Contacts of the helix formed by residues 373 - 382 (chain A) in PDB entry 2Q8I
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 ASN 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A VAL* 3.5 28.0 + - + +
372A PHE* 1.3 88.9 - - - +
374A LYS* 1.3 67.3 + - - +
375A SER* 2.8 32.9 + - - -
376A ALA* 2.8 17.6 + - - +
377A TRP* 2.9 22.5 + - - +
177B GLY 5.5 4.7 + - - +
179B GLU* 3.5 19.6 + - - +
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Residues in contact with LYS 374 (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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373A ASN* 1.3 77.7 - - - +
375A SER* 1.3 55.5 + - - +
377A TRP* 3.4 43.5 - - + +
378A ARG* 2.9 55.5 + - - +
162B GLU* 3.5 28.5 + - + +
163B GLY* 3.4 21.1 - - - +
179B GLU* 2.9 25.2 + - - +
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 4.7 0.2 - - - -
373A ASN* 2.8 19.6 + - - -
374A LYS* 1.3 75.0 - - - +
376A ALA* 1.3 61.2 + - - -
378A ARG* 3.4 25.0 + - - +
379A HIS* 3.3 22.7 + - - -
179B GLU* 3.5 6.0 + - - -
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Residues in contact with ALA 376 (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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63A GLU* 4.1 11.0 - - - +
149A TYR* 3.4 13.4 + - - +
153A ARG* 3.6 26.9 - - - +
371A VAL 3.8 2.7 - - - +
372A PHE* 4.2 5.6 - - + -
373A ASN* 2.8 25.2 + - - +
375A SER* 1.3 76.4 - - - +
377A TRP* 1.3 63.3 + - - +
379A HIS* 3.0 14.2 + - - +
380A TYR* 3.2 18.0 - - + -
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Residues in contact with TRP 377 (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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62A ARG* 6.0 2.5 - - - -
66A LEU* 3.9 29.7 - - + +
372A PHE* 4.2 18.4 - + + -
373A ASN 2.9 13.2 + - - +
374A LYS* 3.4 47.8 - - + +
376A ALA* 1.3 75.2 - - - +
378A ARG* 1.3 88.3 + - + +
380A TYR* 3.0 19.9 + - - +
381A LYS* 3.1 47.8 + - + +
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Residues in contact with ARG 378 (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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374A LYS* 2.9 41.8 + - + +
375A SER* 3.7 28.5 + - - +
376A ALA 3.2 0.2 - - - -
377A TRP* 1.3 99.6 - - + +
379A HIS* 1.3 63.4 + - + +
381A LYS* 3.6 2.8 - - + +
382A THR* 3.0 30.3 + - + +
162B GLU 5.2 0.4 + - - -
163B GLY 3.8 17.8 + - - -
164B ASP* 5.0 7.7 + - - +
179B GLU* 5.0 0.4 + - - -
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Residues in contact with HIS 379 (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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146A ASN* 3.1 14.8 - - - +
149A TYR* 3.4 56.6 - + + +
375A SER* 3.3 25.1 + - - -
376A ALA 3.0 10.0 + - - +
378A ARG* 1.3 77.9 - - + +
380A TYR* 1.3 58.7 + - - +
382A THR* 2.5 28.4 + - - +
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Residues in contact with TYR 380 (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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63A GLU* 2.7 47.7 + - + +
66A LEU* 3.5 52.2 - - + +
67A LEU* 4.2 12.3 - - + -
68A PRO* 6.0 0.2 - - + -
146A ASN* 3.6 27.0 + - - +
149A TYR* 3.8 18.4 - + - -
150A PHE* 3.4 42.6 - + + -
376A ALA 3.2 24.5 - - - -
377A TRP 3.0 6.1 + - - +
379A HIS* 1.3 78.9 - - - +
381A LYS* 1.3 66.7 + - + +
382A THR 3.6 2.8 + - - +
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Residues in contact with LYS 381 (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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66A LEU* 4.0 32.3 - - - +
377A TRP* 3.1 57.6 + - + +
378A ARG* 3.1 6.0 + - - +
380A TYR* 1.3 84.6 - - + +
382A THR* 1.3 61.7 + - - +
383A THR* 3.4 6.8 + - - +
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Residues in contact with THR 382 (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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142A PHE* 3.1 28.1 - - - -
146A ASN* 3.5 9.5 + - - +
378A ARG* 3.0 22.2 + - + +
379A HIS* 2.5 28.9 + - - +
380A TYR 3.3 3.7 - - - +
381A LYS* 1.3 76.2 - - - +
383A THR* 1.3 61.0 + - - +
385A GLU* 5.0 11.2 - - - +
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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