Contacts of the helix formed by residues 699 - 709 (chain F) in PDB entry 4XST
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 699 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698F GLU* 1.4 81.4 + - - +
700F SER* 1.4 52.5 + - - +
702F ARG* 3.1 18.7 + - - +
703F LYS* 2.7 70.9 + - - +
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Residues in contact with SER 700 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E PHE* 4.0 14.3 - - - -
698F GLU* 4.4 12.4 - - - +
699F SER* 1.4 74.1 - - - +
701F PHE* 1.4 57.7 + - - +
703F LYS* 3.5 7.8 + - - +
704F THR* 3.0 32.6 + - - -
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Residues in contact with PHE 701 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PHE* 4.0 17.7 - + - -
89E PHE* 3.8 18.9 - + + -
91E TYR* 3.9 15.5 - + + -
94E VAL* 3.6 29.6 - - + -
96E PHE* 3.8 19.1 - + + -
118E ARG* 3.3 40.4 - - + +
120E GLU* 3.4 15.9 - - - -
698F GLU 3.5 22.8 + - - +
700F SER* 1.4 72.8 - - - +
702F ARG* 1.4 68.6 + - - +
704F THR* 3.1 10.6 + - - -
705F PHE* 3.1 45.0 - + - -
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Residues in contact with ARG 702 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 5.1 8.4 - - + -
118E ARG* 3.9 5.5 - - - +
120E GLU* 3.2 25.9 + - - +
121E LYS* 4.9 9.4 - - - +
144E HIS* 3.5 27.1 + - - -
146E VAL* 5.0 4.2 - - - +
147E LEU* 5.4 5.5 - - - +
698F GLU* 2.9 40.3 + - - +
699F SER* 3.1 16.8 + - - +
701F PHE* 1.4 80.4 - - + +
703F LYS* 1.3 67.0 + - - +
705F PHE* 3.1 18.2 + - - +
706F GLU* 3.2 27.4 + - - +
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Residues in contact with LYS 703 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699F SER* 2.7 55.6 + - - +
700F SER* 3.8 7.4 - - - +
702F ARG* 1.3 76.6 - - - +
704F THR* 1.4 58.4 + - - +
706F GLU* 3.4 34.5 + - - +
707F ASP* 3.0 44.2 + - - +
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Residues in contact with THR 704 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PHE* 4.1 26.2 - - + -
89E PHE* 3.1 25.9 - - + -
700F SER 3.0 10.5 + - - -
701F PHE 3.1 12.5 + - - +
703F LYS* 1.4 74.6 - - - +
705F PHE* 1.3 60.1 + - + +
707F ASP* 3.6 7.0 + - - +
708F TYR* 3.0 27.7 + - + +
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Residues in contact with PHE 705 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU* 6.3 0.7 - - + -
62E LEU* 4.3 12.3 - - + -
64E PHE* 3.5 45.3 - + + -
88E PHE* 3.7 30.1 - + - -
94E VAL* 4.5 3.8 - - + -
96E PHE* 3.3 33.2 - + + -
701F PHE* 3.1 55.0 - + - -
702F ARG 3.1 7.0 + - - +
704F THR* 1.3 75.0 - - + +
706F GLU* 1.4 67.8 + - + +
708F TYR* 2.8 21.0 + + + +
709F LEU* 3.1 18.4 + - + +
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Residues in contact with GLU 706 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702F ARG* 3.2 19.7 + - - +
703F LYS* 3.4 48.0 + - - +
705F PHE* 1.4 77.8 - - + +
707F ASP* 1.3 62.3 + - - +
709F LEU* 3.1 26.7 + - - +
710F HIS* 3.2 17.7 + - - +
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Residues in contact with ASP 707 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703F LYS* 3.0 27.3 + - - +
704F THR* 3.8 6.9 - - - +
706F GLU* 1.3 81.0 - - - +
708F TYR* 1.4 64.2 + - - +
710F HIS* 3.4 27.1 - - - +
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Residues in contact with TYR 708 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ARG* 3.7 23.1 - - - +
36E LEU* 3.4 34.1 - - + +
37E LEU* 3.7 26.0 - - + +
64E PHE* 4.3 16.2 - + - -
704F THR* 3.0 14.8 + - + +
705F PHE* 2.8 17.9 + + + +
707F ASP* 1.4 66.6 - - - +
709F LEU* 1.4 57.7 + - + +
710F HIS 2.8 18.2 + - - +
711F ASN* 3.2 43.3 + - + +
713F VAL* 5.6 1.2 - - - +
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Residues in contact with LEU 709 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 4.0 29.8 - - + -
64E PHE* 4.0 23.3 - - + -
65E ARG* 4.3 28.7 - - - +
97E GLU* 5.3 0.4 - - - +
705F PHE* 3.5 22.2 - - + +
706F GLU* 3.1 14.4 + - - +
708F TYR* 1.4 72.7 - - + +
710F HIS* 1.3 68.9 + - + +
711F ASN* 3.5 14.9 + - - +
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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