEU 3.2 0.2 - - - -
271V ALA* 1.3 78.2 - - + +
273V LYS* 1.3 65.9 + - + +
276V GLY* 4.0 10.0 + - - -
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Residues in contact with LYS 273 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261V GLU* 3.2 36.3 + - - +
262V GLU* 3.2 44.0 - - + +
265V MET* 3.5 39.6 - - - -
269V GLN 3.9 10.1 - - - +
270V LEU* 2.9 9.5 + - - +
272V ILE* 1.3 83.3 - - + +
274V ASN* 1.3 72.4 + - - +
276V GLY* 3.5 0.9 + - - -
277V LYS* 3.4 24.1 + - - +
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Residues in contact with ASN 274 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K ARG* 5.2 4.5 - - - +
122K GLU 5.2 0.2 + - - -
258V ALA* 5.5 8.9 - - - +
262V GLU* 4.7 8.7 + - - +
270V LEU* 2.9 41.4 + - + +
273V LYS* 1.3 80.0 - - - +
275V VAL* 1.3 57.2 + - - +
276V GLY 3.2 1.8 - - - -
277V LYS* 2.7 27.0 - - - +
279V ASP* 3.8 38.6 + - + +
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Residues in contact with VAL 275 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ALA* 4.5 16.2 - - + -
97K ASP 4.9 7.6 - - - +
98K GLN* 4.2 25.8 - - - +
115K ILE* 6.4 0.2 - - + -
121K ARG* 4.6 25.9 - - + +
122K GLU 5.0 1.6 + - - -
124K LEU* 4.1 35.8 - - + +
271V ALA* 3.0 34.5 + - + +
274V ASN* 1.3 73.7 - - - +
276V GLY* 1.3 65.1 + - - +
277V LYS 4.4 0.9 - - - +
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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