Contacts of the helix formed by residues 261 - 269 (chain A) in PDB entry 3N9Z
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 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.9 0.9 - - - -
174A VAL 3.4 12.1 - - - -
175A ILE 3.9 4.0 - - - -
177A GLY* 4.4 4.9 - - - -
259A TYR* 3.3 25.0 - - - -
260A ARG* 1.3 80.0 + - - +
262A ILE* 1.3 66.2 + - - -
263A LEU 3.4 2.6 + - - -
264A TYR* 3.6 4.0 + - - +
265A ARG* 3.3 23.7 + - - +
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 4.1 12.8 - - + +
119A VAL* 3.9 20.2 - - + -
128A PHE* 3.7 34.3 - - + -
174A VAL* 2.9 33.0 + - + +
175A ILE* 3.4 8.7 + - + -
259A TYR* 3.3 2.9 + - - +
261A GLY* 1.3 68.6 - - - -
263A LEU* 1.3 66.4 + - - +
265A ARG* 3.1 8.2 + - - +
266A LEU* 3.0 39.1 + - + +
284A MET* 3.8 28.3 - - + -
428A ILE* 4.1 8.5 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 3.0 24.9 + - + +
176A PHE* 3.5 28.0 - - + -
242A THR* 4.4 17.3 - - + -
245A PHE* 3.5 33.2 - - + -
262A ILE* 1.3 78.7 - - - +
264A TYR* 1.3 57.6 + - - +
266A LEU* 3.3 5.6 + - + +
267A LEU* 2.8 42.1 + - + +
277A ILE* 3.5 31.0 - - + -
281A VAL* 4.0 14.4 - - + -
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Residues in contact with TYR 264 (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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175A ILE 4.5 0.2 + - - -
245A PHE* 3.8 18.9 - + + -
249A LEU* 3.4 36.1 - - + +
254A SER 3.6 8.9 + - - -
255A VAL* 4.0 5.4 - - - +
256A HIS* 3.3 43.0 + + + -
258A ASP 5.7 0.9 - - - -
260A ARG* 3.6 40.2 - - + -
261A GLY 3.6 10.2 + - - +
263A LEU* 1.3 76.3 - - - +
265A ARG* 1.3 66.8 + - + +
267A LEU* 4.2 2.8 - - - +
268A GLY* 2.9 30.6 + - - -
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN 5.4 0.6 + - - -
118A GLU* 3.1 46.6 + - - +
123A GLU 5.2 1.2 + - - -
124A ALA* 4.5 10.9 - - - +
127A ASN* 3.5 24.5 + - - +
259A TYR* 3.7 26.8 - - + +
261A GLY 3.3 13.4 + - - +
262A ILE* 3.1 10.1 + - - +
264A TYR* 1.3 87.1 - - + +
266A LEU* 1.3 57.2 + - - +
269A ASP* 3.0 34.3 + - - +
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Residues in contact with LEU 266 (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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114A ALA 3.9 16.6 - - - +
115A LEU* 3.9 26.9 - - + -
118A GLU* 3.8 24.5 - - + -
262A ILE* 3.0 33.3 + - + +
263A LEU* 3.9 5.4 - - + +
265A ARG* 1.3 74.0 - - - +
267A LEU* 1.3 65.1 + - - +
268A GLY 3.6 0.2 + - - -
270A SER* 3.3 40.9 + - - +
272A MET* 4.9 4.9 - - - +
277A ILE* 3.4 36.7 - - + +
280A ASN* 6.1 0.4 - - + -
281A VAL* 5.5 5.6 - - + -
284A MET* 5.8 1.8 - - - -
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Residues in contact with LEU 267 (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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242A THR 5.4 0.2 - - - +
245A PHE* 4.0 17.5 - - + -
246A TYR* 4.2 25.1 - - + -
249A LEU* 4.4 19.5 - - + -
263A LEU* 2.8 45.8 + - + +
264A TYR 4.2 1.6 - - - +
266A LEU* 1.3 73.7 - - - +
268A GLY* 1.3 62.4 + - - +
270A SER 5.4 0.2 + - - -
274A PHE* 3.7 31.4 - - + -
277A ILE* 4.2 16.8 - - + -
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 5.7 2.6 - - - +
264A TYR* 2.9 22.9 + - - -
265A ARG* 3.9 0.4 - - - -
267A LEU* 1.3 80.0 - - - +
269A ASP* 1.3 62.2 + - - +
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Residues in contact with ASP 269 (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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118A GLU* 4.8 7.4 - - - +
265A ARG 3.0 15.6 + - - +
267A LEU 3.5 0.4 - - - -
268A GLY* 1.3 79.7 - - - +
270A SER* 1.3 65.1 + - - +
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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