Contacts of the helix formed by residues 379 - 385 (chain A) in PDB entry 1CX2
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.9 2.9 - - - +
148A TYR* 3.6 23.7 + - - +
149A THR 2.9 9.5 + - - -
150A ARG* 3.0 26.8 + - - +
219A GLY* 4.9 0.2 - - - -
378A ALA* 1.3 70.5 - - - +
380A GLU* 1.3 54.4 + - - +
382A ASN* 3.0 8.2 + - - +
383A THR* 2.8 32.1 + - - -
458A MET* 3.9 21.9 - - - +
460A TYR* 3.1 17.6 + - - -
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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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150A ARG* 3.2 27.9 - - - +
151A ALA* 3.4 23.5 + - + +
152A LEU 3.4 0.2 + - - -
378A ALA* 4.2 2.2 - - + -
379A SER* 1.3 72.6 - - - +
381A PHE* 1.3 58.7 + - - +
382A ASN 3.0 0.2 + - - -
383A THR* 3.0 2.5 + - - +
384A LEU* 2.7 41.7 + - + +
460A TYR* 3.0 29.6 - - - -
466A TYR* 2.5 36.0 + - + -
503A LEU* 4.6 12.8 - - + -
525A LEU* 5.1 2.7 - - + -
529A PHE* 3.9 19.5 - - + -
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Residues in contact with PHE 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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209A PHE* 4.0 19.5 - + - -
210A PHE* 3.2 30.6 - + + -
377A ILE* 5.3 8.1 - - + -
378A ALA 3.8 14.8 + - - +
379A SER 3.3 0.4 - - - -
380A GLU* 1.3 79.5 - - - +
382A ASN* 1.3 63.5 + - - +
384A LEU* 3.8 6.5 - - + +
385A TYR* 3.1 51.0 + + - +
526A GLY* 3.5 22.7 - - - -
529A PHE* 3.0 46.8 - + + -
530A SER* 3.4 30.3 - - - -
701A S58 4.2 0.2 - - + -
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Residues in contact with ASN 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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148A TYR* 3.7 15.1 + - + -
210A PHE* 2.9 47.9 - - + +
212A THR* 4.2 8.4 + - - -
378A ALA 3.6 8.8 + - - +
379A SER* 3.0 12.3 + - - +
380A GLU 3.0 0.4 - - - -
381A PHE* 1.3 76.1 - - - +
383A THR* 1.3 72.2 + - - +
385A TYR* 3.0 11.3 + - - +
386A HIS* 2.9 29.1 + - - -
682A HEM 3.7 22.5 + - - +
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Residues in contact with THR 383 (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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379A SER 2.8 10.4 + - - -
380A GLU 3.7 3.1 - - - +
382A ASN* 1.3 73.8 + - - +
384A LEU* 1.3 58.1 + - - +
385A TYR 2.6 13.7 + - - -
386A HIS* 2.8 37.7 + - - +
451A SER* 5.5 1.4 - - - -
455A SER* 2.8 27.0 + - - +
458A MET* 4.5 4.7 - - - +
460A TYR* 3.6 31.0 + - + -
503A LEU* 4.6 9.0 - - + -
504A TYR* 4.1 26.4 - - + -
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Residues in contact with LEU 384 (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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380A GLU* 2.7 29.3 + - + +
381A PHE* 3.8 9.6 - - + +
383A THR* 1.3 76.4 - - + +
385A TYR* 1.3 61.5 + - + +
386A HIS 3.2 2.6 - - - +
387A TRP* 3.0 18.8 + - - +
503A LEU* 5.3 1.6 - - + -
504A TYR* 5.3 2.5 - - - -
507A LEU* 3.9 25.4 - - + -
522A MET* 3.3 28.1 - - - +
525A LEU* 3.6 38.8 - - + -
526A GLY* 4.0 12.1 - - - +
529A PHE* 5.0 1.6 - - + -
701A S58 4.1 21.5 - - + -
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Residues in contact with TYR 385 (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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202A ALA 4.4 2.0 - - - -
205A PHE* 5.0 2.4 - - - -
206A THR* 3.1 32.9 - - + +
209A PHE* 5.8 0.2 - + - -
210A PHE* 3.6 15.3 - + + -
348A TYR* 2.8 36.2 + - - -
381A PHE* 3.1 45.4 + + - +
382A ASN 3.0 5.8 + - - +
383A THR 2.6 7.1 + - - -
384A LEU* 1.3 76.3 - - + +
386A HIS* 1.3 54.8 + - - -
387A TRP* 2.7 45.6 + + - +
530A SER* 4.3 8.0 + - - -
682A HEM 3.9 14.4 - - + +
701A S58 3.1 32.2 - - + +
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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