Contacts of the helix formed by residues 188 - 203 (chain A) in PDB entry 2V5E
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 ASN 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 4.3 5.5 + - + +
180A THR 4.1 5.3 + - - -
182A MET* 3.6 29.7 - - + +
187A CYS* 1.3 74.3 - - - +
189A ARG* 1.3 56.2 + - - +
190A ARG* 3.1 26.6 + - - +
191A LYS* 3.2 41.6 + - + +
192A CYS* 3.0 28.4 + - - +
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Residues in contact with ARG 189 (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 CYS* 3.5 15.2 + - - +
188A ASN* 1.3 71.5 + - - +
190A ARG* 1.3 54.2 + - - +
192A CYS* 3.3 3.0 + - - +
193A HIS* 2.8 64.1 + - + +
233A CYS 3.4 25.5 + - - +
234A SER 3.4 23.0 + - - -
235A TYR* 3.5 12.1 + - - +
236A GLU 3.1 25.7 + - - -
237A GLU* 3.5 29.7 + - - +
296A VAL* 4.8 11.9 + - - +
298A THR* 5.2 2.2 - - - -
312A TRP* 5.2 3.8 - - - +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 3.1 14.0 + - - +
189A ARG* 1.3 78.9 - - - +
191A LYS* 1.3 88.9 + - - +
193A HIS* 3.4 6.6 + - - +
194A LYS* 2.9 34.8 + - - +
197A ARG* 5.1 0.5 + - - -
1C GU4 3.0 39.8 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 3.8 14.2 - - + +
188A ASN* 3.2 36.7 + - + +
190A ARG* 1.3 100.5 - - - +
192A CYS* 1.3 65.1 + - - +
194A LYS* 4.3 4.0 - - + -
195A ALA* 3.2 13.7 + - - +
1354A EDO 2.7 32.5 + - - +
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Residues in contact with CYS 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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177A PRO* 4.1 5.5 - - - +
178A CYS* 2.0 56.5 - - - +
188A ASN 3.0 11.9 + - - +
189A ARG 3.6 2.2 - - - +
191A LYS* 1.3 74.9 - - - +
193A HIS* 1.3 65.0 + - - +
195A ALA* 3.2 2.4 + - - -
196A LEU* 2.9 24.5 + - - +
233A CYS* 3.4 30.3 - - - -
234A SER* 3.8 21.8 - - - -
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Residues in contact with HIS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 2.8 50.9 + - + +
190A ARG* 3.6 7.3 - - - +
192A CYS* 1.3 72.0 - - - +
194A LYS* 1.3 63.1 + - - +
196A LEU* 3.1 6.9 + - + +
197A ARG* 3.0 32.6 + - - +
234A SER* 2.8 42.5 + - - -
294A GLY* 3.4 30.0 + - - +
295A THR 3.5 22.2 + - - -
296A VAL* 4.6 6.7 - - + +
298A THR* 3.5 5.1 + - - -
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Residues in contact with LYS 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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190A ARG* 2.9 25.8 + - - +
191A LYS* 3.7 6.5 - - + +
193A HIS* 1.3 77.2 - - - +
195A ALA* 1.3 62.5 + - - +
197A ARG* 3.2 14.0 + - - +
198A GLN* 3.0 35.6 + - - +
1354A EDO 3.5 21.3 - - - +
1C GU4 2.7 55.4 + - - +
2C YYJ 3.2 46.3 + - - -
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Residues in contact with ALA 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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170A TYR* 4.8 1.6 - - - +
173A ALA* 3.3 29.2 - - + +
174A TYR* 3.4 17.6 - - + +
177A PRO* 3.9 4.3 - - + -
191A LYS 3.2 15.7 + - - +
192A CYS 3.8 2.0 - - - +
194A LYS* 1.3 78.0 - - - +
196A LEU* 1.3 57.9 + - - +
198A GLN* 3.4 5.2 + - - +
199A PHE* 2.8 28.4 + - - +
1354A EDO 3.9 17.0 - - - -
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Residues in contact with LEU 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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174A TYR* 3.5 37.9 - - + -
178A CYS* 4.4 0.7 - - - -
