Contacts of the helix formed by residues 684 - 693 (chain B) in PDB entry 2HX4
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 SER 684 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627A ASP* 2.5 37.7 + - - +
630A LEU* 4.2 8.3 - - - +
682A PRO 3.7 7.2 - - - -
683A MET* 4.1 4.9 - - - +
684A SER 3.5 11.7 - - - +
631B VAL* 5.7 0.2 - - - +
651B HIS* 4.4 5.2 - - - -
683B MET* 1.3 79.3 - - - +
685B GLY* 1.3 67.6 + - - +
686B SER 3.4 2.0 - - - -
687B ILE* 3.0 35.0 + - - +
688B THR* 3.6 6.6 - - - +
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Residues in contact with GLY 685 (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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681A PRO 5.7 0.4 - - - -
682A PRO* 3.2 11.8 + - - -
683A MET* 4.2 0.6 - - - +
680B VAL* 3.8 22.4 - - - +
681B PRO* 4.1 3.6 + - - -
683B MET 2.9 7.7 + - - -
684B SER* 1.3 74.9 - - - +
686B SER* 1.3 57.6 + - - +
688B THR* 2.7 29.1 + - - -
691B PHE* 3.3 15.7 - - - +
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Residues in contact with SER 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 2.9 34.0 + - - +
596A ARG* 3.6 10.0 - - - -
600A ASP* 4.2 7.1 + - - +
601A ASN 5.9 0.2 + - - -
682A PRO* 3.0 17.4 + - - +
307B GLU* 5.2 1.4 - - - +
685B GLY* 1.3 67.3 - - - -
687B ILE* 1.3 59.6 + - - +
688B THR 3.1 5.6 - - - -
691B PHE* 3.4 37.1 - - - -
692B HIS* 2.6 27.7 + - - -
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Residues in contact with ILE 687 (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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595A VAL* 5.0 0.7 - - + +
599A CYS* 4.3 13.5 - - + +
601A ASN* 5.3 7.7 + - - +
607A LEU* 3.8 24.5 - - + -
626A LYS* 4.2 32.0 + - + +
627A ASP* 4.1 2.7 - - - +
630A LEU* 3.8 30.1 - - + -
307B GLU* 6.2 0.2 - - - -
652B HIS* 4.0 27.0 + - + -
684B SER* 3.0 40.4 - - - +
686B SER* 1.3 82.8 + - - +
688B THR* 1.3 59.2 + - - +
689B PRO* 4.2 2.6 - - - +
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Residues in contact with THR 688 (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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651B HIS* 4.1 19.7 - - + +
652B HIS* 4.3 7.9 - - + +
655B THR* 3.5 20.4 - - - +
681B PRO* 3.7 22.4 - - + +
684B SER 3.6 15.5 - - - +
685B GLY 2.7 18.6 + - - +
686B SER 4.5 0.2 - - - -
687B ILE* 1.3 82.9 - - - +
689B PRO* 1.3 68.5 - - - +
690B VAL* 3.2 18.2 + - - +
691B PHE* 3.3 11.6 + - - +
692B HIS* 3.7 6.5 - - - -
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Residues in contact with PRO 689 (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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305B ASN* 4.1 6.7 + - - +
307B GLU* 4.3 19.6 - - - +
652B HIS* 4.7 5.2 - - - +
655B THR* 3.3 24.5 - - - +
656B GLU* 3.8 25.6 - - + +
659B ILE* 4.0 14.6 - - + -
687B ILE 4.2 2.7 - - - +
688B THR* 1.3 82.4 - - - +
690B VAL* 1.3 63.3 + - - +
691B PHE 3.3 0.7 + - - -
692B HIS* 3.3 14.9 + - + +
693B GLN* 3.6 9.4 + - - +
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Residues in contact with VAL 690 (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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655B THR* 3.7 32.5 - - + +
658B PHE* 3.8 11.7 - - + -
659B ILE* 3.8 19.1 - - + -
676B TRP* 3.4 10.0 + - - -
679B ILE* 3.6 21.1 - - + -
680B VAL* 4.0 11.7 - - + -
681B PRO* 3.9 11.7 - - + -
688B THR* 3.3 18.6 - - - +
689B PRO* 1.3 73.7 - - - +
691B PHE* 1.3 67.2 + - - +
693B GLN* 3.0 20.5 + - - +
695B MET* 3.7 11.7 - - + +
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Residues in contact with PHE 691 (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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596A ARG* 3.7 26.9 - - - -
677A VAL 5.0 1.3 - - - -
680A VAL 5.3 4.0 - - - -
681A PRO 5.4 0.7 - - - -
682A PRO* 4.2 18.4 - - + -
760A H4B 2.7 59.8 + + - -
676B TRP* 3.1 46.1 + + - -
680B VAL* 4.0 6.1 - - + -
685B GLY* 3.3 23.6 - - - +
686B SER* 3.4 38.6 - - - -
688B THR 3.3 4.8 + - - +
689B PRO 3.3 0.6 - - - -
690B VAL* 1.3 80.2 - - - +
692B HIS* 1.3 63.6 + + + +
693B GLN 3.4 0.9 + - - -
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Residues in contact with HIS 692 (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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596A ARG* 3.9 9.2 + - - -
600A ASP* 3.5 34.4 + - - -
760A H4B 3.5 10.2 + - - -
305B ASN* 3.4 3.6 - - - +
306B TRP* 2.9 37.0 + - + +
307B GLU* 3.9 49.0 + - + +
686B SER* 2.6 29.1 + - - -
688B THR 3.7 12.8 - - - -
689B PRO* 3.3 7.4 + - + +
690B VAL 3.2 0.6 - - - -
691B PHE* 1.3 91.2 - + + +
693B GLN* 1.3 57.5 + - - +
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Residues in contact with GLN 693 (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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760A H4B 3.7 2.9 - - - +
303B VAL* 4.0 15.2 + - - +
304B LYS 3.9 11.3 + - - -
305B ASN* 2.9 33.5 + - - +
310B VAL* 5.3 0.9 + - - +
312B LEU* 4.8 9.9 - - - +
659B ILE* 3.7 30.9 - - + +
662B MET* 3.9 18.8 - - - +
663B GLU* 5.3 3.5 - - - +
676B TRP* 3.3 24.9 - - - -
689B PRO 3.6 2.4 + - - +
690B VAL* 3.0 13.2 + - - +
691B PHE 3.2 0.4 - - - -
692B HIS* 1.3 78.0 - - - +
694B GLU* 1.3 91.4 + - - +
695B MET* 3.5 6.3 - - + +
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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