Contacts of the helix formed by residues 585 - 594 (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 PRO 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A MET* 3.9 20.6 - - + -
583A LEU* 3.6 13.9 - - + -
584A ARG* 1.3 89.3 - - + +
586A GLN* 1.3 63.4 + - - +
587A THR 3.5 2.0 - - - -
588A GLY* 3.0 13.7 + - - -
589A TRP* 3.2 9.9 + - - +
797A MET* 5.9 0.4 - - + -
799A THR* 4.0 16.4 - - + +
806A ILE* 5.3 2.2 - - + -
955A ILE* 4.0 11.4 - - + -
956A LEU* 5.9 0.9 - - + -
959A ALA* 3.6 16.4 - - + -
961A GLU* 3.1 15.3 - - + +
962A THR* 4.4 17.5 - - + -
1006A ILE* 6.0 0.9 - - + -
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Residues in contact with GLN 586 (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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581A GLU 5.5 2.0 + - - -
583A LEU* 3.3 35.2 + - - +
584A ARG 2.7 12.6 + - - +
585A PRO* 1.3 71.5 - - - +
587A THR* 1.3 61.6 + - + +
588A GLY 3.1 0.9 + - - -
589A TRP* 3.1 18.0 + - - +
590A GLN* 2.9 69.9 + - - +
961A GLU* 3.8 0.4 + - - -
1011A THR* 4.1 20.9 - - + -
1012A TRP* 4.5 9.5 - - + -
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Residues in contact with THR 587 (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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585A PRO 3.3 0.8 + - - -
586A GLN* 1.3 78.2 - - + +
588A GLY* 1.3 56.8 + - - +
590A GLN* 3.8 14.4 - - - +
591A PRO* 3.5 10.4 - - - +
911A ASN* 2.9 31.9 + - - +
912A GLY 3.9 22.2 - - - +
913A GLY* 3.9 14.4 - - - +
918A TRP* 3.4 20.3 - - + -
959A ALA* 4.8 0.2 - - - -
960A PRO* 3.2 27.9 - - - +
961A GLU* 4.7 1.2 + - - -
1011A THR* 4.2 15.5 + - + +
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Residues in contact with GLY 588 (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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585A PRO 3.0 9.0 + - - -
587A THR* 1.3 80.2 + - - +
589A TRP* 1.3 62.4 + - - +
590A GLN 3.6 0.2 - - - -
591A PRO* 3.4 12.8 - - - +
592A LEU* 4.2 5.0 + - - +
954A MET* 4.6 0.7 - - - +
955A ILE* 3.8 22.7 + - - +
958A LEU* 3.9 14.5 - - - +
959A ALA* 3.8 22.3 - - - +
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Residues in contact with TRP 589 (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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192A PRO* 3.3 31.6 - - + -
196A MET* 3.3 42.4 + - + +
199A TYR* 3.3 19.5 - + - -
200A ALA* 4.1 3.5 - - + +
583A LEU* 3.5 27.1 - - + +
585A PRO 3.2 10.2 + - - +
586A GLN* 3.1 30.5 + - - +
588A GLY* 1.3 78.8 - - - +
590A GLN* 1.3 67.4 + - + +
592A LEU* 3.1 4.7 + - + +
593A ALA* 2.8 43.8 + - + +
594A PHE* 3.8 31.0 - + - -
955A ILE* 4.0 22.4 - - + +
1208A PHE* 5.8 2.2 - + - -
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Residues in contact with GLN 590 (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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586A GLN* 2.9 51.7 + - - +
587A THR* 3.8 19.6 - - - +
589A TRP* 1.3 86.7 - - + +
591A PRO* 1.3 70.1 - - + +
594A PHE* 2.9 40.8 + - + +
596A LEU* 3.9 14.6 - - + +
912A GLY 4.4 6.9 - - - +
913A GLY* 4.9 3.3 - - - -
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Residues in contact with PRO 591 (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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587A THR* 3.5 22.0 - - - +
588A GLY 3.4 14.8 - - - +
589A TRP 3.6 0.7 - - - -
590A GLN* 1.3 94.1 - - + +
592A LEU* 1.3 58.5 + - - +
595A ALA 3.0 4.5 + - - -
596A LEU* 3.0 40.3 + - + -
597A ASP* 3.1 11.0 - - - +
906A MET* 3.9 30.1 - - + -
911A ASN* 4.3 5.4 - - - +
954A MET* 4.3 5.8 - - + -
958A LEU* 4.2 13.2 - - + -
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Residues in contact with LEU 592 (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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197A VAL* 4.7 2.2 - - + -
200A ALA* 3.8 20.4 - - + -
204A ARG* 2.9 47.4 + - - +
588A GLY 4.3 6.3 - - - +
589A TRP* 3.1 7.5 + - + +
591A PRO* 1.3 81.9 - - - +
593A ALA* 1.3 63.6 + - - +
594A PHE 3.4 0.2 + - - -
823A TRP* 4.3 12.1 - - + -
945A LEU* 4.0 13.0 - - + -
951A ALA* 4.0 20.0 - - + +
954A MET* 3.9 28.0 - - + +
955A ILE* 3.7 31.6 - - + -
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Residues in contact with ALA 593 (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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199A TYR* 4.3 4.7 - - + -
200A ALA* 3.7 19.1 - - + +
203A ALA* 3.0 33.6 - - - +
204A ARG* 3.0 2.1 + - - -
589A TRP* 2.8 53.2 + - + +
590A GLN 4.1 1.6 - - - +
592A LEU* 1.3 75.9 - - - +
594A PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 594 (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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199A TYR* 3.8 20.4 - + - -
203A ALA* 4.2 6.7 - - + -
207A SER* 3.4 26.4 - - - +
213A CYS* 4.1 12.6 - - - -
589A TRP* 3.8 31.2 - + - -
590A GLN* 2.9 34.0 + - + +
593A ALA* 1.3 77.5 - - + +
595A ALA* 1.3 72.1 + - - +
596A LEU* 3.1 23.2 + - + +
599A GLN 4.4 1.6 - - - +
602A ALA* 4.0 9.6 - - + +
604A HIS* 3.2 40.4 - + + +
1208A PHE* 3.7 18.2 - + - -
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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