Contacts of the helix formed by residues 516 - 530 (chain B) in PDB entry 2H3W
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 PHE 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 3.5 34.1 - - - +
49B TYR* 3.6 26.7 - + + -
50B TYR* 3.5 42.4 - + + -
53B ALA* 3.9 7.4 - - + -
469B ARG* 3.4 26.9 - - - -
506B TYR* 3.2 23.1 - + - -
514B GLU 5.3 0.2 - - - +
515B ALA* 1.3 78.9 - - - +
517B ASP* 1.3 76.4 + - - +
518B ARG 3.4 2.0 - - - -
519B HIS* 3.1 5.9 + - - +
520B LEU* 2.8 45.3 + - + +
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Residues in contact with ASP 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ASP* 3.7 3.8 + - - +
467B THR* 3.5 40.3 + - - +
469B ARG* 2.6 49.7 + - - +
506B TYR* 4.2 1.0 + - - -
515B ALA* 4.7 0.2 - - - +
516B PHE* 1.3 88.7 - - - +
518B ARG* 1.3 66.8 + - - +
520B LEU* 3.4 4.6 + - - +
521B LEU* 3.0 22.9 + - - +
543B TYR* 4.9 1.9 + - - -
547B MET* 3.6 20.4 - - + +
549B PHE* 4.3 1.6 - - - -
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Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.5 13.4 - - + -
98B LEU* 3.6 29.0 - - + +
102B TRP* 3.3 47.3 - - - -
452B TYR* 2.8 29.1 + - - -
465B THR* 3.0 38.1 + - - +
466B ASP* 3.2 30.9 + - + +
467B THR* 2.8 26.3 + - - +
516B PHE 3.4 0.2 - - - -
517B ASP* 1.3 84.2 - - - +
519B HIS* 1.3 57.9 + - - +
521B LEU* 3.3 8.1 + - - +
522B GLY 2.8 23.6 + - - -
547B MET* 6.3 0.6 - - - +
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Residues in contact with HIS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.9 8.1 - - + +
41B PRO* 3.0 42.2 + - + +
42B PRO 3.7 7.9 - - - -
43B LEU* 4.1 4.5 - - + -
46B SER* 2.7 30.9 + - - +
84B GLN* 2.8 28.2 + - - -
87B LEU* 3.7 16.6 - - + -
97B TRP* 4.1 9.5 - + + -
466B ASP* 5.1 0.8 + - - -
515B ALA 4.7 0.7 - - - +
516B PHE* 3.1 14.9 + - - +
518B ARG* 1.3 76.9 - - - +
520B LEU* 1.3 64.6 + - + +
522B GLY* 3.1 2.8 + - - -
523B LEU* 3.0 29.8 + - + +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 5.0 10.5 - - - +
47B LEU* 4.1 20.6 - - + -
50B TYR* 3.8 27.8 - - + -
516B PHE* 2.8 45.4 + - + +
517B ASP* 3.9 4.5 - - - +
519B HIS* 1.3 73.6 - - - +
521B LEU* 1.3 63.7 + - - +
523B LEU* 3.3 21.3 + - + -
524B LYS* 3.0 17.2 + - - +
537B ILE* 5.3 3.8 - - + -
538B PHE* 3.3 26.5 - - + -
543B TYR* 4.1 22.9 - - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.6 9.2 - - + -
102B TRP* 3.7 37.0 - - + -
105B THR* 4.7 16.8 - - + -
517B ASP 3.0 15.1 + - - +
518B ARG* 3.4 13.9 - - - +
519B HIS 3.2 0.2 - - - -
520B LEU* 1.3 76.6 - - - +
522B GLY* 1.3 57.1 + - - +
524B LYS* 3.1 26.8 + - - +
525B LEU* 2.9 59.0 + - + +
543B TYR* 4.2 10.0 + - - +
547B MET* 6.1 4.5 - - + -
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Residues in contact with GLY 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.9 6.7 - - - -
97B TRP* 3.8 11.0 - - - -
98B LEU* 5.7 0.2 - - - -
101B TRP* 3.6 25.0 - - - -
518B ARG 2.8 15.1 + - - -
519B HIS 3.1 4.7 + - - -
521B LEU* 1.3 79.1 - - - +
523B LEU* 1.3 51.1 + - - +
