Contacts of the helix formed by residues 516 - 530 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A SER* 3.5 33.2 - - - +
49A TYR* 3.6 28.7 - - + -
50A TYR* 3.4 44.2 - + + -
53A ALA* 4.0 6.1 - - + -
469A ARG* 3.5 26.2 - - - -
506A TYR* 3.2 23.1 + + - -
515A ALA* 1.3 76.9 - - - +
517A ASP* 1.3 75.3 + - - +
518A ARG 3.5 2.5 - - - -
519A HIS* 3.1 4.6 + - - +
520A LEU* 2.8 49.9 + - + +
543A TYR* 6.2 0.2 - + - -
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Residues in contact with ASP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ASP* 3.9 4.1 + - - +
467A THR* 3.5 34.3 + - - +
469A ARG* 2.7 49.6 + - - +
506A TYR* 4.3 3.5 + - - -
515A ALA* 3.9 0.6 - - - +
516A PHE* 1.3 90.7 - - - +
518A ARG* 1.3 66.8 + - - +
520A LEU* 3.4 4.2 + - - +
521A LEU* 3.0 22.5 + - - +
543A TYR* 5.0 2.3 + - - -
547A MET* 3.5 20.9 - - + +
549A PHE* 4.1 4.5 - - - -
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Residues in contact with ARG 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.7 11.4 - - + -
98A LEU* 3.8 28.8 - - + +
102A TRP* 3.3 46.6 - - - -
452A TYR* 2.8 28.1 + - - -
457A LEU* 6.2 0.2 - - + -
465A THR* 2.9 35.5 + - - +
466A ASP* 3.2 34.5 + - - +
467A THR* 2.8 24.2 + - - +
517A ASP* 1.3 81.8 - - - +
519A HIS* 1.3 60.8 + - - +
521A LEU* 3.2 9.0 + - - +
522A GLY* 2.9 24.3 + - - -
547A MET* 6.3 0.8 - - - +
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Residues in contact with HIS 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.1 7.4 - - + +
41A PRO* 3.0 41.2 + - + +
42A PRO 3.8 7.6 - - - -
43A LEU* 3.9 6.1 - - - -
46A SER* 2.8 30.0 + - - +
84A GLN* 2.8 27.8 + - - -
87A LEU* 3.7 16.5 - - + +
97A TRP* 4.1 9.8 - + - -
466A ASP* 5.2 1.0 + - - -
515A ALA 4.5 0.6 + - - +
516A PHE* 3.1 15.9 + - - +
518A ARG* 1.3 77.8 - - - +
520A LEU* 1.3 60.0 + - + +
522A GLY* 2.8 18.4 + - - -
523A LEU* 2.9 22.7 + - + +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.9 0.2 - - + -
46A SER* 4.6 15.7 - - - +
47A LEU* 4.2 20.0 - - + -
50A TYR* 3.8 27.6 - - + -
73A PHE* 6.0 0.2 - - + -
516A PHE* 2.8 46.1 + - + +
517A ASP* 3.8 3.6 - - - +
519A HIS* 1.3 72.7 - - + +
521A LEU* 1.3 62.7 + - - +
523A LEU* 3.2 21.7 + - + -
524A LYS* 3.1 17.5 + - - +
537A ILE* 6.1 2.0 - - + -
538A PHE* 3.3 24.6 - - + -
543A TYR* 4.2 21.8 - - + +
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Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.8 7.4 - - + -
102A TRP* 3.8 35.4 - - + -
105A THR* 4.2 14.8 - - + +
517A ASP 3.0 14.7 + - - +
518A ARG* 3.4 14.6 - - - +
519A HIS 3.1 0.2 - - - -
520A LEU* 1.3 76.9 - - - +
522A GLY* 1.3 63.9 + - - +
524A LYS* 3.2 22.7 + - - +
525A LEU* 3.0 44.9 + - + +
543A TYR* 4.3 10.5 + - - +
547A MET* 5.9 4.7 - - + -
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Residues in contact with GLY 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.6 9.6 - - - +
97A TRP* 3.9 11.4 - - - -
98A LEU* 5.8 0.4 - - - -
101A TRP* 3.6 22.1 - - - -
518A ARG 2.9 10.5 + - - -
519A HIS 2.8 9.1 + - - -
521A LEU* 1.3 79.5 - - - +
523A LEU* 1.3 51.5 + - - +
525A LEU 3.3 0.7 + - - -
526A GLN* 2.8 35.7 + - - +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.6 24.2 - - + -
73A PHE* 4.0 13.9 - - + -
