Contacts of the helix formed by residues 232 - 247 (chain A) in PDB entry 2VES
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 ASP 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A THR* 4.0 28.7 - - + -
172A ALA* 5.0 3.5 - - + +
230A TYR* 3.1 20.8 - - - +
231A GLU* 1.3 80.4 - - - +
233A GLU* 1.3 62.7 + - - +
234A PHE 3.2 3.9 + - - -
235A VAL* 3.3 9.3 + - + +
236A LYS* 3.0 55.3 + - - +
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Residues in contact with GLU 233 (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 ARG 3.8 0.3 - - - +
188A ALA* 3.8 15.6 - - + +
189A ARG* 2.9 46.1 + - - +
215A ILE* 3.5 20.8 - - + +
228A LEU* 3.4 9.0 - - + +
229A ARG* 2.6 43.4 + - - -
230A TYR* 3.2 23.3 + - + +
231A GLU 3.3 2.6 + - - -
232A ASP* 1.3 80.5 + - - +
234A PHE* 1.3 63.7 + - - +
236A LYS* 4.4 0.7 - - - -
237A HIS* 3.1 22.9 + - - +
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 4.1 17.5 - - + -
164A VAL* 5.6 0.7 - - + -
165A PHE* 3.8 23.3 - + - -
168A ARG* 3.6 35.9 - - + -
169A THR 4.8 7.2 - - - +
191A PHE* 3.4 65.3 - + + -
215A ILE* 3.8 24.9 - - + -
217A VAL* 3.9 14.8 - - + -
222A VAL* 4.3 4.3 - - + -
228A LEU* 4.0 21.3 - - + -
231A GLU 5.2 2.2 - - - -
232A ASP 3.2 1.0 + - - -
233A GLU* 1.3 81.2 - - - +
235A VAL* 1.3 63.3 + - - +
237A HIS* 3.3 6.6 + - - +
238A LYS* 3.4 6.4 + - - +
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Residues in contact with VAL 235 (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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156A PHE* 3.5 38.8 - - + +
157A GLU* 4.7 0.2 - - - -
158A ILE* 4.7 5.6 - - + +
169A THR* 4.1 14.6 - - + +
170A GLN* 3.8 21.5 - - - +
171A GLN 4.1 5.6 - - - -
172A ALA* 3.8 26.9 - - + +
232A ASP* 3.4 17.5 - - + +
234A PHE* 1.3 79.9 - - - +
236A LYS* 1.3 64.3 + - - +
238A LYS* 3.2 16.5 + - - +
239A ILE* 3.2 13.4 + - + +
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Residues in contact with LYS 236 (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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172A ALA* 4.5 11.9 - - + -
173A SER 5.5 0.9 - - - -
174A VAL* 3.8 28.0 - - + -
184A GLU* 3.0 48.6 + - - +
185A VAL* 4.0 10.9 - - + +
188A ALA* 3.8 16.4 - - + -
230A TYR* 4.5 3.9 - - + -
232A ASP* 3.0 52.6 + - + +
233A GLU* 4.0 0.9 - - - +
234A PHE 3.3 0.2 - - - -
235A VAL* 1.3 75.6 - - + +
237A HIS* 1.3 60.8 + - - +
239A ILE* 3.2 12.2 + - + +
240A LEU* 2.9 26.2 + - - +
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Residues in contact with HIS 237 (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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78A HIS* 3.1 16.2 - + - -
105A GLY 3.4 9.0 - - - -
188A ALA* 2.9 25.8 + - + +
189A ARG 3.2 20.1 - - - +
190A THR* 3.3 23.5 - - - -
191A PHE* 4.7 7.2 - + + -
233A GLU 3.1 14.3 + - - +
234A PHE 3.7 5.2 - - - +
235A VAL 3.3 0.4 - - - -
236A LYS* 1.3 76.5 - - - +
238A LYS* 1.3 60.3 + - + +
240A LEU* 3.2 8.9 + - + +
241A ASP* 2.8 32.4 + - - -
1295A ZN 2.0 36.7 - - - -
1296A GVR 3.0 5.6 + - - -
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Residues in contact with LYS 238 (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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156A PHE* 3.5 41.1 - - + -
158A ILE* 3.8 21.1 - - + -
160A PHE* 5.9 2.9 - - - -
191A PHE* 4.1 24.3 - - + -
234A PHE 3.4 12.1 + - - +
235A VAL* 3.2 9.7 + - - +
237A HIS* 1.3 77.7 - - + +
239A ILE* 1.3 56.3 + - - +
241A ASP* 3.4 19.4 + - + +
242A ALA* 2.9 27.9 + - - +
261A LYS* 6.3 0.7 - - - +
262A SER 4.5 10.8 + - - +
263A GLY* 5.4 3.6 - - - -
1296A GVR 5.9 4.9 - - - +
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Residues in contact with ILE 239 (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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154A VAL* 3.8 36.1 - - + +
156A PHE* 3.8 16.4 - - + -
172A ALA* 3.8 33.7 - - + +
174A VAL* 4.1 20.9 - - + -
185A VAL* 4.2 15.3 - - + -
235A VAL* 3.2 14.5 + - + +
236A LYS* 3.5 14.1 - - + +
238A LYS* 1.3 74.5 - - - +
240A LEU* 1.3 64.7 + - - +
242A ALA* 3.2 3.0 + - - +
243A ILE* 2.9 39.0 + - + +
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Residues in contact with LEU 240 (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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78A HIS* 3.5 36.8 - - + -
