Contacts of the helix formed by residues 698 - 713 (chain B) in PDB entry 2HRC
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 THR 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B TYR* 3.8 37.7 - - + +
693B GLN 4.3 2.8 + - - -
695B SER* 3.1 22.0 + - - -
697B SER* 1.3 81.9 - - - +
699B THR* 1.3 75.2 + - - +
700B GLY 3.3 0.2 - - - -
701B SER* 3.2 5.7 + - - -
702B SER* 3.2 22.2 + - - -
776B TYR* 5.5 0.5 - - - -
1602B IMD 3.5 47.3 - - + +
1605B CHD 6.0 1.1 - - + -
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Residues in contact with THR 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B THR* 2.7 38.2 + - + +
691B TYR* 3.6 15.0 + - - +
694B TYR* 3.6 25.8 - - + -
695B SER 3.2 2.6 + - - -
698B THR* 1.3 82.2 + - - +
700B GLY* 1.3 64.4 + - - +
702B SER* 3.1 7.8 + - - +
703B LEU* 2.9 35.7 + - + +
725B ASP* 3.5 21.5 + - - +
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Residues in contact with GLY 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B TYR* 3.4 24.5 + - - -
695B SER 3.1 10.1 + - - -
696B CYS* 3.4 12.6 - - - -
699B THR* 1.3 76.5 - - - +
701B SER* 1.3 55.7 + - - +
703B LEU* 3.2 6.0 + - - +
704B ASN* 2.9 40.0 + - - +
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Residues in contact with SER 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B ASP* 3.2 7.8 + - - -
597B ASP* 6.1 1.1 - - - -
598B LEU* 4.8 6.1 + - - +
664B ARG* 2.6 66.4 + - - +
665B TYR* 3.7 5.2 + - - -
696B CYS 3.1 8.2 + - - -
697B SER* 3.7 19.5 - - - -
698B THR 3.2 9.6 + - - -
699B THR 3.2 0.4 - - - -
700B GLY* 1.3 77.0 - - - +
702B SER* 1.3 55.0 + - - +
704B ASN* 3.4 11.5 + - - +
705B ALA 3.2 6.1 + - - -
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Residues in contact with SER 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 3.9 36.4 - - - +
575B ASN 4.3 14.0 + - - -
662B GLY 5.0 1.4 + - - -
664B ARG* 4.3 16.7 - - - +
670B THR* 4.4 3.9 + - - +
689B THR* 5.8 0.2 - - - -
691B TYR* 5.3 2.5 - - - -
698B THR 3.2 8.5 + - - -
699B THR* 3.1 11.2 + - - -
701B SER* 1.3 75.9 - - - +
703B LEU* 1.3 66.0 + - - +
705B ALA* 3.2 17.3 + - - +
706B ILE* 3.4 12.7 + - - +
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 4.0 12.1 - - + -
687B ALA* 3.9 19.1 - - + -
689B THR* 6.0 0.7 - - - -
694B TYR* 4.4 4.0 - - + +
699B THR* 2.9 36.6 + - + +
700B GLY* 3.7 4.0 - - - +
702B SER* 1.3 73.6 - - - +
704B ASN* 1.3 65.9 + - - +
706B ILE* 3.1 16.8 + - + +
707B TYR 3.2 8.8 + - - -
723B THR* 3.7 18.4 - - - +
725B ASP* 4.2 16.6 - - + -
899B LEU* 4.2 24.7 - - + -
914B THR* 3.5 21.5 - - + +
918B PHE* 4.0 15.5 - - + -
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Residues in contact with ASN 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ASP* 4.1 25.5 + - - +
664B ARG* 4.7 2.0 - - - +
696B CYS 4.9 2.6 + - - -
700B GLY* 2.9 30.4 + - - +
701B SER* 3.5 12.8 - - - +
703B LEU* 1.3 77.2 - - - +
705B ALA* 1.3 55.2 + - - +
707B TYR* 3.2 2.8 + - - +
708B ARG* 2.8 34.0 + - - +
908B ASN* 4.8 1.8 - - - +
910B VAL* 3.8 28.6 - - + +
911B CYS* 4.4 9.3 - - - -
914B THR* 2.7 33.8 + - - +
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Residues in contact with ALA 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ARG* 2.6 28.4 - - - +
670B THR* 4.0 20.4 - - + +
671B GLU* 3.9 21.1 - - - +
674B ILE* 4.7 0.5 - - - +
701B SER 3.2 2.6 + - - -
702B SER* 3.4 10.5 - - - +
703B LEU 3.2 0.2 - - - -
704B ASN* 1.3 80.3 - - - +
