Contacts of the helix formed by residues 192 - 201 (chain A) in PDB entry 4GSA
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 LEU 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ASN 3.6 5.7 + - - -
191A ASP* 1.3 73.3 + - - +
193A GLU* 1.3 64.9 + - + +
195A VAL* 3.2 9.3 + - + +
196A LYS* 3.1 42.6 + - - +
226A GLY 4.3 9.6 - - - +
227A PHE* 4.1 20.3 - - + +
230A GLY* 3.8 32.8 - - - +
231A LEU* 4.1 23.8 - - + -
234A ILE* 4.4 11.9 - - + -
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Residues in contact with GLU 193 (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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191A ASP* 3.3 10.1 + - - +
192A LEU* 1.3 76.2 - - + +
194A ALA* 1.3 64.4 + - - +
196A LYS* 3.3 35.7 + - - +
197A ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 194 (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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187A THR* 3.0 25.8 - - - +
188A PRO* 4.2 4.7 - - + -
191A ASP* 3.4 26.5 + - - +
192A LEU 3.4 0.4 - - - -
193A GLU* 1.3 78.7 - - - +
195A VAL* 1.3 56.3 + - - +
197A ALA* 3.5 8.6 - - - +
198A LEU* 3.2 31.7 + - - +
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Residues in contact with VAL 195 (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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144A ILE* 4.4 7.9 - - + -
146A PHE* 3.8 30.7 - - + -
187A THR* 3.9 8.1 - - + -
191A ASP 3.4 17.7 - - - +
192A LEU* 3.3 10.3 - - + +
193A GLU 3.1 0.2 - - - -
194A ALA* 1.3 75.5 - - - +
196A LYS* 1.3 66.8 + - - +
198A LEU* 3.1 18.0 + - - +
199A PHE* 3.2 26.4 + - + -
209A VAL* 4.9 3.8 - - + -
227A PHE* 5.2 0.4 - - + -
231A LEU* 4.1 12.6 - - + -
234A ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 196 (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 LEU* 3.1 31.8 + - + +
193A GLU* 3.3 36.3 + - - +
195A VAL* 1.3 74.4 - - - +
197A ALA* 1.3 62.4 + - - +
199A PHE* 3.2 9.5 + - - +
200A ALA* 3.0 25.9 + - - +
234A ILE* 4.3 30.1 - - + -
238A HIS* 6.4 0.7 - - - -
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Residues in contact with ALA 197 (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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193A GLU 3.0 14.5 + - - +
194A ALA* 3.5 13.0 - - - +
196A LYS* 1.3 76.4 - - - +
198A LEU* 1.3 62.2 + - + +
200A ALA* 3.5 5.8 + - - +
201A GLU* 3.1 30.7 + - - +
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Residues in contact with LEU 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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144A ILE* 4.1 18.4 - - + -
185A LEU* 4.1 30.5 - - + -
186A THR 3.7 24.9 - - - +
187A THR* 3.9 18.6 - - + -
194A ALA* 3.2 15.8 + - + +
195A VAL* 3.1 8.1 + - - +
197A ALA* 1.3 77.1 - - + +
199A PHE* 1.3 61.5 + - - +
201A GLU* 4.2 15.0 - - - +
202A ASN* 2.8 33.0 + - - +
206A ILE* 4.3 3.4 - - - +
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Residues in contact with PHE 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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140A ARG* 5.4 0.7 - - - -
144A ILE* 3.7 19.5 - - + -
195A VAL* 3.2 27.4 + - + -
196A LYS* 3.2 8.5 + - - +
198A LEU* 1.3 72.9 - - - +
200A ALA* 1.3 58.1 + - - +
201A GLU 3.0 10.0 + - - -
202A ASN 3.0 21.8 + - - +
203A PRO* 3.3 6.8 - - - +
206A ILE* 3.7 36.8 - - + -
209A VAL* 4.2 6.7 - - + -
234A ILE* 4.0 24.9 - - + -
235A THR* 4.2 11.0 - - + -
238A HIS* 3.6 52.7 - + + +
240A ALA* 3.8 18.6 - - + -
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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 LYS 3.0 16.7 + - - +
197A ALA* 4.0 6.3 - - - +
199A PHE* 1.3 75.5 - - - +
201A GLU* 1.3 58.3 + - - +
203A PRO* 3.9 12.9 - - - +
238A HIS* 6.1 1.6 - - - -
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Residues in contact with GLU 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 ALA* 3.1 18.7 + - - +
198A LEU* 4.2 14.0 - - - +
199A PHE 3.0 0.6 - - - -
200A ALA* 1.3 78.2 - - - +
202A ASN* 1.3 76.8 + - - +
203A PRO* 3.4 7.9 - - - +
205A GLU* 4.7 1.0 - - - +
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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