Contacts of the strand formed by residues 291 - 296 (chain D) in PDB entry 5MBV
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 291 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D ILE* 4.3 25.3 - - + +
161D ALA 4.3 7.5 + - - +
162D LEU* 4.3 16.3 + - - +
164D ARG 3.9 17.3 - - - -
165D ARG* 3.2 26.5 - - + +
188D LEU* 3.4 39.4 - - - +
264D ASP* 3.2 10.7 + - - -
265D VAL* 3.2 22.0 - - + +
266D LEU 3.0 24.4 + - - -
289D HIS 4.9 6.1 + - - +
290D ALA* 1.3 74.4 - - - +
292D VAL* 1.3 60.5 + - - +
293D ILE* 4.4 7.5 - - + +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 5.2 2.9 - - + -
165D ARG* 3.2 9.1 + - + +
166D ILE* 3.3 16.4 - - + +
167D SER 3.2 23.2 + - - -
266D LEU* 3.4 27.6 - - + +
268D VAL* 4.6 0.7 - - + -
282D LEU* 4.8 3.6 - - + -
286D LEU* 3.6 38.4 - - + -
290D ALA* 4.3 9.6 - - + +
291D ARG* 1.3 78.2 - - - +
293D ILE* 1.3 67.0 + - - +
294D PHE* 3.5 31.9 - - + -
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ALA* 4.2 7.2 - - + +
165D ARG 5.1 0.7 - - - +
167D SER* 3.4 21.5 - - - +
169D ILE* 4.5 12.3 - - + -
181D VAL* 5.7 0.9 - - + -
184D LEU* 4.0 31.4 - - + -
185D LEU* 6.1 1.1 - - + -
188D LEU* 5.4 5.8 - - + -
265D VAL* 4.9 9.0 - - + -
266D LEU 2.9 14.1 + - - +
267D VAL* 3.4 18.1 - - + +
268D VAL 2.9 27.0 + - - +
291D ARG* 4.4 12.6 - - + +
292D VAL* 1.3 84.6 - - - +
294D PHE* 1.3 74.2 - - - +
295D LEU* 4.1 14.8 - - + -
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Residues in contact with PHE 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 5.8 2.9 - + - -
123D PHE* 3.7 13.9 - + - -
166D ILE* 3.7 20.6 - - + -
167D SER 3.2 6.1 + - - -
168D VAL* 3.5 33.2 - - + +
169D ILE 3.1 26.3 + - - +
268D VAL* 3.6 25.1 - - + -
271D ALA* 3.8 17.5 - - + -
274D ILE* 6.3 0.4 - - + -
279D MET* 3.6 37.9 - - + -
282D LEU* 5.1 9.4 - - + -
286D LEU* 6.1 0.7 - - + -
292D VAL* 3.5 26.9 - - + -
293D ILE* 1.3 78.6 - - - +
295D LEU* 1.3 68.5 + - - +
310D LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 5.8 0.4 - - - -
169D ILE* 3.9 16.6 - - + +
177D LYS* 5.4 13.5 - - + +
178D THR* 5.7 4.0 - - - +
181D VAL* 3.6 33.4 - - + -
212D LEU* 4.6 7.6 - - + -
267D VAL* 3.9 17.9 - - + -
268D VAL 2.8 13.3 + - - +
269D ASP* 3.4 34.1 - - + +
270D GLU 3.1 4.0 + - - -
271D ALA* 2.4 38.9 + - - +
293D ILE* 4.1 13.9 - - + -
294D PHE* 1.3 87.0 - - - +
296D GLY* 1.3 54.8 + - - +
310D LEU* 4.8 1.1 - - - -
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Residues in contact with GLY 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 5.7 0.8 - - - +
169D ILE 3.5 3.9 + - - +
170D SER* 3.2 9.5 - - - -
171D GLY 3.0 24.5 + - - +
177D LYS* 4.3 11.7 - - - +
270D GLU* 4.7 6.1 - - - -
271D ALA 4.4 2.2 - - - -
272D SER 4.8 0.2 - - - -
295D LEU* 1.3 76.6 - - - +
297D ASP* 1.3 61.1 + - - -
300D GLN* 4.1 9.0 - - - -
310D LEU* 4.1 13.6 - - - +
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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