Contacts of the strand formed by residues 291 - 296 (chain A) in PDB entry 3MAP
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 MET 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 3.4 33.2 - - + +
110A GLU 3.3 7.2 - - - -
111A ALA* 3.1 42.0 - - + +
130A ILE* 5.1 6.7 - - + -
287A SER 4.5 2.5 - - - +
288A LEU* 3.0 25.6 + - + +
289A GLY 3.5 1.0 - - - -
290A MET* 1.3 77.7 - - - +
292A THR* 1.3 54.1 + - - +
308A ALA* 2.6 54.0 + - + -
331A ALA* 3.3 9.5 - - - +
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Residues in contact with THR 292 (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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108A PHE 3.2 3.8 - - - +
109A ARG* 4.2 1.6 - - - -
110A GLU* 2.8 40.3 + - - +
112A ILE* 3.9 6.6 - - - +
290A MET 3.8 0.2 + - - -
291A MET* 1.3 73.4 - - - +
293A SER* 1.3 72.2 + - - +
294A VAL* 4.2 2.2 - - + +
306A GLU 3.8 6.7 - - - +
307A ALA* 4.6 0.9 - - - +
308A ALA* 4.4 0.7 - - - -
331A ALA* 3.5 10.4 + - - +
334A PHE* 3.1 23.9 - - - +
335A ALA* 4.0 21.1 - - - +
338A ARG* 3.8 30.0 + - + +
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Residues in contact with SER 293 (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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107A VAL* 3.1 19.9 - - - +
108A PHE 3.4 6.3 - - - -
109A ARG* 3.3 27.5 + - - +
292A THR* 1.3 71.7 - - - +
294A VAL* 1.3 73.7 + - - +
295A LEU 4.4 0.2 + - - -
306A GLU* 2.7 61.5 + - - +
308A ALA* 3.8 6.3 - - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 3.3 0.5 - - - +
107A VAL* 4.2 0.9 - - - -
108A PHE* 2.8 45.3 + - + +
199A MET* 5.1 9.2 - - + -
292A THR* 4.2 4.7 - - + +
293A SER* 1.3 83.0 + - - +
295A LEU* 1.3 60.1 + - - +
296A VAL* 3.0 28.0 + - + +
303A VAL* 3.8 27.6 - - + -
304A GLU 3.3 4.7 - - - +
305A ALA* 4.1 3.8 - - + -
338A ARG* 4.0 35.7 - - + +
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Residues in contact with LEU 295 (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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100A ARG* 3.7 29.2 - - + +
103A LEU* 3.9 19.1 - - + -
104A GLY 3.3 27.8 - - - +
105A GLY* 3.5 23.6 - - - +
106A THR 3.7 2.0 - - - -
107A VAL* 3.7 25.6 - - + +
293A SER* 4.4 2.4 + - - -
294A VAL* 1.3 68.2 - - - +
296A VAL* 1.3 59.7 + - - +
297A CYS* 3.5 4.5 + - - -
303A VAL* 3.2 5.5 - - - -
304A GLU* 2.7 56.8 + - + +
306A GLU* 5.3 2.5 - - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 4.1 0.2 - - - -
106A THR 2.9 31.5 + - - -
108A PHE* 3.4 28.5 - - + -
195A SER* 3.0 31.7 + - - +
198A GLN* 4.3 11.9 - - + -
199A MET* 3.6 22.7 - - - +
294A VAL* 3.7 19.3 - - + -
295A LEU* 1.3 68.9 - - - +
297A CYS* 1.3 69.1 + - - +
300A GLY* 5.4 2.2 - - - +
303A VAL* 4.2 14.8 - - + -
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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