Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 3VNG
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 ARG 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.2 2.3 - - - +
240A VAL* 3.4 4.7 - - - -
241A HIS 2.9 34.3 + - - +
242A GLN 3.9 13.3 + - - +
243A GLY* 1.3 84.5 + - - +
245A ILE* 1.3 65.9 + - - +
246A TYR* 3.6 8.0 - - + +
262A CYS* 3.6 27.6 - - - -
263A TYR 3.3 14.8 - - - +
264A ASP* 3.0 34.6 + - - +
265A PRO* 4.1 4.3 - - + -
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Residues in contact with ILE 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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192A CYS* 3.2 27.1 - - - -
194A LEU* 3.5 30.1 - - + -
199A TYR* 5.0 8.5 - - + -
238A ILE* 3.8 31.4 - - + -
239A THR 3.5 1.6 - - - +
240A VAL* 3.2 20.4 - - + -
244A ARG* 1.3 73.5 - - - +
246A TYR* 1.3 67.6 + - - +
247A VAL* 4.3 0.2 - - + -
261A GLU 3.7 0.7 - - - +
262A CYS* 3.1 7.6 - - - -
263A TYR* 2.7 52.1 + - + -
270A TRP* 4.2 13.8 - - + -
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.5 32.8 - - + -
24A TYR* 4.5 11.9 - + - -
26A PRO* 3.7 19.3 - - + +
238A ILE* 3.2 6.6 - - - +
239A THR* 2.8 36.4 + - + +
240A VAL 4.8 0.2 - - - -
241A HIS* 3.6 35.8 + - + -
244A ARG* 3.6 13.4 - - + +
245A ILE* 1.3 78.3 - - - +
247A VAL* 1.3 61.2 + - - +
248A LEU* 3.7 11.4 - - + +
260A VAL* 4.5 9.6 - - + -
261A GLU 3.4 4.3 - - - -
262A CYS* 3.7 26.6 - - + -
273A VAL* 4.2 22.8 - - + +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA* 4.7 0.9 - - + -
229A MET* 3.9 14.6 - - - -
233A ARG* 4.0 11.2 - - - +
236A LEU* 3.6 28.3 - - + -
237A GLY 3.1 3.1 - - - -
238A ILE* 3.9 13.9 - - + -
245A ILE* 4.3 0.4 - - + -
246A TYR* 1.3 78.2 - - - +
248A LEU* 1.3 60.5 + - - +
249A GLY 4.3 0.2 - - - -
259A SER 3.9 0.9 - - - +
260A VAL* 3.3 8.5 - - - +
261A GLU* 3.0 51.6 + - + +
270A TRP* 3.8 26.9 - - + -
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Residues in contact with LEU 248 (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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7A ILE* 4.1 20.6 - - + -
9A THR* 4.5 9.6 - - - -
24A TYR* 5.9 1.1 - - + -
31A TRP* 4.2 23.8 - - + -
236A LEU* 4.8 0.2 - - - +
237A GLY* 2.6 47.9 + - - +
239A THR* 4.7 0.2 - - + -
246A TYR* 3.7 26.5 - - + +
247A VAL* 1.3 80.4 - - - +
249A GLY* 1.3 67.3 + - - +
250A GLY 3.6 0.7 + - - -
259A SER 4.1 2.0 - - - -
260A VAL* 4.0 15.3 - - + -
276A MET* 4.0 13.2 - - + -
280A ARG 4.8 0.3 - - - +
283A VAL* 4.2 6.5 - - + +
285A VAL* 4.3 25.6 - - + -
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Residues in contact with GLY 249 (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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233A ARG* 2.8 33.2 + - - -
236A LEU* 3.8 1.3 - - - +
248A LEU* 1.3 74.1 - - - +
250A GLY* 1.3 59.8 + - - -
257A LEU* 3.2 26.8 - - - +
259A SER 3.1 18.0 + - - -
276A MET* 3.6 11.3 - - - -
280A ARG 3.6 4.7 - - - -
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Residues in contact with GLY 250 (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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233A ARG* 4.5 1.8 - - - -
234A SER 3.3 13.2 - - - -
235A ALA 3.5 14.3 + - - -
236A LEU* 4.0 2.0 - - - -
248A LEU 3.6 1.6 + - - -
249A GLY* 1.3 75.2 - - - -
251A TYR* 1.3 61.1 + - - +
256A PHE* 3.7 3.8 - - - -
257A LEU* 3.0 25.6 + - - -
280A ARG 2.9 14.9 + - - +
281A SER* 3.7 7.0 - - - +
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Residues in contact with TYR 251 (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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209A GLN* 3.1 21.9 - - - +
233A ARG* 3.4 3.1 - - - +
234A SER* 2.9 38.9 + - - +
235A ALA* 4.8 2.5 - - + -
250A GLY* 1.3 74.6 - - - +
252A ASP* 1.3 59.9 + - - +
253A GLY* 3.4 43.6 + - - -
254A HIS 4.3 2.7 - - - -
255A THR 3.4 18.6 - - - -
256A PHE* 3.9 34.8 - + - -
257A LEU* 5.1 0.7 - - - -
281A SER* 4.0 13.2 - - - +
301A FUU 4.3 21.8 - + + -
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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