Contacts of the helix formed by residues 678 - 689 (chain A) in PDB entry 1SIW
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 ASN 678 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A MET* 1.3 76.4 - - - +
679A PRO* 1.3 74.1 - - + +
680A VAL* 3.5 7.7 + - + +
681A ASP* 2.8 43.3 + - - +
682A TYR* 3.0 17.2 + - - +
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Residues in contact with PRO 679 (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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668A ILE* 4.6 1.7 - - + +
669A ALA* 4.4 13.9 - - + +
672A ALA* 3.6 18.2 - - + -
677A MET 3.7 1.7 - - - +
678A ASN* 1.3 86.5 - - + +
680A VAL* 1.3 66.9 + - + +
682A TYR* 3.8 1.0 - - - +
683A THR* 3.0 29.2 + - - -
845A THR* 5.6 1.3 - - + -
847A ILE* 3.8 27.8 - - + -
887A VAL* 3.9 24.5 - - + -
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Residues in contact with VAL 680 (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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678A ASN* 3.3 7.9 + - - +
679A PRO* 1.3 77.6 - - + +
681A ASP* 1.3 70.9 + - - +
683A THR* 3.0 6.1 + - - -
684A VAL* 3.0 32.6 + - + +
847A ILE* 6.4 0.2 - - + -
878A PRO* 5.1 7.4 - - + -
885A ILE* 3.6 41.0 - - + +
887A VAL* 4.1 20.0 - - + -
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Residues in contact with ASP 681 (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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677A MET* 3.6 17.8 - - + +
678A ASN* 2.8 39.6 + - - +
680A VAL* 1.3 79.3 - - - +
682A TYR* 1.3 57.6 - - - +
684A VAL* 3.3 9.2 + - - +
685A LYS* 2.9 31.5 + - - +
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Residues in contact with TYR 682 (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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668A ILE* 3.8 24.7 - - + -
671A GLU* 3.0 47.0 + - + +
672A ALA* 3.5 24.0 - - + -
675A ALA* 4.1 18.8 - - + -
677A MET* 3.5 27.5 - - + +
678A ASN 3.0 18.0 + - - +
679A PRO 3.8 1.1 - - - +
681A ASP* 1.3 77.3 - - - +
683A THR* 1.3 54.1 + - - +
685A LYS* 3.9 17.8 - - - +
686A SER* 2.6 53.9 + - - -
692A ILE* 5.3 4.7 - - + +
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Residues in contact with THR 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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661A LEU* 4.8 13.0 - - + -
668A ILE* 3.4 23.3 - - + +
679A PRO 3.0 20.3 + - - -
680A VAL 3.5 4.0 - - - -
682A TYR* 1.3 76.7 - - - +
684A VAL* 1.3 60.4 + - - +
686A SER* 3.8 5.4 - - - -
687A LEU* 2.9 53.8 + - + +
692A ILE* 5.2 6.3 - - + -
847A ILE* 4.1 12.3 - - + +
849A THR* 6.2 0.7 - - + -
885A ILE* 3.9 23.1 - - + -
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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
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680A VAL* 3.0 23.6 + - + +
681A ASP* 3.7 10.8 - - - +
683A THR* 1.3 75.6 - - - +
685A LYS* 1.3 58.0 + - - +
687A LEU* 3.5 9.9 + - - +
688A LYS* 3.1 39.4 + - + +
876A LEU* 3.9 30.0 - - + +
878A PRO* 4.3 24.5 - - + -
885A ILE* 4.4 10.5 - - + -
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Residues in contact with LYS 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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675A ALA* 5.4 3.4 - - - +
677A MET* 4.5 16.2 - - + -
681A ASP 2.9 17.1 + - - +
682A TYR* 3.9 31.8 - - + +
684A VAL* 1.3 78.1 - - - +
686A SER* 1.3 65.0 + - - +
688A LYS* 3.4 9.0 + - - +
689A GLU* 2.9 69.7 + - + +
691A SER* 5.1 1.8 + - - -
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Residues in contact with SER 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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682A TYR* 2.6 47.6 + - - -
683A THR* 3.8 2.9 - - - -
685A LYS* 1.3 81.7 + - - +
687A LEU* 1.3 54.3 + - - +
689A GLU* 4.6 0.2 - - - -
690A GLY 2.7 27.5 + - - -
691A SER* 2.8 31.9 + - - -
692A ILE* 3.2 26.7 + - - +
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Residues in contact with LEU 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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661A LEU* 4.4 9.9 - - + -
683A THR* 2.9 43.3 + - + +
684A VAL* 3.7 8.5 - - - +
686A SER* 1.3 74.9 - - - +
688A LYS* 1.3 64.7 + - - +
690A GLY* 3.3 10.7 + - - -
692A ILE* 3.5 34.4 - - + +
693A ARG* 4.5 0.7 - - - -
694A PHE* 3.9 35.4 - - + -
849A THR* 6.3 0.9 - - + -
869A TRP* 4.0 14.8 - - + -
870A LYS* 5.7 2.8 + - - -
876A LEU* 4.0 19.1 - - + -
885A ILE* 4.6 14.4 - - + -
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Residues in contact with LYS 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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684A VAL* 3.1 28.2 + - + +
685A LYS* 3.6 9.0 - - - +
686A SER 3.3 0.2 - - - -
687A LEU* 1.3 78.7 - - - +
689A GLU* 1.3 61.4 + - + +
690A GLY* 3.5 0.3 + - - -
869A TRP* 4.4 13.8 + - + +
874A CYS 5.1 1.8 + - - -
875A ASP* 3.3 32.2 + - - +
876A LEU* 3.5 32.3 - - + +
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Residues in contact with GLU 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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685A LYS* 2.9 58.1 + - + +
686A SER 4.0 2.7 - - - +
688A LYS* 1.3 77.7 - - + +
690A GLY* 1.3 61.1 + - - +
691A SER* 3.4 10.6 + - - +
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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