525B LEU 3.3 0.2 + - - -
526B GLN* 2.7 36.6 + - - +
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 24.7 - - + -
73B PHE* 4.2 9.9 - - + -
80B GLY 4.5 0.4 - - - +
83B LEU* 3.8 18.0 - - + +
84B GLN* 3.7 33.4 - - + +
87B LEU* 3.6 19.5 - - + +
519B HIS* 3.0 23.0 + - + +
520B LEU* 3.6 32.3 - - + +
521B LEU 3.3 0.2 - - - -
522B GLY* 1.3 75.4 - - - +
524B LYS* 1.3 63.6 + - - +
526B GLN* 3.3 5.1 + - - +
527B ALA* 2.9 22.3 + - - +
538B PHE* 3.7 11.7 - - + -
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Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 5.9 3.0 - - - +
520B LEU 3.0 13.2 + - - +
521B LEU* 3.1 30.5 + - - +
523B LEU* 1.3 77.2 - - - +
525B LEU* 1.3 73.2 + - - +
527B ALA* 3.1 14.9 + - - +
528B ILE* 3.2 17.8 + - + +
534B MET* 3.7 31.4 - - + +
538B PHE* 3.5 34.5 - - + +
543B TYR* 4.6 15.1 + - + +
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 5.8 0.4 - - + -
101B TRP* 3.5 56.2 + - + +
104B LYS* 6.1 3.6 - - - +
105B THR* 4.0 20.2 - - + +
521B LEU* 2.9 45.3 + - + +
522B GLY* 3.8 3.4 - - - +
524B LYS* 1.3 82.4 - - - +
526B GLN* 1.3 57.7 + - - +
528B ILE* 3.2 22.4 + - + +
529B GLU* 3.0 28.4 + - - +
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Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.6 23.3 - - + +
86B GLY* 3.5 31.8 + - - +
87B LEU* 3.8 6.3 + - + +
89B ARG* 4.8 3.6 - - - +
90B ARG* 4.3 4.9 - - - +
101B TRP* 3.6 21.3 - - + -
522B GLY 2.7 21.7 + - - +
523B LEU* 3.5 9.0 - - - +
524B LYS 3.2 0.2 - - - -
525B LEU* 1.3 73.3 - - - +
527B ALA* 1.3 57.6 + - - +
529B GLU* 3.4 18.2 + - - +
530B ASP* 2.8 68.5 + - - +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.5 16.4 - - + +
523B LEU 2.9 12.5 + - - +
524B LYS* 3.1 10.5 + - - +
526B GLN* 1.3 74.5 - - - +
528B ILE* 1.3 66.1 + - + +
530B ASP 3.2 8.8 + - - -
531B LEU 3.2 4.5 + - - -
532B VAL* 3.2 31.0 + - + +
533B SER 4.7 0.9 - - - +
534B MET* 5.3 1.6 - - - -
535B PRO* 3.7 30.7 - - + -
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Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B LYS* 3.2 19.8 + - + +
525B LEU* 3.5 25.1 - - + +
527B ALA* 1.3 76.0 - - + +
529B GLU* 1.3 63.0 + - - +
531B LEU* 3.2 21.1 + - - +
532B VAL 4.9 3.8 - - - -
534B MET* 4.0 24.9 - - + -
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.1 28.7 + - - -
93B LYS* 5.2 7.8 + - - -
101B TRP* 3.6 11.4 + - + -
525B LEU 3.0 17.4 + - - +
526B GLN* 3.7 22.8 + - - +
527B ALA 3.2 0.2 - - - -
528B ILE* 1.3 74.4 - - - +
530B ASP* 1.3 60.9 + - - +
531B LEU* 3.0 17.3 + - - +
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Residues in contact with ASP 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 4.9 3.8 - - - +
83B LEU* 3.5 20.4 + - - +
86B GLY* 5.3 0.7 - - - -
89B ARG* 4.9 7.1 + - - -
526B GLN* 2.8 49.1 + - - +
527B ALA 3.2 5.3 + - - +
529B GLU* 1.3 75.8 - - - +
531B LEU* 1.3 71.4 + - - +
532B VAL* 3.4 20.1 + - + +
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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