Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 3UGV
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A TYR* 5.3 1.3 - - - -
89A ARG* 5.3 6.7 - - - -
102A MET* 5.3 0.9 - - - -
256A PHE* 3.4 7.2 + - - +
257A TYR* 1.3 73.9 - - - +
259A PRO* 1.3 77.2 - - - +
260A ARG 3.2 2.9 - - - -
261A GLU* 3.1 13.2 + - - +
262A MET 3.3 8.0 + - - -
280A ARG 3.4 6.6 + - - -
281A ILE* 3.5 23.9 - - - +
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Residues in contact with PRO 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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85A TYR* 4.7 6.7 - - - +
89A ARG* 5.4 3.8 - - - +
258A GLY* 1.3 83.5 - - - +
260A ARG* 1.3 57.6 + - - +
262A MET* 3.1 11.3 + - + +
263A HIS* 2.8 29.0 + - - +
281A ILE* 3.9 10.5 - - - +
286A GLY* 3.7 23.6 - - - +
289A ARG* 3.7 24.0 - - + +
290A ALA* 4.1 20.9 - - + +
293A VAL* 4.6 9.9 - - + +
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Residues in contact with ARG 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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257A TYR 6.0 0.2 - - - +
258A GLY* 3.2 1.5 - - - -
259A PRO* 1.3 79.7 - - - +
261A GLU* 1.3 57.9 + - - +
263A HIS* 3.2 16.6 + - + +
264A GLN* 2.8 55.5 + - + +
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Residues in contact with GLU 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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98A ALA* 4.7 6.9 - - - +
233A TYR* 4.8 7.3 - - - -
236A PHE* 4.8 13.0 - - + -
255A ASN 3.5 11.6 - - - +
256A PHE* 3.8 12.0 - - + -
257A TYR* 3.1 48.2 + - - +
258A GLY 3.1 10.8 + - - +
260A ARG* 1.3 75.5 - - - +
262A MET* 1.3 67.5 + - - +
264A GLN* 3.3 17.4 + - - +
265A ALA* 2.9 23.6 + - - +
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Residues in contact with MET 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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256A PHE* 3.7 30.5 - - + -
258A GLY 3.3 6.3 + - - +
259A PRO* 3.1 13.1 + - + +
261A GLU* 1.3 78.5 - - - +
263A HIS* 1.3 63.5 + - - +
265A ALA* 3.0 5.0 + - - +
266A LEU* 3.0 35.7 + - + +
274A VAL* 3.9 20.4 - - + -
276A PRO* 3.4 33.7 - - + -
281A ILE* 4.6 1.6 - - + -
290A ALA* 3.7 31.9 - - + +
293A VAL* 4.4 7.0 - - + -
294A ALA* 4.2 17.0 - - - -
301A MET* 4.3 3.6 - - + -
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Residues in contact with HIS 263 (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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259A PRO 2.8 14.0 + - - +
260A ARG* 3.4 22.2 - - + +
262A MET* 1.3 75.8 - - - +
264A GLN* 1.3 69.6 + - + +
266A LEU* 3.4 5.9 + - - +
267A GLN* 3.0 65.4 + - + +
293A VAL* 4.3 22.4 - - + +
297A TRP* 5.0 8.9 + + - +
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Residues in contact with GLN 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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236A PHE* 4.6 11.9 - - + -
260A ARG* 2.8 42.6 + - - +
261A GLU* 3.7 20.9 - - - +
263A HIS* 1.3 79.8 - - + +
265A ALA* 1.3 64.1 + - - +
267A GLN* 3.5 13.6 + - - +
268A ALA* 3.2 22.5 + - - +
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Residues in contact with ALA 265 (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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236A PHE* 4.0 22.8 - - + -
252A ILE* 4.5 2.0 - - + -
256A PHE* 3.5 33.9 - - + -
261A GLU 2.9 10.7 + - - +
262A MET 3.0 8.0 + - - +
264A GLN* 1.3 75.2 - - - +
266A LEU* 1.3 62.6 + - + +
268A ALA* 3.2 6.9 + - - +
269A GLY 3.2 0.2 + - - -
270A ALA* 3.1 34.9 + - + +
271A CYS* 4.9 3.8 - - - -
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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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262A MET* 3.0 35.6 + - + +
263A HIS 3.8 3.1 - - - +
265A ALA* 1.3 72.2 - - - +
267A GLN* 1.3 64.5 + - - +
268A ALA 3.1 1.6 - - - -
269A GLY* 3.0 14.2 + - - +
270A ALA 4.9 0.9 - - - +
271A CYS* 3.7 21.5 - - - +
274A VAL* 4.5 2.7 - - + -
293A VAL* 4.2 8.1 - - + +
297A TRP* 3.4 61.8 - - + +
299A ILE* 3.6 41.5 - - + -
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Residues in contact with GLN 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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263A HIS* 3.0 59.1 + - + +
264A GLN* 3.8 13.7 - - - +
265A ALA 3.4 0.2 - - - -
266A LEU* 1.3 77.3 - - - +
268A ALA* 1.3 58.3 + - - +
269A GLY 3.2 0.6 + - - -
297A TRP* 4.0 16.0 - - + -
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Residues in contact with ALA 268 (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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236A PHE* 4.3 26.7 - - + +
240A ALA* 3.5 16.5 - - - +
264A GLN 3.2 15.2 + - - +
265A ALA 3.5 6.5 - - - +
266A LEU 3.1 1.0 - - - -
267A GLN* 1.3 80.0 - - - +
269A GLY* 1.3 62.0 + - - +
270A ALA* 3.5 1.3 + - + +
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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