706B ILE* 1.3 57.3 + - - +
708B ARG* 3.8 6.4 - - - +
709B TYR* 2.9 29.6 + - - +
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Residues in contact with ILE 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B LEU* 4.1 8.7 - - + -
574B LEU* 4.2 7.6 - - + -
670B THR* 4.1 8.1 - - + -
674B ILE* 3.9 24.5 - - + -
687B ALA* 3.6 30.7 - - + -
702B SER 3.6 13.7 - - - +
703B LEU* 3.1 8.9 + - + +
705B ALA* 1.3 74.9 - - - +
707B TYR* 1.3 66.8 + - - +
709B TYR* 3.2 10.4 + - - +
710B TYR* 3.4 18.7 - - + -
721B TRP* 4.0 22.0 - - + -
917B PHE* 3.9 23.6 - - + -
918B PHE* 4.1 9.9 - - + -
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Residues in contact with TYR 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU 3.2 5.5 + - - +
704B ASN 3.2 5.3 + - - +
706B ILE* 1.3 82.6 - - - +
708B ARG* 1.3 75.3 + - + +
709B TYR 3.3 0.3 + - - -
710B TYR* 3.4 4.0 + - - +
711B ASN* 2.7 62.4 + - + -
910B VAL* 3.8 23.3 - - + -
913B GLU* 3.0 63.2 + - + +
914B THR* 3.8 22.2 - - + +
917B PHE* 4.2 27.7 - + + -
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Residues in contact with ARG 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ASP* 2.5 44.3 + - - -
664B ARG* 5.9 1.1 - - - +
704B ASN 2.8 24.2 + - - +
705B ALA* 4.0 6.1 - - - +
707B TYR* 1.3 86.3 - - + +
709B TYR* 1.3 65.8 + - - +
711B ASN* 3.8 6.4 - - - +
712B GLN* 2.9 26.2 + - - +
908B ASN* 4.8 1.0 + - - -
909B PRO* 6.0 1.4 - - - +
910B VAL* 3.2 26.5 - - + +
913B GLU* 5.1 3.2 + - - -
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Residues in contact with TYR 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B GLU* 3.7 44.4 - - + -
674B ILE* 3.4 37.9 - - + -
675B GLU* 3.7 25.8 + - + +
678B GLU* 5.1 4.1 - - + +
705B ALA 2.9 19.2 + - - +
706B ILE 3.4 5.6 - - - +
707B TYR 3.2 0.2 - - - -
708B ARG* 1.3 75.6 - - - +
710B TYR* 1.3 80.3 + + - +
712B GLN* 3.2 11.1 + - - +
713B VAL* 3.0 47.1 + - + +
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Residues in contact with TYR 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ILE* 3.5 13.8 - - + +
678B GLU* 2.8 29.7 + - + -
706B ILE* 3.4 23.8 - - + -
707B TYR 3.4 6.5 + - - +
708B ARG 3.4 0.4 - - - -
709B TYR* 1.3 98.2 - + - +
711B ASN* 1.3 63.1 + - - +
713B VAL* 3.2 8.8 - - + +
714B GLY* 3.2 16.8 + - - -
715B ARG* 3.2 27.2 + - + +
716B LYS* 4.1 1.6 - - + -
717B PRO* 3.4 33.5 - - + +
719B MET* 3.3 9.0 - - - +
721B TRP* 2.9 32.5 + + - -
917B PHE* 3.9 15.7 - + + -
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Residues in contact with ASN 711 (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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707B TYR* 2.7 66.2 + - + +
708B ARG* 3.3 10.2 + - - +
709B TYR 3.2 0.6 - - - -
710B TYR* 1.3 80.6 - - - +
712B GLN* 1.3 61.6 + - - +
714B GLY* 3.6 10.1 + - - -
917B PHE* 6.0 0.2 - - - -
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Residues in contact with GLN 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B GLU* 5.6 5.5 - - - +
708B ARG 2.9 18.1 + - - +
709B TYR* 3.7 8.6 - - + +
711B ASN* 1.3 75.3 - - - +
713B VAL* 1.3 58.0 + - - +
714B GLY 3.2 5.7 + - - -
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B TYR* 3.0 37.1 + - + +
710B TYR* 3.2 29.6 - - + +
712B GLN* 1.3 76.4 - - - +
714B GLY* 1.3 61.4 + - - +
715B ARG* 3.0 42.2 + - + +
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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