Contacts of the strand formed by residues 190 - 197 (chain A) in PDB entry 3ARE
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LYS* 4.4 6.3 - - + +
189A PRO* 1.3 81.7 - - - +
191A ALA* 1.3 71.1 + - - +
192A TRP* 3.9 7.3 - - + -
209A HIS 3.7 0.5 - - - +
210A VAL* 3.4 2.4 - - - -
211A SER 2.9 37.5 + - - +
275A ILE* 4.8 1.1 - - - -
12B ARG* 5.6 5.4 - - - +
14B PRO* 4.3 25.1 - - + -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 1.3 82.7 - - - +
192A TRP* 1.3 64.8 + - - +
208A CYS* 4.5 4.3 - - - -
209A HIS 3.0 12.3 - - - +
210A VAL* 4.3 12.6 - - + -
265A VAL* 4.4 7.6 - - + -
275A ILE* 4.2 18.1 - - + +
277A LEU* 3.5 30.5 - - + +
283A HIS* 5.4 2.3 - - - -
287A ASP* 4.8 4.2 - - - +
14B PRO* 5.3 0.3 - - - +
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Residues in contact with TRP 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 VAL* 3.9 12.1 - - + -
191A ALA* 1.3 80.3 - - - +
193A LEU* 1.3 70.3 + - - +
208A CYS* 3.9 0.5 - - - -
209A HIS* 2.9 82.2 + + + -
211A SER* 3.7 32.1 - - - -
246A TYR* 4.2 8.1 - + - -
277A LEU* 3.7 6.3 - - - -
287A ASP* 4.2 19.3 - - + +
291A MET* 4.5 9.8 - - + -
11B SER* 4.2 11.7 - - - -
13B HIS* 3.9 9.0 - - - -
14B PRO* 3.3 51.4 - - + -
15B PRO* 3.6 19.5 - - + +
97B ARG 5.1 1.0 + - - -
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Residues in contact with LEU 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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192A TRP* 1.3 81.2 - - - +
194A SER* 1.3 65.1 + - - +
207A VAL 3.5 2.2 - - - +
208A CYS* 3.8 25.4 - - + -
209A HIS* 4.4 0.2 - - - -
222A TRP* 3.9 15.0 - - + -
263A CYS* 3.8 10.5 - - + -
277A LEU* 3.8 43.9 - - + +
278A TYR 4.1 4.9 - - - +
279A TRP* 4.0 34.5 - - + +
284A HIS* 3.8 32.1 + - + +
287A ASP* 5.4 4.5 + - - +
288A ALA* 5.9 1.7 - - - +
291A MET* 4.5 9.7 - - - +
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Residues in contact with SER 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 TRP* 5.4 0.2 - - - -
193A LEU* 1.3 79.8 - - - +
195A SER* 1.3 67.7 + - - +
206A LEU* 3.5 2.6 - - - -
207A VAL* 2.7 35.3 + - - +
209A HIS* 3.3 24.0 - - - -
279A TRP* 3.7 11.5 - - - -
284A HIS* 5.2 1.3 - - - -
291A MET* 4.6 10.8 - - - -
97B ARG 4.6 0.2 - - - -
98B ASP* 2.5 38.1 + - - +
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Residues in contact with SER 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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194A SER* 1.3 80.0 + - - +
196A VAL* 1.3 68.8 + - - +
204A ARG* 2.6 33.0 + - - -
205A GLN 3.3 11.0 - - - -
206A LEU* 4.0 9.0 - - - -
207A VAL* 4.5 0.4 - - - +
279A TRP* 3.5 24.8 - - - -
98B ASP* 3.7 15.6 + - - +
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Residues in contact with VAL 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 SER* 1.3 79.6 - - - +
197A PRO* 1.3 83.0 - - + +
204A ARG* 3.3 8.9 + - - +
205A GLN* 2.7 51.6 + - + +
207A VAL* 5.2 2.7 - - + -
96B ASP* 4.8 3.6 - - - +
98B ASP* 3.6 34.1 - - + +
99B MET* 4.0 28.5 - - + +
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Residues in contact with PRO 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 VAL* 1.3 103.6 - - + +
198A SER* 1.3 68.0 + - - +
199A SER 3.9 0.2 + - - -
203A HIS 4.2 4.5 - - - +
204A ARG* 3.5 26.2 - - - +
298A HIS* 6.5 2.2 - - + -
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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