81A SER* 2.8 41.9 + - - +
107A ALA* 3.8 13.5 - - + +
181A PHE* 4.8 0.4 - - + -
185A VAL* 3.7 30.2 - - + +
186A SER* 3.7 13.5 - - - +
188A ALA 3.5 24.7 - - - +
236A LYS 2.9 12.9 + - - +
237A HIS* 3.3 11.7 - - + +
239A ILE* 1.3 76.8 - - - +
241A ASP* 1.3 63.9 + - - +
243A ILE* 3.2 2.0 + - - -
244A GLY* 3.1 9.9 + - - -
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Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 3.8 5.8 - - - +
78A HIS* 3.2 8.8 + - - -
237A HIS* 2.8 24.8 + - - +
238A LYS* 3.5 24.6 + - + +
240A LEU* 1.3 73.7 - - - +
242A ALA* 1.3 56.3 + - - +
244A GLY* 3.3 1.7 + - - -
245A ASP* 2.9 35.8 + - - +
264A HIS* 3.8 15.8 + - + -
267A ASN* 4.6 2.5 - - - +
1295A ZN 2.1 36.8 - - - -
1296A GVR 3.0 14.4 + - - +
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Residues in contact with ALA 242 (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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154A VAL* 4.1 12.8 - - + -
156A PHE* 4.7 3.1 - - + -
238A LYS 2.9 14.9 + - - +
239A ILE* 3.5 7.6 - - - +
241A ASP* 1.3 75.1 - - - +
243A ILE* 1.3 57.4 + - - +
246A LEU* 2.9 39.2 + - + +
257A PHE* 3.8 33.0 - - + -
267A ASN* 4.0 13.9 - - - +
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Residues in contact with ILE 243 (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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81A SER* 3.5 19.5 - - - +
84A ALA* 3.8 23.4 - - + +
85A GLY* 4.7 1.8 - - - +
152A PHE* 4.2 17.4 - - + -
154A VAL* 4.0 18.4 - - + -
176A PHE* 3.5 31.9 - - + -
181A PHE* 3.9 19.5 - - + -
185A VAL* 4.3 1.3 - - + -
239A ILE* 2.9 33.1 + - + +
240A LEU 3.2 0.2 + - - -
242A ALA* 1.3 75.2 - - - +
244A GLY* 1.3 62.1 + - - +
246A LEU* 3.9 6.1 - - - +
247A TYR* 3.2 21.3 + - - +
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Residues in contact with GLY 244 (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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77A GLU* 3.4 26.0 - - - -
80A LEU* 3.7 16.3 - - - +
81A SER* 3.5 13.6 + - - -
240A LEU 3.1 10.9 + - - -
241A ASP 3.7 2.2 - - - -
243A ILE* 1.3 74.8 - - - +
245A ASP* 1.3 66.2 + - - +
247A TYR* 3.1 16.1 + - - +
248A LEU* 3.9 2.6 + - - +
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Residues in contact with ASP 245 (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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64A THR* 2.6 27.4 + - - +
77A GLU* 3.3 15.4 - - - +
241A ASP 2.9 16.5 + - - +
242A ALA 3.9 1.1 - - - +
244A GLY* 1.3 74.6 - - - +
246A LEU* 1.3 63.9 + - - +
248A LEU* 3.2 23.0 + - + +
264A HIS* 2.7 29.7 + - - -
267A ASN* 2.9 37.0 + - + +
268A ASN* 5.5 0.9 - - - +
271A LEU* 3.3 15.7 - - - +
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Residues in contact with LEU 246 (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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146A PHE* 3.7 29.2 - - + -
152A PHE* 4.7 12.6 - - + -
154A VAL* 5.2 1.3 - - + -
242A ALA* 2.9 28.0 + - + +
243A ILE* 3.9 4.5 - - - +
245A ASP* 1.3 77.8 - - - +
247A TYR* 1.3 56.5 + - - +
248A LEU 3.1 1.1 - - - -
249A LEU* 3.1 33.6 + - + +
251A ASN 4.8 1.7 - - - +
253A LEU* 4.1 13.2 - - + +
257A PHE* 3.8 38.4 - - + -
267A ASN* 4.7 11.2 - - + +
270A LEU* 4.9 0.7 - - + -
271A LEU* 3.7 24.9 - - + -
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Residues in contact with TYR 247 (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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37A ILE* 4.1 12.3 - - + -
52A ALA* 4.4 2.9 - - - +
80A LEU* 3.9 29.3 - - + +
83A MET* 4.0 7.4 - - + -
84A ALA* 3.6 33.8 - - + -
87A GLY* 4.7 1.9 - - - -
88A ILE 2.6 34.8 + - - -
89A ASP* 3.8 14.0 + - - -
243A ILE 3.2 12.0 + - - +
244A GLY 3.1 13.7 + - - +
246A LEU* 1.3 71.3 - - - +
248A LEU* 1.3 56.4 + - - +
249A LEU 3.1 5.8 - - - -
250A GLY* 2.9 25.7 + - - +
251A ASN* 3.9 31.6 - - - -
252A SER* 4.0 15.3 + - - -
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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
------------------------------------------------------------
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