Contacts of the helix formed by residues 263 - 277 (chain C) 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 GLY 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C LYS* 5.3 4.2 - - - +
238C LYS* 5.1 6.1 - - - -
261C LYS 3.8 0.6 + - - -
262C SER* 1.3 75.5 + - - +
264C HIS* 1.3 62.6 + - - -
265C ALA 3.3 2.9 - - - -
266C LEU* 3.3 6.7 + - - +
267C ASN* 2.9 36.5 + - - -
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 3.9 20.3 + - - +
61C THR 5.0 2.0 - - - -
62C MET* 3.2 20.4 + - - -
63C SER* 3.5 9.2 - - - -
64C THR* 3.5 17.4 + - - +
77C GLU* 3.1 14.4 + - + -
241C ASP* 3.7 21.4 + - + +
245C ASP* 2.7 30.7 + - - +
263C GLY* 1.3 72.0 - - - -
265C ALA* 1.3 57.3 + - - +
267C ASN* 3.7 0.9 - - - +
268C ASN* 2.9 31.5 + - - +
1301C GVR 2.8 38.2 + - - +
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 3.3 31.2 + - - +
139C GLU* 4.7 10.5 - - - +
263C GLY* 3.3 0.8 - - - -
264C HIS* 1.3 79.6 - - - +
266C LEU* 1.3 57.4 + - - +
268C ASN* 3.6 3.0 - - - +
269C GLN* 2.9 29.2 + - - +
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 3.5 22.4 - - + +
138C GLU 4.0 7.9 - - - -
139C GLU* 3.8 32.1 + - + +
142C LYS* 3.7 15.7 - - + -
143C ARG* 3.5 44.0 - - - +
144C ALA* 3.6 3.1 - - + +
262C SER* 3.4 16.4 - - - +
263C GLY 3.3 9.3 + - - +
265C ALA* 1.3 75.7 - - - +
267C ASN* 1.3 60.6 + - - +
269C GLN* 3.2 16.6 + - - +
270C LEU* 2.8 30.2 + - - +
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Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ALA* 5.2 0.9 - - - -
156C PHE* 5.1 2.4 - - - -
238C LYS 5.5 0.2 + - - -
241C ASP* 4.4 3.0 - - - +
242C ALA* 3.7 24.0 - - - +
245C ASP* 2.9 34.7 + - + +
246C LEU* 4.4 7.5 - - + +
257C PHE* 3.5 22.2 - - - -
262C SER* 3.0 21.0 + - - -
263C GLY* 2.9 25.5 + - - +
264C HIS* 3.7 4.6 + - - +
266C LEU* 1.3 76.4 - - - +
268C ASN* 1.3 61.6 + - - +
270C LEU* 3.4 7.5 + - - +
271C LEU* 3.1 27.4 + - - +
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Residues in contact with ASN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 3.8 19.5 + - - +
57C VAL* 3.6 40.1 - - + +
60C THR* 4.4 11.3 - - + +
64C THR* 6.1 1.3 - - + +
245C ASP* 5.3 1.9 - - + +
248C LEU* 5.1 3.2 - - + +
264C HIS 2.9 18.5 + - - +
265C ALA 3.6 3.9 - - - +
267C ASN* 1.3 76.5 - - - +
269C GLN* 1.3 58.9 + - - +
271C LEU* 3.3 9.7 + - - +
272C ARG* 3.0 35.8 + - - +
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Residues in contact with GLN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 3.8 25.8 - - + +
138C GLU 4.7 8.3 + - - +
139C GLU* 5.2 3.3 - - - +
265C ALA 2.9 17.6 + - - +
266C LEU* 3.2 19.7 + - - +
268C ASN* 1.3 73.1 - - - +
270C LEU* 1.3 56.9 + - - +
272C ARG* 3.4 33.7 + - - +
273C THR* 2.7 39.7 + - - +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.7 25.6 - - + +
136C SER* 3.9 8.7 - - - +
