Contacts of the helix formed by residues 428 - 441 (chain R) in PDB entry 1HI0
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 ASP 428 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125R LEU* 3.8 14.9 - - - +
426R ILE 3.8 0.2 - - - -
427R LYS* 1.3 88.9 - - - +
429R MET* 1.3 65.7 + - - +
430R PRO* 3.0 17.3 - - + +
431R SER* 2.6 37.6 + - - -
432R ALA* 2.9 23.2 + - - +
434R ARG* 4.5 1.7 + - - -
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Residues in contact with MET 429 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125R LEU* 3.5 34.8 - - + +
128R ARG* 3.7 34.8 - - + +
129R ALA* 3.9 7.0 - - - +
132R ARG* 3.2 37.9 - - + +
343R GLU* 4.0 5.2 - - - +
428R ASP* 1.3 73.8 - - - +
430R PRO* 1.3 63.8 - - + +
432R ALA* 2.9 3.4 + - - +
433R CYS* 2.6 44.8 + - - -
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Residues in contact with PRO 430 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428R ASP* 3.0 17.7 - - + +
429R MET* 1.3 92.2 - - + +
431R SER* 1.3 65.2 + - - +
433R CYS* 3.1 5.6 + - + +
434R ARG* 2.8 46.0 + - - +
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Residues in contact with SER 431 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425R ARG 3.2 23.1 - - - +
427R LYS* 2.8 33.8 + - - -
428R ASP* 2.6 33.2 + - - -
430R PRO* 1.3 72.1 - - - +
432R ALA* 1.3 54.3 + - - +
434R ARG* 3.3 27.0 + - - +
435R PHE* 2.9 24.1 + - - +
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Residues in contact with ALA 432 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R LEU* 4.2 12.8 - - + +
126R LEU* 4.9 3.2 - - + +
129R ALA* 4.1 16.8 - - + -
426R ILE* 3.8 25.6 - - + -
428R ASP 2.9 21.4 + - - +
429R MET* 3.1 7.2 - - - +
431R SER* 1.3 74.4 + - - +
433R CYS* 1.3 68.3 + - - +
435R PHE* 2.9 4.6 + - - +
436R LEU* 2.8 24.9 + - - +
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Residues in contact with CYS 433 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R ALA* 4.0 19.0 - - - +
132R ARG* 4.2 17.9 - - - -
133R LEU* 3.9 15.3 - - + +
429R MET* 2.6 46.3 + - - +
430R PRO* 3.6 5.4 - - + +
432R ALA* 1.3 71.5 - - - +
434R ARG* 1.3 59.3 + - + +
436R LEU* 3.8 1.9 - - - +
437R ASP* 2.8 35.2 + - - +
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Residues in contact with ARG 434 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425R ARG 5.5 0.2 + - - -
428R ASP* 4.5 2.0 + - - -
430R PRO* 2.8 28.5 + - - +
431R SER* 3.3 46.4 + - - +
433R CYS* 1.3 77.8 - - + +
435R PHE* 1.3 62.0 + - - +
437R ASP* 3.6 4.8 - - - +
438R SER* 3.0 23.0 + - - -
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Residues in contact with PHE 435 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R LEU* 4.4 6.7 - - + -
411R LEU* 4.0 31.4 - - + -
415R LEU* 4.5 12.3 - - + -
422R LEU* 4.2 19.5 - - + -
425R ARG* 3.5 37.9 - - + +
426R ILE* 3.8 34.1 - - + -
431R SER 2.9 18.6 + - - +
432R ALA 3.5 2.9 - - - +
434R ARG* 1.3 76.4 - - - +
436R LEU* 1.3 56.7 + - - +
438R SER* 3.0 7.5 + - - -
439R TYR* 2.8 41.7 + - + +
444R GLU* 3.9 26.7 - - + -
446R ILE* 4.7 2.7 - - + -
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Residues in contact with LEU 436 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R LEU* 3.9 10.1 - - + +
129R ALA* 3.7 10.8 - - + -
130R ALA* 3.3 42.8 - - + +
133R LEU* 3.7 13.9 - - + -
408R ILE* 3.9 13.9 - - + -
411R LEU* 4.0 17.0 - - + -
432R ALA 2.8 17.1 + - - +
433R CYS 3.8 3.1 - - - +
435R PHE* 1.3 76.6 - - - +
437R ASP* 1.3 58.0 + - - +
439R TYR* 3.1 8.0 + - + +
440R TRP* 2.8 58.5 + - + +
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Residues in contact with ASP 437 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R LEU* 3.4 17.9 - - + +
297R LYS* 3.4 19.1 + - - -
298R TYR* 2.8 25.3 + - - -
433R CYS 2.8 20.0 + - - +
434R ARG* 3.6 6.6 - - - +
436R LEU* 1.3 78.5 - - - +
438R SER* 1.3 64.7 + - - +
440R TRP 3.3 0.2 + - - -
441R GLN* 2.8 39.5 + - - +
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Residues in contact with SER 438 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425R ARG* 4.7 3.9 + - - -
434R ARG 3.0 13.2 + - - -
435R PHE* 3.0 11.0 + - - -
437R ASP* 1.3 80.2 + - - +
439R TYR* 1.3 62.6 + - - +
441R GLN* 3.2 7.4 + - - +
443R HIS* 3.2 43.6 + - - +
444R GLU* 2.4 28.0 + - - -
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Residues in contact with TYR 439 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301R THR* 4.1 4.3 - - - +
407R SER 4.9 0.4 - - - -
410R TYR 4.8 0.2 - - - -
411R LEU* 3.7 37.5 - - + -
414R GLN* 2.7 27.7 + - - -
435R PHE* 2.8 20.4 + + + +
436R LEU* 3.4 17.7 - - + +
438R SER* 1.3 76.3 - - - +
440R TRP* 1.3 75.1 + + - +
442R GLY* 2.9 21.8 + - - -
443R HIS 4.2 0.2 + - - -
444R GLU* 3.8 16.1 - - + +
446R ILE* 3.1 39.0 - - + +
447R ARG* 3.9 5.1 - - - -
448R GLN* 3.4 39.6 + - + +
457R LEU* 4.9 0.2 - - - +
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Residues in contact with TRP 440 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R ALA* 3.8 28.9 - - + -
133R LEU* 3.7 38.8 - - + -
134R MET* 3.9 26.2 - - + -
298R TYR* 3.5 39.2 - + + +
300R TYR* 3.7 1.0 - - - +
301R THR* 3.0 46.3 + - - +
302R PHE* 3.6 17.7 - + - -
404R LEU* 5.7 1.3 - - + -
407R SER* 2.9 27.2 + - - -
408R ILE* 4.4 4.6 - - + +
436R LEU* 2.8 35.9 + - + +
437R ASP 3.3 0.4 + - - +
439R TYR* 1.3 91.5 - + - +
441R GLN* 1.3 58.9 + - - +
442R GLY 3.1 0.4 - - - -
448R GLN* 4.7 0.2 - - - -
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Residues in contact with GLN 441 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297R LYS* 3.9 30.1 - - - +
298R TYR* 4.0 7.5 - - + -
300R TYR* 3.5 18.9 - - - +
437R ASP* 2.8 39.9 + - - +
438R SER* 3.7 9.1 - - - +
439R TYR 3.1 1.8 - - - -
440R TRP* 1.3 76.3 - - - +
442R GLY* 1.3 61.4 + - - +
443R HIS* 3.4 37.4 + - + +
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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
------------------------------------------------------------
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