Contacts of the strand formed by residues 373 - 380 (chain A) in PDB entry 1B4V
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 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TRP* 3.9 13.0 - - + -
173A PHE* 5.9 0.3 - - - +
327A ALA* 3.8 6.3 - - + -
328A ARG 3.6 4.9 - - - +
329A ALA* 5.4 0.7 - - - -
330A ASN* 4.0 0.4 - - - -
336A THR* 3.4 17.9 + - - +
340A GLN* 5.0 1.6 + - - +
365A MET* 3.5 31.5 - - - +
371A THR* 3.0 20.3 + - - +
372A TRP* 1.3 80.0 - - - +
374A SER* 1.3 71.8 + - - +
375A LEU 4.1 0.2 + - - -
429A ARG* 3.4 37.5 - - + +
432A LEU* 3.8 21.3 - - + -
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Residues in contact with SER 374 (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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173A PHE 4.8 1.7 + - - -
176A VAL* 4.7 2.3 - - - +
177A SER* 3.3 15.1 + - - -
327A ALA* 3.2 6.2 - - - +
328A ARG* 2.9 39.5 + - - -
330A ASN* 2.9 24.6 + - - -
336A THR* 3.8 9.3 - - - +
362A ILE* 6.2 1.1 - - - -
373A VAL* 1.3 72.7 - - - +
375A LEU* 1.3 59.7 + - - +
376A TYR* 3.3 27.1 + - - -
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Residues in contact with LEU 375 (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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76A LEU 4.2 17.0 - - - +
77A GLY* 4.5 13.0 - - - -
325A MET* 3.9 24.5 - - + -
326A THR 3.5 16.2 - - - +
327A ALA* 4.0 11.7 - - + -
362A ILE* 3.8 2.8 - - - +
363A ALA* 2.9 52.6 + - + +
364A PRO 4.1 5.2 - - - +
365A MET* 3.9 30.0 - - + -
366A PRO* 6.3 0.7 - - + -
373A VAL 4.0 1.8 + - - -
374A SER* 1.3 72.1 - - - +
376A TYR* 1.3 70.8 + - - +
432A LEU* 4.5 5.4 - - + -
433A PHE* 4.7 1.8 - - + -
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Residues in contact with TYR 376 (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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177A SER* 2.7 36.7 + - - -
325A MET* 3.4 11.7 - - - +
326A THR* 3.0 44.1 + - + +
327A ALA* 4.5 0.7 - - - -
328A ARG* 3.0 40.0 + - + -
348A ILE* 4.1 11.9 - - + -
360A ALA* 4.6 3.4 - - + -
361A GLU 3.3 12.8 - - - +
362A ILE* 4.2 10.3 - - + -
363A ALA* 4.4 1.1 - - - +
374A SER* 3.3 25.2 - - - -
375A LEU* 1.3 80.8 - - - +
377A LEU* 1.3 58.8 + - - +
378A ALA 3.8 1.0 + - - -
417A PHE* 3.4 46.9 - + + -
420A ILE* 5.3 1.9 - - + +
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Residues in contact with LEU 377 (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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323A ASN* 4.0 24.5 - - + +
324A ILE 3.7 4.0 - - - +
325A MET* 3.9 18.8 - - + -
359A PHE 3.9 0.9 - - - +
360A ALA* 3.5 1.8 - - - -
361A GLU* 2.9 61.0 + - - +
363A ALA* 4.7 2.1 - - + +
376A TYR* 1.3 71.9 - - - +
378A ALA* 1.3 74.2 + - - +
379A ILE* 3.9 8.8 + - + +
444A PHE* 4.3 8.7 - - + -
446A TYR* 3.5 38.6 - - + -
447A HIS* 4.6 9.6 - - + +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLY 3.2 4.4 - - - +
323A ASN* 3.4 4.2 - - - -
324A ILE* 2.7 40.3 + - + +
326A THR* 5.7 1.8 - - + -
358A VAL* 4.0 20.9 - - + -
359A PHE 3.8 4.0 - - - -
360A ALA* 4.1 7.4 - - + -
376A TYR 3.8 1.4 - - - -
377A LEU* 1.3 76.9 - - - +
379A ILE* 1.3 60.8 + - - +
380A THR* 4.4 3.8 - - + -
413A ALA* 4.1 21.8 - - + -
417A PHE* 4.4 8.1 - - + -
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Residues in contact with ILE 379 (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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321A ASN* 3.3 24.7 - - - +
322A GLY 3.8 2.5 - - - -
323A ASN* 4.2 11.9 - - - +
351A TRP* 3.4 6.8 - - + -
358A VAL* 3.4 5.4 - - - -
359A PHE* 2.9 43.9 + - + +
361A GLU* 6.3 2.0 - - + +
377A LEU* 4.5 6.7 - - + +
378A ALA* 1.3 76.0 - - - +
380A THR* 1.3 60.3 + - - +
447A HIS* 3.9 16.6 - - + -
483A GLY* 3.6 30.5 - - - +
484A VAL* 3.4 31.6 - - - +
485A ASN* 3.6 12.3 - - - +
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Residues in contact with THR 380 (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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321A ASN 4.0 4.2 - - - +
322A GLY* 2.9 35.4 + - - +
324A ILE* 4.9 0.7 - - + -
351A TRP* 3.6 12.8 - - - -
357A SER 3.7 7.2 - - - -
358A VAL* 4.1 20.2 - - + -
378A ALA* 4.4 6.5 - - + -
379A ILE* 1.3 79.8 - - - +
381A LYS* 1.3 61.9 + - - +
382A ASN* 3.8 2.3 + - - +
409A ALA* 3.2 41.5 - - - +
412A ALA* 4.1 6.7 - - + -
413A ALA* 4.1 9.9 - - + +
481A SER* 4.3 6.2 + - - -
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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