Contacts of the helix formed by residues 379 - 385 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D VAL* 5.0 3.1 - - - +
148D TYR* 3.6 23.3 + - - +
149D THR 2.9 8.9 + - - -
150D ARG* 3.0 26.7 + - - +
219D GLY* 4.9 0.4 - - - -
378D ALA* 1.3 72.3 - - - +
380D GLU* 1.3 54.2 + - - +
382D ASN* 3.0 9.0 + - - +
383D THR* 2.7 31.4 + - - -
458D MET* 3.9 20.8 - - - +
460D TYR* 3.2 17.7 + - - -
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Residues in contact with GLU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ARG* 3.2 28.3 - - - +
151D ALA* 3.3 20.5 + - + +
152D LEU 3.3 2.4 + - - -
378D ALA* 4.1 2.5 - - + -
379D SER* 1.3 72.7 - - - +
381D PHE* 1.3 66.9 + - - +
383D THR* 3.0 1.8 + - - -
384D LEU* 2.7 33.7 + - + +
460D TYR* 3.1 28.5 - - - -
466D TYR* 2.6 32.8 + - + -
503D LEU* 4.5 13.2 - - + -
525D LEU* 5.1 2.2 - - + -
529D PHE* 3.8 22.9 - - + -
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Residues in contact with PHE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PHE* 4.0 20.0 - + - -
210D PHE* 3.2 32.3 - + - -
377D ILE* 5.4 7.6 - - + -
378D ALA 3.9 15.2 + - - +
379D SER 3.3 0.2 - - - -
380D GLU* 1.3 79.5 - - - +
382D ASN* 1.3 62.0 + - - +
384D LEU* 3.8 5.6 - - + +
385D TYR* 3.1 50.3 + + - +
526D GLY* 3.4 22.7 - - - -
529D PHE* 2.9 50.3 - + + -
530D SER* 3.5 30.3 - - - -
701D S58 4.1 0.2 - - + -
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Residues in contact with ASN 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR* 3.6 16.1 + - + -
210D PHE* 2.9 40.3 - - + +
212D THR* 4.2 6.2 + - - -
378D ALA 3.7 5.5 + - - +
379D SER* 3.0 16.1 + - - +
381D PHE* 1.3 74.4 - - - +
383D THR* 1.3 63.0 + - - +
385D TYR* 3.0 10.7 + - - +
386D HIS* 2.7 39.5 + - - -
682D HEM 3.1 35.4 + - - +
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Residues in contact with THR 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D SER 2.7 11.0 + - - -
380D GLU 3.0 3.0 + - - +
382D ASN* 1.3 75.8 + - - +
384D LEU* 1.3 58.0 - - + +
385D TYR 2.6 14.2 + - - -
386D HIS* 2.8 37.4 + - - +
451D SER* 4.9 1.4 + - - -
455D SER* 2.8 26.8 + - - +
458D MET* 4.6 4.2 - - - +
460D TYR* 3.5 29.7 + - + -
503D LEU* 4.6 8.1 - - + -
504D TYR* 4.1 26.6 - - + -
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D GLU* 2.7 30.0 + - + +
381D PHE* 3.8 8.5 - - + +
383D THR* 1.3 77.1 - - + +
385D TYR* 1.3 62.3 + - + +
386D HIS 3.2 2.9 + - - +
387D TRP* 3.0 19.5 + - - +
503D LEU* 5.4 1.6 - - + -
504D TYR* 5.3 2.7 - - - -
507D LEU* 3.8 26.9 - - + -
522D MET* 3.4 26.8 - - - +
525D LEU* 3.6 40.2 - - + -
526D GLY* 4.1 11.7 - - - +
529D PHE* 5.0 0.9 - - + -
701D S58 4.2 21.3 - - + -
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Residues in contact with TYR 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ALA 4.4 2.2 - - - -
205D PHE* 5.1 1.9 - - - -
206D THR* 3.0 34.9 - - + +
209D PHE* 5.8 0.2 - + - -
210D PHE* 3.6 15.5 - + + -
348D TYR* 3.0 35.0 + - - -
381D PHE* 3.1 44.9 + + - +
382D ASN 3.0 4.7 + - - +
383D THR 2.6 7.3 + - - -
384D LEU* 1.3 76.1 - - + +
386D HIS* 1.3 58.2 + - - -
387D TRP* 2.8 34.7 + + - +
530D SER* 4.2 8.5 + - - -
682D HEM 3.4 17.5 - - + +
701D S58 2.9 35.7 - - + +
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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