137C VAL* 3.9 12.7 - - + +
144C ALA* 3.6 24.7 - - + +
145C VAL 4.1 4.3 - - - +
146C PHE* 3.5 34.5 - - + -
246C LEU* 4.8 2.0 - - + -
257C PHE* 3.7 33.4 - - + -
266C LEU 2.8 13.8 + - - +
267C ASN 3.5 7.6 - - - +
269C GLN* 1.3 77.4 - - - +
271C LEU* 1.3 62.6 + - - +
273C THR* 3.3 2.1 + - - -
274C LEU* 2.9 23.2 + - - +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 4.2 15.9 - - + -
146C PHE* 4.1 12.3 - - + -
245C ASP 3.2 26.0 - - - +
246C LEU* 3.5 37.2 - - + +
248C LEU* 4.0 16.2 - - + -
249C LEU* 4.1 22.7 - - + +
267C ASN 3.1 17.8 + - - +
268C ASN* 3.5 14.6 - - - +
270C LEU* 1.3 76.1 - - - +
272C ARG* 1.3 63.5 + - - +
274C LEU* 3.2 4.8 + - + +
275C ILE* 2.9 31.7 + - + +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 5.3 3.9 - - + +
268C ASN* 3.0 24.5 + - - +
269C GLN* 3.7 36.2 + - - +
270C LEU 3.3 0.2 - - - -
271C LEU* 1.3 75.9 - - - +
273C THR* 1.3 64.8 + - - +
275C ILE* 3.4 9.3 + - - +
276C ALA* 3.1 27.5 + - + +
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Residues in contact with THR 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.6 21.0 - - + +
136C SER 4.6 4.7 - - - +
137C VAL* 3.5 19.4 - - + +
269C GLN* 2.7 25.8 + - - +
270C LEU 3.6 4.5 - - - -
271C LEU 3.2 0.2 - - - -
272C ARG* 1.3 80.3 + - - +
274C LEU* 1.3 67.0 + - - +
276C ALA* 3.6 4.5 + - - +
277C ASP* 3.4 20.4 + - + +
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE* 4.9 5.8 - - + -
131C ILE* 3.6 28.5 - - + -
135C VAL* 3.8 27.5 - - + +
146C PHE* 3.6 28.0 - - + -
249C LEU* 4.3 28.5 - - + -
253C LEU* 4.6 0.4 - - + -
270C LEU 2.9 14.0 + - - +
271C LEU* 3.5 7.4 - - + +
273C THR* 1.3 75.0 - - - +
275C ILE* 1.3 65.7 + - - +
277C ASP* 3.0 14.3 + - - +
280C ALA* 4.0 9.6 - - + +
281C TRP* 3.1 32.9 + - + -
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 4.0 22.2 - - + -
55C GLU* 4.0 27.1 - - - +
248C LEU 5.6 0.2 - - - +
249C LEU* 3.6 33.2 - - + +
271C LEU* 2.9 25.3 + - + +
272C ARG* 3.9 6.5 - - - +
274C LEU* 1.3 72.3 - - - +
276C ALA* 1.3 62.7 + - + +
277C ASP 4.1 0.5 - - - -
278C LYS* 4.3 7.5 + - - +
281C TRP* 3.1 34.6 + - + +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ARG* 3.1 19.6 + - + +
273C THR* 4.1 4.7 - - - +
274C LEU 3.2 0.2 - - - -
275C ILE* 1.3 80.4 - - + +
277C ASP* 1.3 56.0 + - - +
278C LYS* 3.5 10.8 + - - +
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Residues in contact with ASP 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 4.8 6.9 + - - -
134C GLU 5.5 1.2 - - - +
135C VAL* 5.1 4.8 - - + +
273C THR* 3.4 14.7 + - + +
274C LEU* 3.0 7.4 + - - +
276C ALA* 1.3 74.5 - - - +
278C LYS* 1.3 58.2 + - - +
279C ASP* 3.3 22.8 + - - +
280C ALA* 2.9 35.3 + - + +
281C TRP* 3.1 14.4 - - - -
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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