Contacts of the helix formed by residues 253 - 262 (chain A) in PDB entry 3RLG
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 TYR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 5.7 1.8 - - + -
53A CYS 5.1 6.1 + - - -
54A GLY* 4.9 11.1 + - - -
55A ARG* 5.9 1.4 - - - -
200A ASN* 5.6 0.7 - - - -
233A ASP* 3.5 44.6 - - + -
251A THR* 2.9 13.4 + - - +
252A ASN* 1.4 92.6 - - + +
254A PRO* 1.4 70.6 - - - +
255A ASP* 3.1 11.2 - - - +
256A VAL* 2.9 32.5 + - + +
257A ILE 3.4 6.8 + - - -
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Residues in contact with PRO 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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9A ILE* 4.0 7.1 - - + +
11A GLY* 4.6 1.3 - - - -
23A PHE* 3.7 35.9 - - + +
26A LEU* 3.5 24.7 - - + +
27A GLY 4.0 0.9 - - - -
28A ALA* 3.6 25.1 - - + +
251A THR* 3.7 17.0 - - + -
252A ASN 3.7 8.1 - - - +
253A TYR* 1.4 86.6 - - - +
255A ASP* 1.3 59.8 + - - +
257A ILE* 3.3 4.0 + - + +
258A THR* 3.0 30.7 + - - -
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Residues in contact with ASP 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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26A LEU* 3.3 40.0 + - + +
235A ARG* 5.8 0.7 + - - -
253A TYR* 3.4 23.5 - - - +
254A PRO* 1.3 72.4 - - - +
256A VAL* 1.4 67.5 + - - +
258A THR* 3.6 5.4 - - - -
259A ASP* 2.9 39.2 + - - +
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Residues in contact with VAL 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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233A ASP 3.8 22.9 - - - +
234A LYS 4.1 2.9 - - - -
235A ARG* 3.6 53.6 - - + +
238A THR* 4.8 2.2 - - - +
251A THR* 5.5 0.2 - - - +
253A TYR* 2.9 30.9 + - + +
255A ASP* 1.4 82.6 - - - +
257A ILE* 1.4 67.0 + - + +
259A ASP* 3.3 3.8 + - - +
260A VAL* 3.1 22.5 + - - +
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Residues in contact with ILE 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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7A ILE* 5.6 1.1 - - + -
9A ILE* 3.9 26.5 - - + -
232A VAL 3.8 20.0 - - - +
238A THR* 3.3 36.8 - - + +
249A ILE* 4.0 25.1 - - + -
251A THR* 3.6 30.1 - - + +
253A TYR 3.7 3.8 - - - +
254A PRO 3.3 5.5 + - - +
256A VAL* 1.4 79.1 - - + +
258A THR* 1.3 65.2 + - - +
260A VAL* 3.2 4.5 + - - +
261A LEU* 3.0 28.1 + - + +
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Residues in contact with THR 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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9A ILE* 3.6 20.8 - - + +
26A LEU 4.6 2.0 - - - +
27A GLY* 3.9 17.4 + - - -
254A PRO 3.0 18.1 + - - -
255A ASP* 3.6 9.2 - - - +
257A ILE* 1.3 76.6 - - - +
259A ASP* 1.3 65.6 + - - +
261A LEU* 3.2 5.9 + - + +
262A ASN* 2.9 41.1 + - - +
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Residues in contact with ASP 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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235A ARG* 2.8 35.0 + - - +
255A ASP* 2.9 28.0 + - - +
256A VAL 3.5 5.6 - - - +
258A THR* 1.3 79.8 - - - +
260A VAL* 1.3 61.5 + - - +
262A ASN* 3.2 16.5 + - - +
263A GLU* 3.3 17.1 + - - +
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Residues in contact with VAL 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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235A ARG* 3.7 39.7 - - + +
238A THR* 3.8 22.2 - - + -
239A ARG* 3.8 24.7 - - + +
242A LEU* 4.0 11.9 - - + -
256A VAL 3.1 15.6 + - - +
257A ILE 3.2 6.0 + - - +
259A ASP* 1.3 71.6 - - - +
261A LEU* 1.3 65.6 + - - +
262A ASN 3.0 1.6 - - - -
263A GLU* 3.0 28.3 + - - +
266A TYR* 3.3 17.2 - - + +
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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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7A ILE* 4.4 13.7 - - + -
9A ILE* 3.4 37.7 - - + -
242A LEU* 3.6 32.1 - - + -
257A ILE* 3.0 19.7 + - + +
258A THR* 3.2 8.7 + - + +
260A VAL* 1.3 75.3 - - - +
262A ASN* 1.3 63.4 + - - +
266A TYR* 3.8 4.1 - - - +
267A LYS* 3.4 26.9 + - - +
270A PHE* 3.6 32.9 - - + +
271A ARG* 5.4 1.3 - - - +
272A VAL* 4.3 15.9 - - + +
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Residues in contact with ASN 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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258A THR* 2.9 38.4 + - - +
259A ASP* 3.2 11.3 + - - +
260A VAL 3.0 0.6 - - - -
261A LEU* 1.3 79.2 - - - +
263A GLU* 1.3 66.9 + - - +
264A ALA 3.5 1.7 + - - -
267A LYS* 3.8 35.4 + - - +
293A PEG 4.6 2.3 + - - -
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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
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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