Contacts of the helix formed by residues 531 - 539 (chain A) in PDB entry 3H0G
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 GLN 531 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LEU* 6.0 8.1 - - + -
530A VAL* 1.3 90.3 - - + +
532A ASP* 1.3 65.8 + - + +
533A THR 3.3 0.2 - - - -
534A LEU* 2.8 23.5 + - - +
535A ALA* 3.0 11.9 + - - +
757A SER* 4.1 18.2 + - - -
758A LYS* 4.1 26.3 - - - +
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Residues in contact with ASP 532 (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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478A LEU* 4.8 7.2 - - - +
531A GLN* 1.3 82.8 + - - +
533A THR* 1.3 90.3 + - - +
535A ALA* 3.8 7.4 - - - +
536A GLY 2.9 19.9 + - - -
660A ASN* 4.5 12.0 + - - -
663A LEU* 3.4 20.8 - - + +
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Residues in contact with THR 533 (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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478A LEU* 4.8 7.4 - - + -
529A ILE* 3.3 22.6 - - - +
530A VAL 4.3 9.5 + - - +
531A GLN 3.3 0.6 - - - -
532A ASP* 1.3 92.3 + - - +
534A LEU* 1.3 58.5 + - - +
536A GLY 3.6 0.2 + - - -
537A VAL* 3.1 30.3 + - - +
655A ILE* 4.9 3.4 + - - +
656A GLN* 3.6 33.5 - - + +
659A VAL* 3.6 9.4 - - - +
660A ASN* 2.9 33.0 - - - +
663A LEU* 5.2 0.7 - - - -
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Residues in contact with LEU 534 (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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529A ILE* 3.4 37.5 - - + +
530A VAL* 3.9 14.6 - - + -
531A GLN 2.8 11.2 + - - +
533A THR* 1.3 77.2 + - - +
535A ALA* 1.3 67.0 + - - +
536A GLY 2.9 1.6 - - - -
537A VAL* 2.9 16.4 + - + +
538A ARG 3.6 3.1 + - - -
624A ASP* 4.0 10.5 - - - -
625A LYS* 3.7 41.3 - - + +
628A VAL* 4.5 5.4 - - + -
755A ALA* 4.1 10.1 - - + +
756A GLY 4.2 1.1 - - - -
757A SER* 3.8 26.0 - - - +
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Residues in contact with ALA 535 (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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531A GLN 3.0 10.5 + - - +
532A ASP* 3.8 11.4 - - - +
534A LEU* 1.3 77.1 - - - +
536A GLY* 1.3 59.9 + - - +
538A ARG* 3.8 6.2 - - - +
539A LYS* 3.4 21.0 + - - +
663A LEU* 5.4 1.6 - - + -
668A PHE* 4.8 22.2 - - + -
752A MET* 5.1 6.5 - - + -
755A ALA* 3.9 15.4 - - + +
757A SER* 4.1 16.2 - - - +
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Residues in contact with GLY 536 (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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532A ASP 2.9 17.2 + - - -
533A THR 3.8 2.0 - - - -
535A ALA* 1.3 76.7 - - - +
537A VAL* 1.3 67.6 + - - +
539A LYS* 3.1 23.9 + - - +
540A PHE* 3.2 6.4 - - - +
659A VAL* 3.8 10.8 - - - -
662A TRP* 4.8 0.8 - - - -
663A LEU* 3.6 20.9 - - - -
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Residues in contact with VAL 537 (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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529A ILE* 5.0 7.0 - - + -
533A THR 3.1 18.7 + - - +
534A LEU* 2.9 14.2 + - + +
536A GLY* 1.3 75.7 - - - +
538A ARG* 1.3 70.2 + - - +
540A PHE* 3.4 4.6 - - - +
541A SER* 2.7 20.5 + - - +
584A LEU* 4.6 6.5 - - + -
623A VAL* 3.0 47.3 - - + +
624A ASP* 4.7 1.8 - - - -
628A VAL* 5.1 4.0 - - + -
655A ILE* 4.0 16.6 - - + -
659A VAL* 3.8 22.0 - - + +
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Residues in contact with ARG 538 (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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534A LEU 3.6 2.4 + - - -
535A ALA 3.8 9.0 - - - +
537A VAL* 1.3 81.3 - - - +
539A LYS* 1.3 64.5 + - - +
540A PHE 2.4 17.7 + - - -
541A SER* 2.8 12.9 + - - -
542A LEU* 3.4 31.7 - - + +
622A VAL* 4.4 13.5 - - + -
623A VAL 3.3 14.1 + - - +
624A ASP* 5.0 4.0 - - + +
745A ASP* 4.3 14.6 + - - +
746A SER* 5.7 0.4 - - - +
751A GLN* 3.0 60.6 - - - +
754A ALA* 4.2 13.6 - - - +
755A ALA* 4.1 23.8 - - + +
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Residues in contact with LYS 539 (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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535A ALA 3.4 12.2 + - - +
536A GLY* 3.1 10.2 + - - +
538A ARG* 1.3 90.3 - - - +
540A PHE* 1.3 63.0 + - - +
542A LEU* 3.9 14.6 - - + -
545A ASN* 5.5 1.3 - - - -
662A TRP* 3.3 13.0 + - - -
663A LEU* 6.1 0.2 - - - +
666A ASN* 3.3 22.9 + - - +
667A GLY 4.5 13.5 + - - +
668A PHE* 4.2 17.4 - - + +
746A SER* 6.4 0.7 - - - -
748A ASN* 5.1 1.8 + - - -
751A GLN* 3.5 31.9 + - - +
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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