Contacts of the strand formed by residues 189 - 196 (chain A) in PDB entry 3C9G
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 VAL 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN* 1.3 74.7 + - - +
190A GLU* 1.3 63.8 + - - +
191A ILE* 3.6 10.7 + - + +
232A TYR* 4.1 19.5 - - - +
234A LEU* 4.4 18.2 - - + -
293A PHE* 4.1 22.2 - - + -
294A ARG 3.5 4.0 - - - +
295A LEU* 3.7 19.5 - - + -
298A ILE* 3.6 24.0 - - + -
303A PHE* 4.0 26.5 - - + -
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Residues in contact with GLU 190 (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 ASN* 3.6 19.1 + - - +
189A VAL* 1.3 72.6 - - - +
191A ILE* 1.3 60.5 + - - +
192A GLU* 4.3 5.8 - - + -
230A ARG* 3.7 32.7 + - - +
232A TYR* 3.2 33.4 + - - -
292A THR 3.5 1.6 - - - +
293A PHE* 3.2 4.9 - - - -
294A ARG* 2.5 60.6 + - + +
296A ASN* 4.3 4.9 - - - +
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Residues in contact with ILE 191 (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 VAL* 4.1 8.1 - - + +
190A GLU* 1.3 75.6 - - - +
192A GLU* 1.3 63.0 + - - +
193A ILE* 3.7 23.6 - - + -
214A PHE* 4.1 14.6 - - + -
230A ARG* 3.2 11.5 - - - +
231A ALA* 2.9 50.5 + - + +
232A TYR 3.7 27.6 - - - +
233A SER 4.2 2.0 - - - +
234A LEU* 3.8 14.6 - - + -
291A VAL* 4.1 14.6 - - + -
292A THR 3.7 2.0 - - - -
293A PHE* 3.5 27.8 - - + -
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Residues in contact with GLU 192 (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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190A GLU* 4.3 10.1 - - + +
191A ILE* 1.3 75.8 - - - +
193A ILE* 1.3 61.3 + - - +
194A ARG* 5.7 2.9 - - + -
229A GLY 3.6 4.9 - - - +
230A ARG* 3.1 42.0 + - - +
262A GLU* 4.3 9.0 - - - +
290A LYS* 3.5 6.9 + - - +
291A VAL* 3.3 6.1 - - - -
292A THR* 2.8 67.6 + - - +
294A ARG* 4.5 7.9 - - - +
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Residues in contact with ILE 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 ILE* 3.7 26.2 - - + -
192A GLU* 1.3 74.7 - - - +
194A ARG* 1.3 72.7 + - - +
210A ILE* 4.0 29.4 - - + -
214A PHE* 3.9 22.9 - - + -
217A ALA* 5.2 2.5 - - + -
219A ILE* 5.7 0.2 - - + -
227A VAL* 3.5 4.6 - - + +
228A TYR* 3.5 3.6 - - - -
229A GLY* 2.8 54.5 + - - +
230A ARG 4.5 1.3 - - - +
231A ALA* 4.9 5.4 - - + +
289A ILE* 3.6 22.9 - - + -
290A LYS 3.4 1.3 - - - -
291A VAL* 3.9 14.4 - - + -
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Residues in contact with ARG 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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192A GLU* 5.2 3.1 - - + -
193A ILE* 1.3 81.5 - - - +
195A THR* 1.3 68.1 + - - +
226A GLU* 2.6 46.0 + - - +
227A VAL 2.9 28.1 + - - +
228A TYR* 3.2 33.3 + - + -
288A PRO 3.7 0.3 - - - +
289A ILE* 3.5 0.4 - - - -
290A LYS* 2.6 78.1 + - + +
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Residues in contact with THR 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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193A ILE* 5.4 0.7 - - + -
194A ARG* 1.3 80.9 + - - +
196A LYS* 1.3 66.9 + - - +
206A VAL* 4.4 5.2 - - + -
210A ILE* 4.2 7.4 - - + -
226A GLU* 4.8 0.7 - - - -
227A VAL* 2.7 54.8 + - + -
269A LYS* 3.6 14.1 + - + +
287A SER* 3.7 3.5 + - - -
288A PRO 2.6 29.5 + - - -
289A ILE* 3.8 23.1 - - + -
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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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195A THR* 1.3 85.8 + - - +
197A ILE* 1.3 67.6 + - - +
198A HIS* 3.4 23.0 + - + +
201A GLU* 3.3 2.3 - - - +
206A VAL* 4.7 0.3 - - - +
225A GLY 3.3 11.4 - - - +
226A GLU* 4.3 22.2 + - - +
227A VAL* 4.2 1.3 - - - -
269A LYS* 2.9 27.0 + - - +
287A SER* 2.8 31.0 - - - +
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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