Contacts of the strand formed by residues 293 - 298 (chain A) in PDB entry 4MQP
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 ALA 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.6 9.0 - - - -
121A SER* 2.9 31.0 + - - +
123A SER 3.3 33.4 - - - +
124A GLY* 4.0 3.1 - - - +
127A SER* 3.9 10.1 - - - +
281A VAL 3.3 15.5 - - - +
282A GLY* 4.3 1.8 - - - -
285A LEU* 3.9 7.4 - - - -
292A LEU* 1.3 76.5 - - - +
294A ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 294 (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 LEU* 4.2 5.4 - - + -
118A VAL* 4.0 14.4 - - + -
119A PHE 3.4 8.3 - - - +
120A PHE* 3.9 19.7 - - + -
121A SER 4.6 0.7 - - - +
127A SER* 3.9 4.1 - - - -
279A MET 3.8 0.6 - - - +
280A CYS* 3.4 3.3 - - - -
281A VAL* 2.9 50.5 + - + +
285A LEU* 4.7 1.1 - - + -
293A ALA* 1.3 76.5 - - - +
295A THR* 1.3 63.8 + - - +
296A LEU* 4.4 3.4 - - + -
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Residues in contact with THR 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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117A THR 3.9 0.7 - - - +
118A VAL* 3.7 0.5 - - - -
119A PHE* 2.8 35.6 + - - +
121A SER* 5.1 0.3 + - - -
127A SER* 2.8 32.1 + - - +
130A VAL* 3.8 15.7 - - - +
131A ALA* 3.8 22.7 - - + +
134A MET* 3.8 14.1 - - + +
278A ILE* 3.6 29.2 - - + -
279A MET 3.2 6.5 - - - +
280A CYS* 4.4 1.1 - - - -
294A ALA* 1.3 71.3 - - - +
296A LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 296 (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 LEU* 4.0 17.9 - - + +
108A VAL* 4.4 0.7 - - + +
111A THR* 3.7 29.8 - - + +
115A LEU* 3.8 25.0 - - + +
117A THR 3.1 5.2 - - - +
118A VAL* 3.8 27.6 - - + -
278A ILE* 3.2 6.5 - - - +
279A MET* 2.8 44.6 + - + +
281A VAL* 4.1 30.1 - - + -
294A ALA* 4.4 6.1 - - + -
295A THR* 1.3 79.2 - - - +
297A CYS* 1.3 63.1 + - - +
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Residues in contact with CYS 297 (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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115A LEU* 3.8 7.0 - - - -
116A ASP 3.1 20.1 + - - -
117A THR* 2.9 41.5 + - - -
134A MET* 4.1 11.2 - - - -
277A ASP 3.4 12.1 - - - +
278A ILE* 4.0 6.1 - - + -
296A LEU* 1.3 77.3 - - - +
298A THR* 1.3 71.9 + - - +
301A VAL* 3.8 22.4 - - + -
302A ALA 3.9 2.0 - - - -
22B TRP* 3.8 24.9 - - - -
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Residues in contact with THR 298 (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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114A GLY* 3.2 25.6 - - - +
115A LEU* 4.2 1.1 - - + -
116A ASP* 4.8 1.1 - - - -
117A THR* 4.9 0.4 - - - -
275A SER* 6.3 0.4 - - - -
276A PRO 4.0 8.1 - - - +
277A ASP* 3.2 29.2 + - - +
297A CYS* 1.3 81.8 - - - +
299A ALA* 1.3 65.1 + - - +
300A ASP* 3.6 8.0 + - - +
301A VAL* 3.1 26.7 + - - +
302A ALA* 3.0 20.4 + - - +
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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