Contacts of the helix formed by residues 195 - 210 (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 SER 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLY* 4.1 13.3 - - - -
51A VAL* 5.3 0.2 - - - +
192A PRO 3.1 4.7 + - - +
194A MET* 1.3 82.4 - - - +
196A MET* 1.3 65.3 + - - +
198A SER* 3.1 8.5 + - - -
199A TYR* 3.0 17.0 + - - +
713A ARG* 2.9 33.0 + - - +
791A TRP* 6.1 0.2 - - - -
794A LYS* 4.9 2.2 - - - -
796A ASP* 3.2 23.1 - - - -
797A MET 3.4 6.1 - - - -
809A LEU* 4.6 7.0 - - - -
1247A GDP 4.6 3.4 + - - -
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PRO 2.9 19.2 + - - +
193A ALA 4.2 1.3 - - - +
195A SER* 1.3 70.4 - - - +
197A VAL* 1.3 58.9 + - + +
199A TYR* 3.3 2.3 + - - +
200A ALA* 2.9 29.1 + - - +
583A LEU* 3.7 18.2 - - + -
585A PRO* 3.9 22.9 - - + -
589A TRP* 3.3 21.1 + - + +
796A ASP* 3.4 4.0 + - - +
797A MET* 3.3 26.9 + - + +
798A ASN* 3.8 21.1 - - - +
799A THR* 3.6 40.4 - - + +
806A ILE* 4.4 2.9 - - + -
955A ILE* 4.0 12.8 - - + -
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Residues in contact with VAL 197 (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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196A MET* 1.3 71.9 - - + +
198A SER* 1.3 57.5 + - - +
200A ALA* 3.2 7.1 + - - +
201A SER* 2.9 28.8 + - - -
592A LEU* 4.7 0.9 - - + -
795A ASP 5.0 0.2 - - - +
796A ASP* 2.9 23.8 + - + +
797A MET* 5.1 0.9 - - + +
823A TRP* 3.6 27.1 - - + -
948A ALA* 4.1 22.0 - - + +
951A ALA* 3.8 13.5 - - + -
952A ALA* 4.0 29.6 - - + +
955A ILE* 4.1 15.5 - - + -
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Residues in contact with SER 198 (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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195A SER* 3.1 7.1 + - - -
197A VAL* 1.3 77.3 - - - +
199A TYR* 1.3 56.9 + - - +
201A SER* 2.8 21.2 + - - -
712A TRP* 3.0 14.4 + - - -
713A ARG* 3.8 11.9 - - - -
794A LYS* 2.7 29.0 + - - +
795A ASP 5.2 0.9 + - - -
796A ASP* 2.8 25.2 + - - +
822A ASP* 3.3 26.8 + - - +
823A TRP* 5.1 2.2 + - - +
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Residues in contact with TYR 199 (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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189A SER* 3.3 31.0 - - - -
190A PRO 3.7 15.3 - - - -
192A PRO* 3.5 27.6 - - + -
195A SER 3.0 10.5 + - - +
196A MET 3.6 6.7 - - - +
198A SER* 1.3 75.2 - - - +
200A ALA* 1.3 71.5 + - - +
201A SER 3.1 1.2 + - - -
203A ALA* 3.3 35.4 + - + +
213A CYS* 4.9 3.3 - - - +
214A LEU 4.6 3.6 + - - -
216A PHE* 5.3 4.0 - + - -
589A TRP* 3.3 31.0 - + - -
593A ALA* 4.3 0.4 - - + -
594A PHE* 3.8 7.9 - + - -
712A TRP* 3.4 14.0 - + - +
713A ARG* 3.8 14.5 - - - +
1208A PHE* 3.6 29.1 - - - -
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Residues in contact with ALA 200 (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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196A MET 2.9 17.5 + - - +
197A VAL* 3.2 5.1 + - - +
199A TYR* 1.3 84.8 - - - +
201A SER* 1.3 55.8 + - - +
203A ALA* 4.3 0.7 - - - -
204A ARG* 2.8 35.2 + - - +
589A TRP* 4.1 1.6 - - - +
592A LEU* 3.8 26.7 - - + -
593A ALA* 3.7 26.6 - - + +
823A TRP* 4.9 2.5 - - + -
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Residues in contact with SER 201 (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 2.9 12.6 + - - -
198A SER 2.8 18.5 + - - -
200A ALA* 1.3 77.5 - - - +
202A GLY* 1.3 69.2 + - - +
205A TYR 3.3 4.0 + - - -
822A ASP* 3.5 10.3 + - - +
823A TRP* 3.6 42.8 - - - -
826A TYR* 3.2 18.9 - - - +
899A PHE* 3.3 26.1 - - - -
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Residues in contact with GLY 202 (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 3.5 3.4 + - - -
201A SER* 1.3 82.2 + - - +
203A ALA* 1.3 60.1 + - - +
205A TYR* 3.2 2.1 + - - +
206A LEU* 2.9 33.5 + - - +
712A TRP* 3.4 14.8 - - - -
826A TYR* 3.2 33.1 - - - -
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Residues in contact with ALA 203 (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* 3.3 42.9 + - + +
