Contacts of the helix formed by residues 251 - 262 (chain A) in PDB entry 4GR0
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A ASP* 4.7 5.6 - - - -
233A LYS* 3.7 29.7 + - - -
234A ALA* 3.3 13.2 - - - +
249A ARG 3.6 1.8 + - - -
250A LEU* 1.3 76.7 - - - +
252A ALA* 1.3 64.0 + - - +
253A ASP* 3.2 6.1 + - - +
254A ASP* 2.9 35.9 + - - -
255A ILE* 3.0 23.8 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LEU 4.1 0.2 + - - -
251A SER* 1.3 74.0 - - - +
253A ASP* 1.3 57.0 + - - +
255A ILE* 3.5 10.1 + - - +
256A ARG* 3.0 28.1 + - - +
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 2.6 37.7 + - - +
231A ASP* 4.2 16.7 + - + +
234A ALA* 4.7 0.4 - - + -
251A SER* 3.0 8.3 + - - +
252A ALA* 1.3 78.4 - - - +
254A ASP* 1.3 60.6 + - - +
256A ARG* 3.1 35.1 + - - +
257A GLY* 2.9 27.0 + - - -
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TRP* 4.0 8.1 - - + -
226A LEU* 4.5 2.5 - - - +
229A SER* 5.1 0.7 - - - -
234A ALA* 3.4 6.1 - - - +
235A VAL* 2.8 31.1 + - - +
236A MET* 3.2 34.1 + - - +
250A LEU* 3.9 16.9 - - + -
251A SER* 2.9 36.0 + - - +
253A ASP* 1.3 75.2 - - - +
255A ILE* 1.3 58.5 + - - +
257A GLY* 3.4 2.1 + - - -
258A ILE* 3.0 31.8 + - - +
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 4.1 19.7 - - + -
250A LEU* 4.0 33.4 - - + +
251A SER 3.0 19.5 + - - +
252A ALA* 3.9 8.1 - - - +
254A ASP* 1.3 74.1 - - - +
256A ARG* 1.3 64.1 + - - +
258A ILE* 3.5 5.0 + - - +
259A GLN* 2.9 55.2 + - + +
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Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA 3.0 18.2 + - - +
253A ASP* 3.1 36.6 + - - +
255A ILE* 1.3 75.4 - - - +
257A GLY* 1.3 84.8 + - - +
259A GLN* 3.8 4.0 - - - +
260A SER* 3.0 33.0 + - - -
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.5 20.3 - - - +
253A ASP 2.9 16.5 + - - -
254A ASP* 3.8 1.6 - - - -
255A ILE 3.2 0.2 - - - -
256A ARG* 1.3 96.6 - - - +
258A ILE* 1.3 60.1 + - - +
260A SER* 2.6 22.5 + - - -
261A LEU* 3.6 4.3 + - - +
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TRP* 3.8 22.0 - - + -
144A VAL* 3.9 13.7 - - + -
145A THR* 3.6 29.2 - - + -
224A LEU* 3.9 34.5 - - + -
226A LEU* 3.7 26.7 - - + +
254A ASP 3.0 20.7 + - - +
255A ILE* 3.6 6.1 - - - +
257A GLY* 1.3 75.8 - - - +
259A GLN* 1.3 63.0 + - + +
261A LEU* 3.1 6.9 + - + +
262A TYR* 3.1 36.6 + - + +
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 2.9 32.1 + - - +
145A THR* 5.3 0.2 - - - -
255A ILE* 2.9 39.7 + - + +
256A ARG* 3.8 4.2 - - - +
258A ILE* 1.3 75.4 - - + +
260A SER* 1.3 61.7 + - - +
261A LEU 3.1 0.4 - - - -
262A TYR 3.2 21.8 + - - +
263A GLY* 4.8 1.7 - - - -
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 4.2 7.1 - - - +
256A ARG* 3.0 24.7 + - - -
257A GLY* 2.6 22.1 + - - -
259A GLN* 1.3 77.4 - - - +
261A LEU* 1.3 69.7 + - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 3.6 42.7 - - + +
106A GLY 5.4 2.5 - - - +
108A VAL* 3.9 11.8 - - + +
224A LEU 3.8 12.6 - - - +
225A GLY* 3.6 34.5 - - - +
226A LEU* 3.7 17.5 - - + +
257A GLY 3.7 9.9 - - - +
258A ILE* 3.1 4.4 + - + +
260A SER* 1.3 88.8 - - - +
262A TYR* 1.3 82.7 + - + +
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.5 12.3 - - + -
109A TRP* 3.0 55.5 + + + -
111A LYS 4.9 0.4 - - - -
112A HIS* 4.4 12.3 - + - +
145A THR* 4.6 3.7 - - - +
146A PRO* 4.0 18.4 - - + +
147A LEU* 3.8 41.1 - - + -
224A LEU* 2.7 31.0 + - + -
258A ILE* 3.1 24.5 + - + +
259A GLN* 3.2 26.9 - - - +
260A SER 3.7 0.2 - - - -
261A LEU* 1.3 94.3 - - + +
263A GLY* 1.3 58.0 + - - +
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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