Contacts of the helix formed by residues 257 - 268 (chain H) in PDB entry 6GYS
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 SER 257 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H GLN* 6.2 6.5 - - - -
255H LEU 3.6 3.3 + - - -
256H THR* 1.3 73.2 - - - +
258H ILE* 1.3 54.1 + - - +
259H SER* 3.2 16.6 - - - -
260H VAL* 2.8 17.9 + - - +
261H ILE* 2.8 32.6 + - - +
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Residues in contact with ILE 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H PRO* 5.5 4.5 - - + -
256H THR 3.8 1.2 + - - -
257H SER* 1.3 71.0 - - - +
259H SER* 1.3 60.8 + - - +
261H ILE* 3.8 16.4 - - + +
262H ARG* 2.9 30.5 + - - +
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Residues in contact with SER 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H ILE* 3.5 18.2 - - - +
173H ASP 6.0 0.7 - - - -
177H PRO* 4.3 28.4 - - - +
180H VAL* 4.1 17.1 - - - +
257H SER* 3.8 8.9 - - - -
258H ILE* 1.3 78.6 - - - +
260H VAL* 1.3 68.3 + - - +
262H ARG* 3.4 6.5 + - - +
263H THR* 2.5 37.1 + - - -
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Residues in contact with VAL 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H ILE* 3.8 11.4 - - + -
201H PHE* 3.6 27.4 - - + -
202H GLY 5.3 0.9 - - - +
203H GLN 5.9 1.1 - - - +
256H THR* 5.0 8.3 - - + -
257H SER* 2.8 23.4 + - - +
259H SER* 1.3 88.6 + - - +
261H ILE* 1.3 60.8 + - - +
263H THR* 3.2 6.9 + - - -
264H ILE* 2.9 49.9 + - + +
283H LEU* 4.5 19.3 - - + -
287H LEU* 5.1 8.5 - - + -
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Residues in contact with ILE 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H THR* 3.3 39.0 - - - +
257H SER 2.8 15.0 + - - +
258H ILE* 3.8 16.4 - - + +
259H SER 3.3 0.2 - - - -
260H VAL* 1.3 77.7 - - - +
262H ARG* 1.3 57.0 + - - +
264H ILE* 3.2 9.4 + - + +
265H ARG* 3.0 38.5 + - + +
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Residues in contact with ARG 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H PRO 5.4 1.3 - - - +
180H VAL* 3.7 17.3 - - + -
181H ASP* 2.4 56.9 + - + +
184H LEU* 3.2 38.5 - - + +
185H SER* 3.2 21.6 - - - +
258H ILE 2.9 17.8 + - - +
259H SER* 3.6 4.9 - - - +
261H ILE* 1.3 75.9 - - - +
263H THR* 1.3 62.5 + - - +
265H ARG* 2.8 59.7 - - - +
266H SER* 3.5 1.2 + - - -
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Residues in contact with THR 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H PHE* 5.2 4.5 - - + -
172H ILE* 3.3 29.4 - - + +
180H VAL* 4.4 0.5 - - - +
184H LEU* 4.4 4.0 - - - -
199H VAL* 4.5 17.9 - - + -
201H PHE* 4.0 15.5 - - + -
259H SER 2.5 21.3 + - - -
260H VAL* 3.3 11.4 - - - -
261H ILE 3.1 0.2 - - - -
262H ARG* 1.3 75.8 - - - +
264H ILE* 1.3 60.5 + - - +
266H SER* 2.9 22.6 + - - +
267H MET* 2.9 32.9 + - + +
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Residues in contact with ILE 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H PHE* 5.3 0.4 - - + -
256H THR* 5.6 6.3 - - + -
260H VAL* 2.9 39.6 + - + +
261H ILE* 3.9 7.2 - - + +
263H THR* 1.3 71.5 - - - +
265H ARG* 1.3 60.2 + - - +
267H MET* 3.0 45.1 + - + +
268H GLU* 4.1 3.6 + - - +
287H LEU* 5.8 5.8 - - + -
299H LYS* 5.3 11.0 - - - +
300H THR 3.5 28.3 - - - +
301H ILE* 4.6 15.5 - - + -
302H SER* 5.3 6.8 - - - -
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H ILE* 3.0 19.7 + - + +
262H ARG* 2.8 65.1 + - - +
264H ILE* 1.3 77.9 - - - +
266H SER* 1.3 61.0 + - - +
269H SER* 6.0 0.2 - - - -
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Residues in contact with SER 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H LEU* 3.3 39.8 - - - +
193H PHE* 5.2 6.1 - - - -
262H ARG 3.9 0.7 - - - -
263H THR* 2.9 16.0 + - - +
265H ARG* 1.3 84.4 - - - +
267H MET* 1.3 65.0 + - - +
268H GLU 3.3 2.5 - - - -
269H SER* 3.1 22.7 + - - -
270H MET* 3.3 22.8 - - - +
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Residues in contact with MET 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H VAL* 4.4 8.7 - - + -
201H PHE* 3.7 30.1 - - + -
263H THR* 2.9 24.8 + - + +
264H ILE* 3.0 34.8 + - + +
266H SER* 1.3 77.8 - - - +
268H GLU* 1.3 61.4 + - - +
270H MET* 3.3 22.2 - - - +
273H LEU* 3.7 18.5 - - + +
276H ILE* 4.9 6.5 - - - -
301H ILE* 3.8 27.6 - - + +
302H SER* 5.4 1.1 - - - -
305H VAL* 3.6 23.7 - - + +
331H TRP* 6.4 0.4 - - - -
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Residues in contact with GLU 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264H ILE 4.1 2.9 + - - +
266H SER 3.3 0.6 - - - -
267H MET* 1.3 76.0 - - - +
269H SER* 1.3 61.8 + - - +
270H MET 3.0 7.8 + - - -
271H LYS 3.6 0.3 + - - -
302H SER* 3.2 28.9 + - - +
304H ILE* 3.1 23.2 - - + +
305H VAL* 3.8 20.8 - - + +
308H ARG* 2.3 64.9 + - - -
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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