192A CYS* 2.9 24.6 + - - +
193A HIS* 3.1 13.0 + - + +
195A ALA* 1.3 74.7 - - - +
197A ARG* 1.3 64.2 + - - +
199A PHE* 3.2 4.7 + - - +
200A PHE* 3.1 38.7 + - + -
229A ILE* 3.8 19.7 - - + +
234A SER* 3.6 31.2 - - - +
293A ILE* 4.2 27.8 - - + -
294A GLY* 4.3 3.4 - - - +
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Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG 5.1 0.8 + - - -
193A HIS* 3.0 22.6 + - - +
194A LYS* 3.5 15.8 - - - +
196A LEU* 1.3 73.2 - - - +
198A GLN* 1.3 58.5 + - - +
200A PHE* 3.2 5.1 + - - +
201A ASP* 2.9 30.8 + - - +
255A ILE* 4.0 28.4 - - - +
259A ARG* 5.0 7.4 + - - +
293A ILE 3.6 19.0 + - - +
294A GLY* 2.9 27.1 + - - +
295A THR* 4.7 2.5 - - + -
1351A EDO 4.2 7.2 + - - +
1352A EDO 3.2 11.0 - - - +
1C GU4 2.8 46.7 + - - -
2C YYJ 2.7 42.1 - - - -
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Residues in contact with GLN 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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170A TYR* 4.1 21.0 - - + -
173A ALA* 6.1 1.0 - - - +
194A LYS* 3.0 28.1 + - - +
195A ALA* 3.8 5.3 - - - +
197A ARG* 1.3 75.5 - - - +
199A PHE* 1.3 56.8 + - - +
202A LYS* 2.8 36.4 + - - +
1352A EDO 3.2 27.6 - - - -
1354A EDO 2.6 26.2 + - - -
2C YYJ 2.7 38.5 - - - -
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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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167A CYS* 3.8 31.4 - - - -
170A TYR* 3.6 16.5 - - + +
171A ARG* 3.5 34.8 - - + -
174A TYR* 3.7 28.5 - + + -
195A ALA 2.8 18.6 + - - +
196A LEU* 3.2 9.1 + - - +
198A GLN* 1.3 73.2 - - - +
200A PHE* 1.3 84.0 + + + +
203A VAL* 3.0 42.3 + - + +
208A SER* 3.6 30.5 - - - -
211A MET* 4.7 13.5 - - + -
228A THR* 5.8 1.6 - - + -
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Residues in contact with PHE 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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174A TYR* 5.9 1.1 - + - -
196A LEU* 3.1 34.1 + - + +
197A ARG* 4.1 3.1 - - - +
199A PHE* 1.3 93.9 - + - +
201A ASP* 1.3 61.6 + - - +
203A VAL 3.8 10.7 - - - +
208A SER* 3.7 41.4 + - - -
209A TYR* 4.9 4.7 - + + -
212A LEU* 3.7 33.0 - - + -
228A THR* 5.2 5.8 - - + -
229A ILE* 5.0 3.8 - - + -
259A ARG* 6.2 1.1 - - - +
290A SER* 4.1 26.5 - - - +
291A GLY* 5.8 2.0 - - - -
293A ILE* 4.0 33.0 - - + +
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Residues in contact with ASP 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 ARG 2.9 17.5 + - - +
198A GLN 4.1 0.2 - - - +
200A PHE* 1.3 77.7 - - - +
202A LYS* 1.3 69.0 + - - +
203A VAL 4.9 0.7 - - - +
259A ARG* 4.7 6.0 + - - +
1351A EDO 2.8 28.3 + - - +
1352A EDO 2.7 29.8 + - - +
2C YYJ 4.5 1.7 - - - -
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 4.0 8.7 - - - +
170A TYR* 3.7 37.5 - - + +
198A GLN* 2.8 16.5 + - - +
201A ASP* 1.3 86.4 + - - +
203A VAL* 1.3 63.2 - - - +
204A PRO* 3.8 6.8 - - - +
1352A EDO 2.5 33.3 + - - +
2C YYJ 2.9 20.4 - - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 4.1 2.7 - - + +
167A CYS* 3.8 35.7 - - + +
170A TYR* 3.5 36.6 - - + -
199A PHE* 3.0 26.0 + - + +
200A PHE 3.8 10.6 - - - +
201A ASP 4.9 1.0 - - - +
202A LYS* 1.3 80.5 - - - +
204A PRO* 1.3 85.4 - - + +
205A ALA* 3.4 1.6 + - - -
207A HIS* 3.9 9.2 - - + -
208A SER* 3.4 16.5 + - - +
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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