Contacts of the helix formed by residues 682 - 691 (chain A) in PDB entry 4UHX
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 682 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611A PHE* 3.9 9.9 - - - +
680A ALA* 3.2 3.7 - - - +
681A ASP* 1.3 78.4 - - - +
683A GLU* 1.3 63.0 + - - +
684A VAL* 3.5 10.9 - - - +
685A GLN* 2.8 39.2 + - - +
686A ALA* 3.2 23.6 + - - +
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Residues in contact with GLU 683 (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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33A LYS* 3.0 31.3 + - - +
276A LYS* 5.8 1.6 + - - -
611A PHE* 3.6 48.0 - - + +
682A SER* 1.3 72.1 - - - +
684A VAL* 1.3 70.4 + - + +
686A ALA* 3.2 3.5 + - - +
687A LYS* 3.0 49.4 + - + +
835A VAL* 5.1 1.7 - - - +
837A GLU* 4.5 6.9 - - - +
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Residues in contact with VAL 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A SER* 3.5 13.0 - - - +
683A GLU* 1.3 78.5 - - + +
685A GLN* 1.3 68.0 + - + +
687A LYS* 3.4 6.6 + - - +
688A ARG* 2.9 59.1 + - - +
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Residues in contact with GLN 685 (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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635A MET* 5.3 0.5 - - - +
636A PRO* 3.5 29.1 - - + +
637A GLY* 3.7 21.2 - - - +
638A VAL* 4.5 0.3 - - - +
680A ALA* 4.1 8.3 - - + -
681A ASP* 3.6 13.4 - - - +
682A SER* 2.8 38.0 + - - +
683A GLU 3.3 0.4 - - - -
684A VAL* 1.3 83.3 - - + +
686A ALA* 1.3 58.2 + - - +
688A ARG* 3.7 14.1 - - - +
689A ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 686 (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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611A PHE* 4.2 17.0 - - + +
613A THR* 3.5 23.3 - - + +
678A VAL* 3.7 12.8 - - - +
680A ALA* 3.6 16.0 - - + +
682A SER 3.2 15.8 + - - +
683A GLU 3.2 4.9 + - - +
685A GLN* 1.3 76.1 - - - +
687A LYS* 1.3 59.5 + - - +
689A ALA* 3.4 0.9 + - - -
690A ALA* 2.9 30.7 + - - +
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Residues in contact with LYS 687 (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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611A PHE* 4.5 6.0 - - - -
613A THR* 3.3 29.4 - - + +
683A GLU* 3.0 46.4 + - + +
684A VAL* 3.8 5.8 - - - +
686A ALA* 1.3 75.8 - - - +
688A ARG* 1.3 62.3 - - - +
690A ALA* 3.4 6.9 + - + +
691A LYS* 3.3 37.9 + - - +
835A VAL 4.7 5.1 + - - -
837A GLU* 2.8 35.0 + - - +
840A GLU* 3.6 18.3 + - - +
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Residues in contact with ARG 688 (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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22A ASP* 5.4 3.6 + - - -
24A GLU* 3.6 14.8 + - - +
240A ARG* 3.1 57.8 - - - +
635A MET* 3.7 16.7 - - + +
636A PRO* 6.3 1.2 - - - +
684A VAL* 2.9 44.8 + - - +
685A GLN* 3.7 12.6 - - - +
687A LYS* 1.3 76.9 - - + +
689A ALA* 1.3 62.1 - - - +
691A LYS* 3.4 19.1 + - - +
692A ARG* 3.7 17.3 + - - +
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Residues in contact with ALA 689 (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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632A ALA* 3.2 33.9 - - + +
635A MET* 3.8 15.7 - - + +
638A VAL* 3.4 33.0 - - + -
678A VAL* 4.2 9.0 - - + -
685A GLN 3.0 13.4 + - - +
686A ALA 3.9 3.1 - - - +
688A ARG* 1.3 74.7 - - - +
690A ALA* 1.3 64.6 + - - +
692A ARG* 3.2 8.5 + - - -
693A VAL* 3.5 1.3 + - - -
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Residues in contact with ALA 690 (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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613A THR* 4.2 10.8 - - + +
614A PHE 5.0 4.9 - - - +
615A VAL* 3.8 16.8 - - + +
678A VAL* 4.0 22.8 - - + +
686A ALA 2.9 18.8 + - - +
687A LYS* 3.5 8.7 - - + +
688A ARG 3.3 0.2 - - - -
689A ALA* 1.3 77.0 - - - +
691A LYS* 1.3 59.7 + - + +
693A VAL* 3.3 21.8 + - - +
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Residues in contact with LYS 691 (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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275A VAL 5.0 6.1 + - - -
276A LYS 4.5 14.6 + - - -
277A PHE* 6.0 0.8 - - - +
279A GLY* 5.6 10.3 - - - +
687A LYS* 3.3 24.2 + - - +
688A ARG* 3.7 13.5 - - - +
689A ALA 3.2 1.0 - - - -
690A ALA* 1.3 76.8 - - + +
692A ARG* 1.3 61.0 + - + +
693A VAL 3.4 4.8 + - - +
694A LYS* 5.3 3.5 - - - +
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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