Contacts of the helix formed by residues 376 - 382 (chain A) in PDB entry 1CX4
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 VAL 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A ALA 5.0 2.7 - - - +
309A ASP* 3.0 25.0 + - + +
353A LEU* 4.1 34.1 - - + +
375A ASP* 1.3 73.5 - - + +
377A GLN* 1.3 82.3 + - - +
379A PHE* 3.4 7.6 + - + +
380A GLU* 3.0 50.5 + - + +
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Residues in contact with GLN 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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199A ILE* 4.0 13.2 - - + -
212A ASN 3.0 25.8 + - - +
213A TYR* 3.4 46.1 - - + +
375A ASP* 3.0 17.5 + - - +
376A VAL* 1.3 93.1 - - - +
378A ALA* 1.3 60.8 + - - +
380A GLU* 3.4 6.0 + - - +
381A ARG* 3.0 29.8 + - - +
440A CMP 4.3 13.7 + - + +
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Residues in contact with ALA 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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289A VAL* 3.8 25.6 - - + +
374A MET* 3.5 23.5 - - + +
375A ASP* 2.7 22.4 + - - +
377A GLN* 1.3 70.2 - - - +
379A PHE* 1.3 61.0 + - - +
381A ARG* 4.5 15.0 - - - +
382A LEU* 2.8 36.8 + - + +
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Residues in contact with PHE 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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311A PHE* 3.7 41.1 - + + -
350A GLU* 4.5 5.2 - - + -
353A LEU* 3.9 30.3 - - + -
354A VAL* 4.2 13.9 - - + -
374A MET* 3.8 11.2 - - - -
375A ASP 3.0 14.1 + - - +
376A VAL* 3.4 11.4 - - - +
378A ALA* 1.3 77.7 - - - +
380A GLU* 1.3 72.2 + - + +
383A LEU* 2.9 55.0 + - + +
387A MET* 3.9 24.8 - - + +
390A MET* 4.1 19.5 - - - -
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Residues in contact with GLU 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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210A VAL 3.9 18.3 - - - +
211A GLY* 5.5 1.3 - - - -
353A LEU 4.8 8.3 - - - +
376A VAL* 3.0 37.2 + - + +
377A GLN* 3.4 5.6 + - - +
379A PHE* 1.3 91.3 - - + +
381A ARG* 1.3 62.2 + - - +
384A GLY* 4.4 10.9 + - - +
387A MET* 5.8 4.7 - - + -
440A CMP 5.3 1.8 - - - +
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Residues in contact with ARG 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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221A GLU* 4.7 4.4 + - - -
222A LEU* 3.5 39.0 - - - +
226A TYR* 5.4 1.6 + - - -
285A LYS* 4.8 11.9 + - - +
289A VAL* 3.8 23.4 - - - +
377A GLN 3.0 16.5 + - - +
378A ALA* 3.8 10.9 - - - +
380A GLU* 1.3 80.0 - - - +
382A LEU* 1.3 93.0 + - + +
384A GLY 5.0 1.1 + - - -
385A PRO* 5.7 0.9 - - - +
440A CMP 3.6 51.7 + - + +
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Residues in contact with LEU 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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278A LEU* 3.3 23.0 - - + +
282A GLU* 4.1 18.5 - - + +
285A LYS* 4.1 24.5 - - + +
286A VAL* 3.9 31.0 - - + -
289A VAL* 4.0 20.4 - - + -
374A MET* 5.1 3.8 - - + -
378A ALA 2.8 18.1 + - - +
381A ARG* 1.3 111.3 - - + +
383A LEU* 1.3 69.5 + - + +
384A GLY 3.4 2.7 - - - -
385A PRO* 3.5 5.5 - - - +
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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