Contacts of the strand formed by residues 357 - 363 (chain B) in PDB entry 3L82
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 TRP 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.4 23.6 - - + -
116A THR* 3.6 27.8 - - - +
117A ALA* 3.6 27.1 + - + +
120A LEU* 4.1 17.9 - - + -
325B LEU* 3.4 25.4 - - + +
327B VAL* 5.6 1.1 - - + -
345B ALA* 4.0 15.9 - - + -
350B LEU* 3.6 44.6 + - + +
351B ASN* 3.4 21.7 + - - -
355B HIS 3.5 14.4 - - - +
356B PRO* 1.3 75.4 - - + +
358B LEU* 1.3 73.4 + - - +
359B VAL* 3.7 16.4 - - + -
376B TRP* 3.8 10.5 - - - -
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 4.4 7.2 - - - -
115A LEU 3.1 35.4 - - - +
116A THR* 4.3 12.1 - - + -
325B LEU 3.2 4.5 + - - +
326B LEU* 3.8 12.3 - - + +
327B VAL* 2.9 28.5 + - - +
357B TRP* 1.3 80.8 - - - +
359B VAL* 1.3 76.3 + - - +
360B GLN* 4.7 11.0 - - + +
372B ASN 5.3 0.7 - - - +
373B GLY* 4.9 3.1 - - - -
376B TRP* 3.4 57.7 - - + +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 3.1 8.2 - - - -
115A LEU* 2.9 40.4 + - + +
327B VAL* 3.4 18.2 - - + +
329B SER* 3.2 26.2 - - - +
341B CYS* 4.0 19.3 - - + +
344B LEU* 5.1 4.5 - - + -
345B ALA* 4.3 11.9 - - + +
350B LEU* 3.9 17.9 - - + -
357B TRP* 3.7 22.0 - - + -
358B LEU* 1.3 78.6 - - - +
360B GLN* 1.3 60.9 + - - +
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 3.6 16.2 + - - -
114A SER* 4.0 11.5 - - - -
326B LEU* 4.5 8.7 - - + -
327B VAL 3.0 9.4 + - - +
328B LEU* 3.5 8.5 - - + -
329B SER* 3.0 23.6 + - - -
358B LEU* 4.7 6.7 - - + +
359B VAL* 1.3 75.6 - - - +
361B ASP* 1.3 90.2 + - - +
362B THR* 3.6 4.2 + - - +
369B GLY* 3.4 32.9 - - - +
372B ASN* 3.8 20.5 + - - +
373B GLY* 4.1 17.4 + - - -
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU 3.9 6.3 - - - +
113A SER* 3.0 39.0 + - - +
329B SER* 3.5 9.6 - - - -
338B ARG* 3.6 39.9 + - - +
339B MSE 5.6 0.2 - - - +
340B PRO* 5.9 0.5 - - - +
341B CYS* 3.7 25.7 + - - +
360B GLN* 1.3 87.6 + - - +
362B THR* 1.3 60.9 + - - +
368B THR* 3.6 1.1 - - - +
369B GLY* 3.5 10.7 - - - -
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Residues in contact with THR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.7 10.3 - - + -
328B LEU* 3.3 31.2 - - + +
329B SER 2.8 12.8 + - - +
330B CYS* 3.4 21.6 - - - -
331B ILE* 3.3 27.5 + - - +
338B ARG* 3.7 3.8 + - - -
360B GLN 3.6 2.6 + - - -
361B ASP* 1.3 77.9 + - - +
363B GLU* 1.3 78.9 + - - +
367B LEU* 4.8 0.7 - - - -
368B THR 3.2 12.1 - - - +
369B GLY 4.4 4.0 - - - -
370B PHE* 4.3 20.0 - - + +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ILE* 3.6 22.1 - - + +
332B SER 5.1 0.7 - - - +
333B GLN* 3.9 2.8 - - - +
334B GLY* 3.1 35.8 + - - +
338B ARG* 5.1 2.0 - - - +
362B THR* 1.3 83.1 - - - +
364B ALA* 1.3 60.1 + - - +
365B GLU 4.7 1.1 - - - +
366B THR* 3.3 32.5 + - - +
367B LEU* 2.8 31.9 + - - +
368B THR* 3.2 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