Contacts of the helix formed by residues 606 - 615 (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 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A SER* 3.1 6.7 - - - -
218A ASP* 3.4 16.3 + - - +
605A MET* 1.3 83.9 - - - +
607A SER* 1.3 62.4 + - - +
608A THR* 3.4 2.1 - - - +
609A SER* 2.7 30.2 + - - +
610A TYR* 3.2 15.8 + - - +
655A LEU* 4.6 7.0 - - - +
656A PRO* 3.5 22.2 - - - +
1206A TYR* 3.5 22.6 + - + +
1211A TYR 4.7 1.8 - - - +
1212A GLY* 4.5 3.2 - - - -
1213A THR* 3.5 20.0 + - - +
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Residues in contact with SER 607 (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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188A PHE* 3.9 4.3 - - - -
214A LEU* 3.1 22.8 - - - +
215A SER* 2.7 35.8 + - - -
219A TRP* 3.9 16.8 - - - -
605A MET 3.4 2.0 + - - -
606A ASN* 1.3 68.3 - - - +
608A THR* 1.3 58.5 + - - +
610A TYR* 3.7 9.0 - - - -
611A PHE* 2.8 48.9 + - - -
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Residues in contact with THR 608 (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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218A ASP* 3.8 3.6 + - - +
219A TRP* 3.7 30.8 + - - +
606A ASN* 3.3 2.3 + - - +
607A SER* 1.3 76.7 - - - +
609A SER* 1.3 58.6 + - - +
611A PHE* 4.0 0.7 - - - +
612A TYR* 2.8 31.9 + - + +
1190A ILE* 3.7 28.4 - - + +
1192A PRO* 5.5 2.0 - - + -
1213A THR* 2.8 45.5 + - - +
1214A VAL* 3.9 12.1 - - - +
1215A GLY 3.9 2.3 + - - +
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Residues in contact with SER 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A MET* 4.2 6.5 - - - -
606A ASN* 2.7 32.4 + - - +
608A THR* 1.3 78.0 - - - +
610A TYR* 1.3 64.1 + - - +
612A TYR* 3.6 9.0 - - - +
613A ASN* 2.9 27.4 + - - +
646A ASN* 2.8 39.2 + - - -
655A LEU* 4.3 1.7 - - - +
1192A PRO* 6.5 0.7 - - - -
1213A THR* 3.0 10.5 + - - +
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Residues in contact with TYR 610 (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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183A ASP 5.5 1.5 + - - -
186A ALA* 3.4 17.3 - - + +
212A THR* 4.9 2.4 + - + -
214A LEU* 3.7 34.5 - - + -
605A MET* 3.7 24.1 - - + +
606A ASN 3.2 12.3 + - - +
607A SER* 3.5 10.5 - - - +
608A THR 3.2 0.2 - - - -
609A SER* 1.3 80.4 - - - +
611A PHE* 1.3 79.4 + + - +
613A ASN* 4.7 1.1 - - - -
614A HIS* 3.0 46.4 + + + +
658A ALA* 3.3 39.0 - - + -
659A PRO* 4.9 0.2 - - + -
706A PRO* 3.1 36.7 - - + +
709A LEU* 5.5 2.7 - - + +
731A LEU* 6.5 0.2 - - + -
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Residues in contact with PHE 611 (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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188A PHE* 4.5 4.0 - + - -
214A LEU* 4.0 19.7 - - + -
219A TRP* 3.8 36.1 - + + -
607A SER* 2.8 48.6 + - - +
610A TYR* 1.3 86.9 - + - +
612A TYR* 1.3 66.1 + - - +
613A ASN 3.1 1.6 - - - -
614A HIS* 5.7 0.7 - - + -
615A SER* 2.5 34.7 + - - +
617A GLN* 4.9 2.9 - - - +
709A LEU* 5.3 6.5 - - + -
716A LEU* 3.9 27.8 - - + -
727A MET* 3.4 24.9 - - + -
731A LEU* 4.0 23.8 - - + -
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Residues in contact with TYR 612 (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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608A THR 2.8 19.8 + - - +
609A SER* 3.6 9.4 - - - +
611A PHE* 1.3 76.3 - - - +
613A ASN* 1.3 59.1 + - + +
617A GLN* 3.1 33.3 + - + -
618A TRP* 3.2 38.9 - - + -
621A GLU* 2.6 24.6 + - - +
641A HIS* 3.2 21.0 + - - -
642A LEU* 4.0 2.3 - - - +
643A ILE* 4.0 24.2 - - + -
646A ASN* 5.9 4.5 - - + -
1190A ILE* 3.3 46.8 - - + +
1192A PRO* 3.4 28.8 - - + +
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Residues in contact with ASN 613 (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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609A SER 2.9 18.1 + - - +
610A TYR* 3.7 3.8 - - - +
612A TYR* 1.3 78.1 - - + +
614A HIS* 1.3 84.0 + - + +
616A SER* 3.1 17.3 + - - -
618A TRP* 3.3 21.6 + - - +
643A ILE* 4.3 14.0 - - + +
696A ALA* 4.9 13.0 + - - +
699A PRO* 3.3 32.8 - - - +
764A LYS* 4.1 1.9 + - - -
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Residues in contact with HIS 614 (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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610A TYR* 3.0 46.1 + + + +
611A PHE* 5.0 1.6 - - + -
613A ASN* 1.3 94.9 + - - +
615A SER* 1.3 57.6 + - - +
616A SER 3.0 5.6 + - - -
658A ALA 2.7 26.7 + - - -
659A PRO* 3.5 7.3 - - + +
699A PRO* 4.9 6.0 - - + +
704A ASN 3.3 25.6 - - - -
705A HIS* 4.0 7.0 - - - +
706A PRO* 3.3 20.9 - - + +
730A TYR* 4.0 1.6 - - - +
731A LEU* 3.5 18.5 - - + +
764A LYS* 2.9 33.8 + - + +
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A PHE* 2.5 32.2 + - - +
614A HIS* 1.3 72.1 - - - +
616A SER* 1.3 64.0 + - - +
617A GLN* 2.9 24.4 + - - +
726A PHE* 3.6 7.8 - - - +
727A MET* 4.1 24.7 - - - -
730A TYR* 3.1 26.7 - - - -
731A LEU* 4.0 21.0 - - - +
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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