200A ALA 3.9 1.6 - - - +
202A GLY* 1.3 76.9 - - - +
204A ARG* 1.3 53.5 + - - +
206A LEU* 4.5 1.6 - - - -
207A SER* 2.7 37.2 + - - -
213A CYS* 3.8 21.3 - - - -
593A ALA 3.0 15.5 - - - +
594A PHE* 4.2 1.8 - - + -
712A TRP* 3.5 6.4 - - + -
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ALA 2.8 18.3 + - - +
201A SER 3.8 4.0 - - - +
203A ALA* 1.3 75.6 - - - +
205A TYR* 1.3 65.5 + - - +
207A SER* 4.0 3.7 - - - -
208A LEU* 3.1 35.3 + - + +
591A PRO 3.6 3.2 + - - -
592A LEU* 2.9 41.8 + - - +
593A ALA 3.0 6.5 + - - -
595A ALA* 3.6 9.3 - - + +
597A ASP* 2.9 42.2 + - - -
598A TRP* 3.7 3.8 - - - -
823A TRP* 4.5 6.3 - - - -
898A ARG 3.1 11.1 + - - -
899A PHE* 3.1 36.3 + - + +
901A SER 3.0 18.6 + - - -
945A LEU* 3.5 13.3 - - - +
954A MET* 5.2 0.2 - - - +
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Residues in contact with TYR 205 (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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170A ALA* 5.1 0.7 - - - -
173A ASN* 2.7 29.8 + - - +
201A SER 3.3 10.7 + - - +
202A GLY 3.2 7.3 + - - +
204A ARG* 1.3 79.6 - - - +
206A LEU* 1.3 67.8 + - + +
208A LEU* 3.4 5.5 + - - +
209A ILE* 3.0 48.0 + - + +
710A PHE* 4.0 15.9 - + - -
826A TYR* 4.2 24.0 - + + +
829A ILE* 3.6 19.4 - - + +
830A ALA* 3.9 35.7 - - + -
833A PHE* 3.5 25.1 - + + +
895A THR* 4.3 6.7 - - + -
899A PHE* 3.8 14.0 - - + -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.9 30.3 - - + +
186A ALA* 4.0 14.6 - - - -
187A GLY* 3.4 29.6 - - - +
202A GLY* 2.9 21.1 + - - +
203A ALA 3.9 2.9 - - - +
205A TYR* 1.3 82.0 - - + +
207A SER* 1.3 61.9 + - - +
209A ILE* 3.3 7.7 + - + +
210A GLY 3.0 4.5 + - - -
211A GLY* 2.8 34.1 + - - -
212A THR 3.9 6.1 - - - +
213A CYS* 4.2 14.1 - - - -
710A PHE* 4.0 14.8 - - + -
712A TRP* 4.0 13.7 - - + -
826A TYR* 6.1 0.7 - - + -
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Residues in contact with SER 207 (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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203A ALA 2.7 23.0 + - - -
204A ARG 4.0 2.5 - - - -
205A TYR 3.4 0.2 - - - -
206A LEU* 1.3 76.4 - - - +
208A LEU* 1.3 63.4 + - - +
210A GLY* 3.4 8.9 + - - -
211A GLY 4.7 5.2 - - - -
213A CYS* 3.7 13.4 - - - -
594A PHE* 3.4 41.2 - - - +
595A ALA* 4.1 2.0 - - - -
599A GLN* 3.6 3.8 + - - -
602A ALA* 4.0 15.9 - - - +
603A ARG 5.3 1.1 + - - +
890A ARG* 3.5 12.0 + - - -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A ARG* 3.1 28.6 + - + +
205A TYR* 3.8 3.8 - - - +
206A LEU 3.2 0.2 - - - -
207A SER* 1.3 78.6 - - - +
209A ILE* 1.3 61.8 + - - +
210A GLY 3.2 0.9 + - - -
595A ALA* 3.6 21.8 - - + -
598A TRP* 4.2 10.8 - - + -
599A GLN* 3.5 31.7 + - - +
890A ARG* 3.6 12.5 + - - +
892A TYR* 4.9 0.9 - - - -
895A THR* 3.7 39.3 + - + +
898A ARG* 4.0 19.7 - - + -
899A PHE* 3.7 28.0 - - + +
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Residues in contact with ILE 209 (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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173A ASN* 5.7 1.3 - - - +
177A ILE* 4.1 17.6 - - + +
182A PRO* 3.1 11.3 - - - +
185A VAL* 4.3 17.7 - - + -
205A TYR* 3.0 33.4 - - + +
206A LEU* 3.4 9.2 - - + +
208A LEU* 1.3 75.1 - - - +
210A GLY* 1.3 56.0 + - - +
211A GLY* 3.4 22.2 - - - +
833A PHE* 3.6 33.2 - - + -
890A ARG* 4.1 0.7 - - - -
892A TYR* 3.0 32.7 + - + -
895A THR* 3.9 20.0 - - + +
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Residues in contact with GLY 210 (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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182A PRO* 3.6 13.0 - - - +
206A LEU 3.0 4.0 + - - -
207A SER* 3.4 5.1 + - - -
208A LEU 3.2 4.6 + - - -
209A ILE* 1.3 79.1 - - - +
211A GLY* 1.3 66.0 + - - +
603A ARG* 2.9 27.6 + - - -
890A ARG* 3.6 27.3 - - - -
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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