Contacts of the strand formed by residues 252 - 260 (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 SER 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C LYS* 3.7 20.9 - - - +
127C LYS 4.2 2.0 + - - -
128C PHE* 3.4 24.3 - - - -
129C ILE* 2.9 25.3 + - - +
152C PHE* 6.1 0.3 - - - -
247C TYR* 3.8 14.7 - - - -
251C ASN* 1.3 74.4 - - - +
253C LEU* 1.3 60.6 + - - +
294C ILE* 3.6 7.4 - - - +
296C TYR* 2.5 29.7 + - - -
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Residues in contact with LEU 253 (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* 3.5 13.7 - - + +
131C ILE* 3.9 24.7 - - + -
146C PHE* 3.7 31.6 - - + -
152C PHE* 3.6 47.5 - - + +
246C LEU* 5.0 6.7 - - + +
249C LEU* 3.5 27.8 - - + -
251C ASN 3.6 2.8 + - - +
252C SER* 1.3 74.1 + - - +
254C ILE* 1.3 65.9 + - - +
255C GLY* 3.8 8.1 - - - +
256C GLU 4.8 0.4 - - - +
274C LEU* 4.6 2.9 - - + -
294C ILE* 3.1 19.2 - - - +
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Residues in contact with ILE 254 (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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128C PHE* 3.6 37.7 - - + -
129C ILE 2.8 12.7 + - - +
130C ARG* 3.8 21.7 - - + +
131C ILE* 2.9 29.3 + - - +
149C PHE 3.5 15.9 - - - +
150C ASP* 4.5 3.8 - - - +
151C GLY 3.3 15.3 - - - +
253C LEU* 1.3 75.7 - - - +
255C GLY* 1.3 57.4 + - - +
284C VAL* 4.1 8.1 - - + -
286C PHE* 3.8 25.4 - - + -
293C PRO* 3.9 16.8 - - + -
294C ILE* 3.9 7.4 - - + -
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Residues in contact with GLY 255 (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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131C ILE* 4.0 10.1 - - - -
147C VAL 3.8 8.5 - - - -
149C PHE* 3.5 18.8 - - - -
151C GLY 2.9 7.4 + - - +
152C PHE* 3.3 12.1 - - - -
153C LYS 3.2 20.4 + - - -
253C LEU* 3.8 6.2 - - - +
254C ILE* 1.3 75.5 - - - +
256C GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 256 (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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131C ILE* 4.8 0.2 - - - +
145C VAL 3.7 0.7 - - - +
146C PHE* 3.2 11.2 - - - -
147C VAL* 2.9 47.3 + - + +
148C PRO 4.7 1.0 - - - +
149C PHE* 3.6 24.6 - - + +
153C LYS* 3.2 38.5 + - + +
155C SER* 4.4 3.5 + - - -
253C LEU* 4.8 1.2 - - - +
255C GLY* 1.3 74.3 - - - +
257C PHE* 1.3 67.4 + - - +
258C ARG* 2.9 43.4 + - - +
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Residues in contact with PHE 257 (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* 4.1 9.6 - - + -
145C VAL 3.3 6.5 - - - -
146C PHE* 4.1 5.2 - + + -
152C PHE* 5.1 3.0 - - + -
153C LYS 2.8 10.0 + - - +
154C VAL* 3.5 23.3 - - + -
155C SER* 2.8 33.3 + - - -
156C PHE* 3.9 10.5 - + - -
242C ALA* 3.8 16.8 - - + -
246C LEU* 3.7 35.2 - - + -
256C GLU* 1.3 74.8 - - - +
258C ARG* 1.3 60.3 + - - +
259C GLY* 3.4 28.3 - - - -
262C SER* 4.5 0.2 - - - -
267C ASN* 3.5 25.6 - - - -
270C LEU* 3.7 30.3 - - + -
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Residues in contact with ARG 258 (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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198A GLU* 4.6 18.8 + - - +
202A SER* 3.9 26.1 - - - -
143C ARG 4.1 0.5 - - - +
144C ALA* 3.5 3.3 - - - -
145C VAL* 2.9 49.5 + - + +
147C VAL* 3.9 21.1 - - - +
155C SER* 3.4 14.6 - - - -
256C GLU* 2.9 39.1 + - + +
257C PHE* 1.3 81.6 - - - +
259C GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 259 (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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143C ARG 3.5 6.1 - - - -
155C SER 2.9 12.2 + - - -
156C PHE* 3.3 13.9 - - - -
157C GLU* 2.9 25.9 + - - +
257C PHE* 3.4 18.8 - - - -
258C ARG* 1.3 74.6 - - - +
260C PHE* 1.3 60.7 + - - +
261C LYS 4.1 1.1 - - - -
262C SER* 4.3 1.3 - - - -
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Residues in contact with PHE 260 (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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195A ARG* 3.6 52.7 - - + -
196A ASP* 5.7 2.7 - - - -
141C ASP* 3.2 31.4 - - + -
142C LYS* 3.4 2.6 - - - -
143C ARG* 2.9 51.0 + - + +
157C GLU* 3.4 27.1 - - + -
159C ASP* 4.1 11.2 - - + -
259C GLY* 1.3 72.8 - - - +
261C LYS* 1.3 97.7 + - + +
262C SER 3.1 0.6 + - - +
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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