Contacts of the strand formed by residues 189 - 198 (chain A) in PDB entry 2RD0
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 GLN 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-15A ILE* 4.2 5.4 - - - +
185A LEU* 3.4 24.9 + - - +
187A LYS* 3.0 25.4 - - - +
188A GLY* 1.3 80.8 - - - +
190A ILE* 1.3 61.9 + - - +
210A LYS* 3.6 42.4 + - + +
211A ILE* 3.0 23.1 - - - +
212A ASN* 3.6 18.7 + - - +
213A HIS 4.1 4.9 - - - +
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Residues in contact with ILE 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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-17A TYR* 6.1 0.2 - - - +
-15A ILE* 5.5 2.7 - - - -
185A LEU* 3.5 14.1 - - + -
189A GLN* 1.3 73.4 - - - +
191A ILE* 1.3 81.9 + - - +
192A VAL* 4.1 11.7 + - + +
209A LEU 3.9 0.2 - - - +
210A LYS* 3.3 2.8 - - - -
211A ILE 2.8 40.4 + - - +
212A ASN 4.2 2.0 - - - +
213A HIS* 3.8 25.6 - - + +
267A LEU* 5.1 7.4 - - + -
273A ILE* 4.2 19.7 - - + -
276A CYS* 5.6 0.2 - - + -
277A ILE* 4.4 15.0 - - + -
281A ARG 5.3 1.8 - - - +
283A PRO* 3.6 31.6 - - + -
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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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-17A TYR* 4.2 11.2 + - - +
-15A ILE* 3.5 37.7 - - + +
190A ILE* 1.3 84.1 - - - +
192A VAL* 1.3 62.5 + - - +
208A THR* 3.6 23.6 - - + -
209A LEU 3.2 10.5 - - - +
210A LYS* 3.8 32.5 - - + +
282A MET* 3.4 23.6 - - - +
283A PRO* 3.4 20.1 - - - +
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Residues in contact with VAL 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 ILE* 4.5 11.7 - - + +
191A ILE* 1.3 77.9 - - - +
193A VAL* 1.3 71.4 + - - +
194A ILE* 4.0 3.8 - - + +
207A TYR 4.2 0.2 - - - +
208A THR* 3.4 7.1 - - - +
209A LEU* 2.9 36.5 + - + +
211A ILE* 4.4 20.2 - - + -
220A VAL* 5.4 10.3 - - + -
267A LEU* 4.6 15.7 - - + -
282A MET* 4.6 0.4 - - - -
283A PRO* 3.4 28.9 - - + +
285A LEU* 3.9 24.0 - - + -
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Residues in contact with VAL 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 VAL* 1.3 79.0 - - - +
194A ILE* 1.3 59.5 + - - +
195A TRP* 3.2 37.0 - - + +
206A LYS* 3.5 30.3 - - + -
207A TYR 4.0 4.9 - - - +
208A THR* 3.9 15.0 - - + +
282A MET* 3.6 35.9 - - + -
283A PRO 2.9 13.6 + - - +
284A ASN* 3.3 7.3 - - - +
285A LEU 3.2 14.9 + - - -
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Residues in contact with ILE 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 VAL* 5.4 4.0 - - + +
193A VAL* 1.3 73.1 - - - +
195A TRP* 1.3 63.2 + - - +
196A VAL* 5.7 0.4 - - + -
207A TYR* 3.1 49.6 + - + +
209A LEU* 3.9 15.7 - - + -
220A VAL* 4.5 14.4 - - + +
221A ILE* 4.8 0.7 - - - -
224A ALA* 3.6 30.5 - - + -
252A LEU* 3.4 18.6 - - + -
285A LEU* 3.6 13.2 - - + +
287A LEU* 3.3 41.5 - - + +
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Residues in contact with TRP 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 VAL* 3.2 35.0 + - + +
194A ILE* 1.3 75.8 - - - +
196A VAL* 1.3 67.7 + - - +
197A ILE 4.3 0.2 - - - -
204A LYS* 3.8 40.4 - - + -
205A GLN 3.5 4.5 - - - -
206A LYS* 3.9 45.8 - - + -
255A CYS* 4.0 2.7 - - - -
284A ASN* 3.6 7.3 - - - +
285A LEU 2.9 18.2 + - - +
286A MET* 3.8 3.8 - - + +
287A LEU* 3.1 26.5 + - - +
789A MET* 3.4 33.4 - - + -
792A LEU* 4.9 2.7 - - + -
793A LEU* 3.4 39.5 - - + +
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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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194A ILE* 5.5 0.7 - - + +
195A TRP* 1.3 80.5 - - - +
197A ILE* 1.3 74.6 + - - +
198A VAL* 3.8 6.8 + - + +
203A ASP 3.8 0.7 - - - +
204A LYS* 3.4 2.5 - - - -
205A GLN* 2.8 38.1 + - + +
207A TYR* 4.3 21.8 - - + -
228A LYS* 3.5 31.4 - - + +
250A TYR* 6.0 5.6 - - + +
286A MET* 5.6 0.4 - - - -
287A LEU* 3.8 33.2 - - + +
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Residues in contact with ILE 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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195A TRP 4.3 0.2 - - - -
196A VAL* 1.3 80.7 - - - +
198A VAL* 1.3 65.9 + - - +
199A SER* 3.6 25.1 - - - +
202A ASN 3.3 26.0 - - - +
203A ASP 3.5 0.7 - - - -
204A LYS* 4.0 19.5 - - + -
286A MET* 4.5 24.0 - - - -
287A LEU 5.4 2.6 + - - -
788A ILE* 4.8 20.4 - - + +
789A MET* 4.7 9.2 - - + -
792A LEU* 5.8 1.3 - - + -
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Residues in contact with VAL 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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196A VAL* 3.9 17.7 - - + +
197A ILE* 1.3 79.7 - - - +
199A SER* 1.3 63.4 + - - +
201A ASN* 3.1 27.9 + - + +
203A ASP* 2.6 25.2 + - + +
205A GLN* 4.0 22.4 - - - +
228A LYS* 4.3 9.2 - - - +
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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