Contacts of the strand formed by residues 357 - 367 (chain A) in PDB entry 3CMQ
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 VAL 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ILE* 4.3 10.4 - - + +
294A ARG* 3.2 21.1 + - - -
349A VAL* 3.9 29.4 - - + -
350A ARG* 4.7 4.3 + - - +
353A GLY* 3.9 17.0 - - - -
354A GLY 3.6 8.6 + - - +
355A ASP 3.3 0.4 - - - -
356A LEU* 1.3 78.8 - - - +
358A GLU* 1.3 62.4 + - - +
359A LYS 3.7 15.7 - - - +
360A VAL* 4.1 5.6 - - + -
380A ILE* 3.9 14.8 - - + -
381A THR 3.7 8.7 - - - +
382A TYR* 3.8 27.1 - - + +
401A LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 358 (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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147A ILE* 4.0 3.6 - - - +
148A ASP* 3.2 22.0 + - - -
149A SER* 4.6 10.2 - - - +
292A ASP* 4.1 12.1 - - - +
294A ARG* 3.6 22.9 + - - +
323A LYS* 4.2 9.4 + - - -
356A LEU 3.7 1.8 + - - -
357A VAL* 1.3 74.2 - - - +
359A LYS* 1.3 73.6 + - + +
381A THR* 2.8 25.1 + - + +
383A ARG* 2.7 51.8 + - + -
385A MET* 5.7 0.9 - - - +
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Residues in contact with LYS 359 (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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147A ILE* 3.2 17.7 - - - +
148A ASP* 3.7 17.9 - - + +
149A SER 5.0 0.2 - - - +
357A VAL* 3.6 2.1 - - - +
358A GLU* 1.3 93.5 - - + +
360A VAL* 1.3 66.8 + - - +
361A ASP* 3.3 35.8 + - - +
379A ARG 3.7 1.4 - - - +
381A THR* 3.0 48.3 + - + +
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Residues in contact with VAL 360 (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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146A GLN* 5.6 2.1 - - - +
147A ILE* 3.1 27.8 + - + +
345A PHE* 4.2 6.1 - - + -
346A TYR* 3.7 34.5 + - + -
349A VAL* 4.0 28.9 - - + -
357A VAL* 4.1 7.4 - - + -
359A LYS* 1.3 79.2 - - - +
361A ASP* 1.3 71.5 + - - +
362A LEU 4.3 0.2 + - - -
378A TYR* 3.8 27.1 - - + -
379A ARG 3.5 4.3 - - - +
380A ILE* 4.1 12.6 - - + -
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Residues in contact with ASP 361 (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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359A LYS* 3.3 35.7 + - + +
360A VAL* 1.3 79.9 - - - +
362A LEU* 1.3 61.4 + - - +
363A ILE* 3.2 17.8 + - + +
378A TYR* 3.1 5.4 - - - -
379A ARG* 2.6 45.3 + - + +
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Residues in contact with LEU 362 (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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342A GLU* 3.7 25.6 - - - +
346A TYR* 4.3 8.0 + - - +
360A VAL 4.3 0.6 + - - -
361A ASP* 1.3 69.5 + - - +
363A ILE* 1.3 59.5 + - - +
364A ASP 3.6 17.0 - - - +
365A LYS* 3.5 29.6 - - + +
376A HIS* 3.5 29.8 - - + +
377A CYS 3.6 16.4 - - - +
378A TYR* 3.6 20.9 - - + -
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Residues in contact with ILE 363 (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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330A ASP* 4.1 5.6 - - - +
361A ASP* 3.2 19.7 + - + +
362A LEU* 1.3 74.8 - - - +
364A ASP* 1.3 64.1 + - + +
377A CYS* 2.9 36.3 + - + +
379A ARG* 3.9 48.2 - - + +
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Residues in contact with ASP 364 (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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362A LEU* 3.6 6.8 - - - +
363A ILE* 1.3 86.8 - - + +
365A LYS* 1.3 77.3 + - - +
366A PHE* 3.8 22.3 - - - +
375A SER 4.2 0.7 - - - -
376A HIS* 3.5 1.2 - - - -
377A CYS* 2.8 44.5 + - + +
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Residues in contact with LYS 365 (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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342A GLU* 4.8 4.4 + - - -
362A LEU* 3.5 29.0 - - + +
364A ASP* 1.3 86.1 + - - +
366A PHE* 1.3 65.9 + - - +
374A THR* 4.9 3.6 - - + -
375A SER 2.9 12.6 - - - +
376A HIS* 3.9 22.7 + - + +
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Residues in contact with PHE 366 (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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334A TRP* 3.8 19.7 - + - -
364A ASP* 3.8 24.5 - - - +
365A LYS* 1.3 75.6 - - - +
367A VAL* 1.3 75.8 + - - +
368A HIS* 4.5 8.1 - - + -
374A THR* 3.3 4.0 - - - +
375A SER* 2.7 58.9 + - - +
414A ARG* 3.5 29.6 - - - -
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Residues in contact with VAL 367 (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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366A PHE* 1.3 85.9 - - - +
368A HIS* 1.3 68.5 + - - +
369A PRO* 3.6 7.7 - - + +
372A HIS* 3.5 29.6 - - - +
373A LYS 3.2 4.3 - - - +
374A THR* 3.8 17.7 - - + +
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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