Contacts of the helix formed by residues 685 - 694 (chain B) in PDB entry 1SQN
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 PRO 685 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683B LEU 3.4 8.7 - - - +
684B ILE* 1.3 94.7 - - + +
686B PRO* 1.3 77.2 - - + +
687B LEU 3.3 0.2 - - - -
688B ILE* 3.1 27.4 + - + -
689B ASN* 3.1 9.4 + - - +
851B GLU* 3.3 21.8 - - - +
854B LYS* 4.2 27.6 - - + +
858B LEU* 4.0 14.8 - - + -
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Residues in contact with PRO 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ILE 3.5 3.6 - - - +
685B PRO* 1.3 84.6 - - + +
687B LEU* 1.3 60.9 + - - +
689B ASN* 3.1 10.5 + - + +
690B LEU* 2.9 28.9 + - - +
851B GLU* 5.3 0.2 - - - +
854B LYS* 6.0 1.8 - - - +
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Residues in contact with LEU 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B PRO 3.3 0.6 - - - -
686B PRO* 1.3 80.7 - - - +
688B ILE* 1.3 58.7 + - - +
690B LEU* 3.2 10.8 + - + +
691B LEU* 2.8 35.7 + - + +
737B PRO* 3.7 34.3 - - + -
847B SER* 5.1 8.1 - - - +
848B TYR* 3.7 36.1 - - + +
851B GLU* 3.5 36.4 + - + +
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Residues in contact with ILE 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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684B ILE* 3.9 6.7 - - + -
685B PRO* 3.1 29.0 + - + +
687B LEU* 1.3 73.8 - - - +
689B ASN* 1.3 61.3 + - - +
691B LEU* 3.1 8.2 + - - +
692B MET* 2.9 27.1 + - + +
816B GLU* 3.6 36.1 - - + +
819B LEU* 4.1 10.0 - - + +
820B CYS* 3.9 9.6 - - - -
851B GLU* 3.6 28.4 + - + +
855B ALA* 3.7 36.3 - - + -
858B LEU* 4.9 0.2 - - + -
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Residues in contact with ASN 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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684B ILE* 3.2 48.9 - - - +
685B PRO 3.1 6.8 + - - +
686B PRO* 3.1 11.6 + - + +
688B ILE* 1.3 75.5 - - - +
690B LEU* 1.3 62.8 + - - +
692B MET* 3.2 9.9 + - - +
693B SER* 3.0 22.2 + - - -
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Residues in contact with LEU 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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686B PRO 2.9 13.0 + - - +
687B LEU* 3.5 13.0 - - + +
688B ILE 3.1 0.2 - - - -
689B ASN* 1.3 77.3 - - - +
691B LEU* 1.3 64.3 + - + +
693B SER* 2.8 26.7 + - - +
694B ILE* 3.1 23.1 + - + +
735B SER 4.3 3.8 - - - +
737B PRO* 3.5 43.7 - - + -
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Residues in contact with LEU 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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687B LEU* 2.8 21.0 + - + +
688B ILE* 3.1 11.4 + - - +
690B LEU* 1.3 76.1 - - - +
692B MET* 1.4 62.8 + - - +
694B ILE* 3.3 23.3 + - + +
695B GLU* 3.4 15.4 + - - +
732B TRP* 5.0 4.3 + - - +
736B LEU* 3.5 32.5 - - + -
737B PRO* 4.5 4.9 - - + -
819B LEU* 3.9 41.3 - - + +
820B CYS* 4.3 14.1 - - - +
823B VAL* 4.0 7.6 - - + -
848B TYR* 4.1 22.4 - - + +
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Residues in contact with MET 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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688B ILE 2.9 12.8 + - - +
689B ASN* 3.2 14.1 + - - +
691B LEU* 1.4 75.9 - - - +
693B SER* 1.3 62.6 + - - +
695B GLU* 3.3 31.9 + - + +
815B GLN* 3.1 43.3 - - + +
819B LEU* 3.8 12.0 - - + +
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Residues in contact with SER 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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689B ASN 3.0 12.5 + - - -
690B LEU* 2.8 24.2 + - - +
692B MET* 1.3 77.3 - - - +
694B ILE* 1.3 67.0 + - - +
695B GLU 3.4 3.4 + - - +
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Residues in contact with ILE 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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690B LEU* 3.1 31.8 + - + +
691B LEU* 3.4 17.7 - - + +
693B SER* 1.3 84.4 - - - +
695B GLU* 1.3 68.9 + - - +
696B PRO* 3.4 2.8 - - - +
732B TRP* 3.5 39.2 - - + +
735B SER* 3.7 43.3 - - - +
736B LEU* 3.8 14.6 - - - -
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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