Contacts of the helix formed by residues 699 - 706 (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 TYR 699 (chain B).
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Specific contacts
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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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Residues in contact with ALA 700 (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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696B ARG 5.2 0.9 - - - -
697B ASN 4.8 4.5 + - - +
698B ASN 3.8 2.0 + - - -
699B TYR* 1.4 71.1 - - - +
701B GLU* 1.4 52.4 + - - +
703B HIS* 3.1 9.4 + - - +
704B ALA* 2.6 36.3 + - - +
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Residues in contact with GLU 701 (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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670B LYS* 2.2 46.2 + - - +
673B ARG* 2.4 48.5 + - - +
675B ASN* 5.2 2.0 - - - -
699B TYR 2.9 4.0 + - - -
700B ALA* 1.4 76.5 - - - +
702B MET* 1.4 60.2 + - + +
704B ALA* 3.5 13.6 + - + +
705B TYR* 3.6 8.8 + - - +
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Residues in contact with MET 702 (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* 3.4 41.1 - - + +
669B LYS* 5.1 8.7 - - + -
670B LYS 6.2 0.2 - - - +
673B ARG* 4.2 19.7 - - - +
683B PHE* 4.9 9.1 - - + -
695B ILE* 4.0 12.3 - - + -
699B TYR* 2.6 42.2 + - + +
701B GLU* 1.4 70.1 - - + +
703B HIS* 1.4 63.0 + - - +
705B TYR* 4.0 3.3 + - - +
706B MET* 2.8 30.0 + - - +
730B ILE* 3.6 28.0 - - + -
757B PHE* 3.8 15.9 - - + -
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Residues in contact with HIS 703 (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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695B ILE* 3.9 3.6 - - - +
696B ARG* 2.5 83.2 + - + +
699B TYR 2.7 15.4 + - - +
700B ALA* 3.3 11.7 - - - +
702B MET* 1.4 68.5 - - - +
704B ALA* 1.4 60.0 + - - +
706B MET* 2.6 39.8 + - - +
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Residues in contact with ALA 704 (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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700B ALA 2.6 19.7 + - - +
701B GLU* 3.5 11.2 + - + +
703B HIS* 1.4 75.9 - - - +
705B TYR* 1.3 63.9 + - - +
706B MET 3.2 0.7 + - - -
707B GLY* 4.2 5.4 + - - -
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Residues in contact with TYR 705 (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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673B ARG* 3.4 45.7 - - + +
674B PRO* 5.0 6.5 - - + -
679B PRO* 3.8 29.6 - - + +
681B PHE 2.6 24.8 + - - -
682B ARG* 3.6 8.0 - - - +
683B PHE* 3.6 39.3 - + - -
701B GLU 3.6 4.5 + - - +
702B MET 4.2 6.7 - - - +
703B HIS 2.8 4.2 + - - -
704B ALA* 1.3 75.4 - - - +
706B MET* 1.3 50.2 + - + +
707B GLY* 2.7 16.6 + - - -
709B PHE* 3.2 52.8 - + - -
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Residues in contact with MET 706 (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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683B PHE* 3.7 23.6 - - + +
684B GLY* 4.5 1.8 - - - -
685B THR* 3.3 34.1 - - + +
692B GLU* 4.8 5.4 - - + +
695B ILE* 3.4 27.1 - - + -
696B ARG* 3.4 33.7 + - - +
702B MET* 2.8 24.9 - - - +
703B HIS* 2.6 20.5 + - - +
704B ALA 4.4 1.3 - - - -
705B TYR* 1.3 68.0 - - + +
707B GLY* 1.4 62.3 + - - +
708B LYS 3.6 0.9 - - - -
709B PHE* 4.1 9.9 - - + +
710B ASN* 3.6 17.5 + - - +
730B ILE* 5.0 7.0 - - - -
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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