Contacts of the helix formed by residues 689 - 699 (chain B) in PDB entry 1S2S
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 GLY 689 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A LYS* 3.8 16.4 - - - -
686B VAL* 4.7 4.0 - - - -
687B PRO 3.2 3.6 + - - -
688B ASN* 1.3 77.0 - - - +
690B SER* 1.3 57.7 + - - -
691B THR 3.4 2.0 - - - -
692B GLU* 3.4 4.4 + - - +
693B ARG* 2.6 50.8 + - - +
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Residues in contact with SER 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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488A LYS* 5.2 0.8 - - - +
514A THR* 2.6 40.9 + - - -
516A ASN* 3.3 26.0 + - - +
519A ARG* 4.1 1.8 + - - +
534A ILE* 5.5 0.9 - - - -
689B GLY* 1.3 70.2 - - - +
691B THR* 1.3 55.1 + - - +
693B ARG* 3.6 8.4 - - - +
694B ASN* 2.7 37.5 + - - +
760B THR* 4.5 9.2 - - - -
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Residues in contact with THR 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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514A THR* 5.8 1.7 - - - +
534A ILE* 3.7 38.0 - - + +
685B THR* 4.0 11.2 - - + -
686B VAL* 4.4 19.9 - - - +
689B GLY 3.4 0.4 - - - -
690B SER* 1.3 79.1 - - - +
692B GLU* 1.4 65.8 + - - +
694B ASN* 3.2 1.3 + - - +
695B ILE* 2.9 28.0 + - + +
730B ILE 3.7 23.3 - - - +
731B TYR* 4.3 5.8 - - + -
732B ASP* 3.6 16.6 + - - -
760B THR* 5.0 2.4 + - - +
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Residues in contact with GLU 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B THR* 3.5 15.5 - - - +
686B VAL 3.2 19.8 + - - +
687B PRO* 3.1 7.2 - - - +
688B ASN* 2.5 39.8 + - - +
689B GLY 3.4 3.1 + - - +
691B THR* 1.4 78.3 - - - +
693B ARG* 1.3 56.2 + - - +
696B ARG* 2.5 87.7 + - + +
706B MET* 4.8 2.2 - - + -
710B ASN* 2.8 17.2 + - - +
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Residues in contact with ARG 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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489A LYS* 5.3 7.1 + - - +
516A ASN* 4.3 16.6 - - - +
518A GLU* 2.4 41.9 + - - +
688B ASN* 5.8 0.6 - - - -
689B GLY* 2.6 37.0 + - - +
690B SER* 3.6 7.2 - - - +
692B GLU* 1.3 71.3 - - - +
694B ASN* 1.4 56.0 + - - +
696B ARG* 4.5 2.0 - - - -
697B ASN* 2.6 60.0 + - - +
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Residues in contact with ASN 694 (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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534A ILE* 5.3 3.6 - - + -
690B SER 2.7 21.6 + - - +
691B THR* 3.8 4.3 - - - +
693B ARG* 1.4 72.3 - - - +
695B ILE* 1.3 58.7 + - + +
697B ASN* 4.9 0.2 - - - -
698B ASN* 2.6 70.6 + - - +
699B TYR* 4.0 12.7 - - - -
758B ALA* 3.2 32.8 - - + +
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Residues in contact with ILE 695 (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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534A ILE* 3.9 16.6 - - + -
685B THR* 4.1 11.0 - - + -
691B THR* 2.9 24.7 + - - +
692B GLU 4.0 0.9 - - - +
694B ASN* 1.3 84.0 - - + +
696B ARG* 1.3 64.0 + - - +
699B TYR* 2.7 41.8 + - + +
702B MET* 4.0 12.8 - - + -
703B HIS* 3.9 12.5 - - - +
706B MET* 3.4 33.7 - - + -
730B ILE* 3.8 35.2 - - + -
757B PHE* 5.7 2.5 - - + -
758B ALA* 5.0 2.2 - - + -
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Residues in contact with ARG 696 (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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692B GLU* 2.5 61.2 + - + +
693B ARG* 4.5 0.7 - - - -
695B ILE* 1.3 76.1 - - + +
697B ASN* 1.3 66.8 + - - +
699B TYR 4.8 0.2 + - - -
700B ALA* 5.0 1.4 + - - -
703B HIS* 2.5 96.7 + - + +
706B MET* 3.4 29.6 + - + +
710B ASN* 3.8 8.9 - - - +
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Residues in contact with ASN 697 (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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693B ARG* 2.6 48.5 + - - +
696B ARG* 1.3 85.4 - - - +
698B ASN* 1.4 71.7 + - - +
699B TYR 3.6 0.6 + - - -
700B ALA* 4.8 3.9 + - - +
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Residues in contact with ASN 698 (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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694B ASN* 2.6 56.4 + - - +
697B ASN* 1.4 88.6 - - - +
699B TYR* 1.4 68.2 + - + +
700B ALA 3.8 1.6 + - - -
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Residues in contact with TYR 699 (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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666B LEU* 4.3 20.8 - - + +
694B ASN* 4.0 21.8 - - - -
695B ILE* 2.7 28.8 + - + +
698B ASN* 1.4 81.6 - - + +
700B ALA* 1.4 65.1 + - - +
701B GLU 3.3 2.5 - - - -
702B MET* 2.6 54.8 + - + -
703B HIS 2.7 11.4 + - - -
757B PHE* 2.5 43.5 + - + +
758B ALA* 4.6 0.7 - - + -
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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