80A GLY 4.4 2.7 - - - +
83A LEU* 3.5 18.1 - - + +
84A GLN* 3.7 34.1 - - + +
87A LEU* 3.4 22.0 - - + +
519A HIS* 2.9 20.8 + - + +
520A LEU* 3.2 28.9 + - + +
522A GLY* 1.3 75.4 - - - +
524A LYS* 1.3 57.3 + - - +
526A GLN* 3.5 3.5 + - - +
527A ALA* 3.0 26.9 + - - +
538A PHE* 3.7 11.4 - - + -
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Residues in contact with LYS 524 (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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520A LEU 3.1 10.7 + - - +
521A LEU* 3.2 26.4 + - - +
523A LEU* 1.3 74.1 - - - +
525A LEU* 1.3 76.1 + - - +
527A ALA* 3.2 5.5 + - - +
528A ILE* 3.1 28.7 + - + +
534A MET* 3.7 28.7 - - + +
538A PHE* 3.4 40.8 - - + +
543A TYR* 4.6 16.8 - - + -
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 6.1 0.2 - - + -
101A TRP* 3.4 58.1 + - + +
104A LYS* 5.5 4.5 - - - +
105A THR* 4.1 24.7 - - + -
521A LEU* 3.0 42.0 + - + +
522A GLY 3.9 2.0 - - - +
524A LYS* 1.3 84.0 - - - +
526A GLN* 1.3 56.3 + - - +
528A ILE* 3.2 21.2 + - + +
529A GLU* 2.9 29.1 + - - +
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Residues in contact with GLN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.6 24.7 - - + +
86A GLY* 3.6 30.0 + - - +
87A LEU* 3.8 7.1 + - + +
89A ARG* 4.8 3.4 - - - +
90A ARG* 4.3 4.3 - - - +
101A TRP* 3.5 20.9 - - + -
522A GLY 2.8 18.0 + - - +
523A LEU* 3.6 8.7 - - - +
525A LEU* 1.3 75.3 - - - +
527A ALA* 1.3 55.1 + - - +
529A GLU* 3.1 18.5 + - - +
530A ASP* 2.7 75.9 + - - +
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Residues in contact with ALA 527 (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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83A LEU* 3.5 21.7 - - + +
523A LEU 3.0 14.5 + - - +
524A LYS 3.2 9.8 + - - +
526A GLN* 1.3 75.5 - - - +
528A ILE* 1.3 62.7 + - + +
530A ASP 3.3 0.7 + - - -
531A LEU 3.2 3.3 + - - -
532A VAL* 3.2 39.3 + - + +
534A MET* 5.2 1.6 - - - -
535A PRO* 3.7 30.5 - - + -
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Residues in contact with ILE 528 (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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524A LYS* 3.1 22.1 + - + +
525A LEU* 3.4 26.9 - - + +
527A ALA* 1.3 76.8 - - - +
529A GLU* 1.3 62.4 + - - +
531A LEU* 3.0 22.5 + - - +
532A VAL 4.9 3.8 - - - -
534A MET* 4.0 24.5 - - + -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.2 28.4 + - - -
93A LYS* 5.3 7.6 + - - -
101A TRP* 3.7 12.7 + - + +
525A LEU 2.9 16.2 + - - +
526A GLN* 3.1 19.9 + - - +
528A ILE* 1.3 74.8 - - - +
530A ASP* 1.3 61.6 + - - +
531A LEU* 2.9 20.4 + - - +
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Residues in contact with ASP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 4.6 5.7 - - - +
83A LEU* 3.7 19.2 - - - +
86A GLY* 5.3 0.2 - - - -
89A ARG* 5.0 8.6 + - - -
526A GLN* 2.7 50.1 + - - +
527A ALA 3.3 5.6 + - - +
529A GLU* 1.3 73.2 - - - +
531A LEU* 1.3 70.6 + - - +
532A VAL* 3.2 21.4 + - + +
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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
------------------------------------------------------------
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