Contacts of the strand formed by residues 379 - 385 (chain A) in PDB entry 1W21
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A THR* 3.6 1.4 - - - -
373A ILE 3.0 15.4 + - - -
374A SER* 3.2 17.0 + - - -
377A SER* 2.8 11.2 + - - -
378A ARG* 1.3 74.8 - - - +
380A GLY* 1.3 68.2 + - - +
406A ASN* 2.7 28.4 + - - -
408A ASN 3.4 12.1 - - - -
409A TRP* 3.9 7.6 - - - -
410A SER* 3.4 1.7 + - - -
1478A SIA 3.5 30.4 + - - -
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Residues in contact with GLY 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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372A THR* 3.3 7.1 - - - -
373A ILE* 3.5 5.8 - - - -
379A SER* 1.3 79.1 - - - +
381A TYR* 1.3 63.2 + - - +
404A VAL* 3.0 17.3 - - - -
405A ASN 3.3 14.1 - - - -
406A ASN* 3.6 6.4 - - - +
408A ASN 2.7 14.5 + - - -
410A SER* 2.9 19.4 + - - -
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Residues in contact with TYR 381 (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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358A GLY* 4.9 0.7 - - - -
359A PHE* 3.1 19.2 + + - -
370A GLY* 3.2 18.3 + - - -
371A ARG* 3.4 33.5 - - - -
372A THR* 3.9 8.5 - - + -
373A ILE* 3.5 5.2 - - - +
380A GLY* 1.3 77.7 - - - +
382A GLU* 1.3 77.6 + - - +
383A MET* 4.1 10.1 - - - -
402A VAL* 3.8 2.4 - - - +
403A ILE* 2.8 33.8 + - + -
404A VAL* 2.7 33.8 + - + +
410A SER* 4.4 5.2 - - - -
411A GLY 4.7 3.4 - - - -
413A SER* 2.7 37.1 + - - -
430A PHE* 4.6 0.4 - + - -
432A VAL* 3.9 30.1 - - + -
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Residues in contact with GLU 382 (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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369A LEU 3.9 0.5 - - - +
370A GLY* 3.4 3.5 - - - -
371A ARG* 2.8 77.6 + - + +
372A THR 3.8 6.1 - - - +
373A ILE* 3.9 25.5 - - + +
381A TYR* 1.3 80.2 - - - +
383A MET* 1.3 62.4 + - - +
384A LEU* 4.1 12.8 - - + -
401A GLN 3.6 8.5 - - - +
402A VAL* 4.7 1.3 - - - -
403A ILE 4.4 0.2 - - - +
1485A MAN 3.5 6.0 + - - -
1487A MAN 2.6 44.5 + - - +
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Residues in contact with MET 383 (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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103A TRP* 3.6 46.2 - - + +
359A PHE* 3.6 37.2 - - + -
368A TRP* 3.8 21.3 - - + -
369A LEU 3.5 0.9 - - - -
370A GLY* 3.7 17.3 - - - +
381A TYR* 4.1 4.3 - - - -
382A GLU* 1.3 73.5 - - - +
384A LEU* 1.3 62.2 + - - +
400A ASN* 3.2 5.9 - - - -
401A GLN* 2.9 36.4 + - + +
403A ILE* 3.8 12.6 - - + -
430A PHE* 3.7 26.2 - - + -
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Residues in contact with LEU 384 (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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328A VAL* 3.8 18.6 - - + -
368A TRP* 3.4 3.8 - - - -
369A LEU* 2.8 44.4 + - + +
371A ARG* 3.7 37.5 - - + +
382A GLU* 3.8 11.2 - - + +
383A MET* 1.3 83.3 - - - +
385A LYS* 1.3 61.5 + - - +
386A VAL* 3.4 15.3 + - + +
397A PRO* 4.3 10.1 - - + -
399A SER 3.6 4.0 - - - +
400A ASN* 3.6 13.9 - - + -
1485A MAN 3.3 31.0 - - - +
1487A MAN 3.8 5.2 - - - +
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Residues in contact with LYS 385 (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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99A GLU* 5.4 2.0 - - - +
100A VAL 3.0 24.6 + - - +
101A ASN* 3.0 19.0 + - - +
365A GLU 3.8 20.6 - - - +
366A ASN* 4.3 9.8 + - - +
367A SER 3.3 14.6 - - - +
368A TRP* 3.5 29.1 - - + +
384A LEU* 1.3 70.4 - - - +
386A VAL* 1.3 57.4 + - - +
387A PRO* 3.4 3.1 - - + +
397A PRO* 3.3 1.9 - - - +
398A ILE* 2.9 51.3 + - + +
399A SER* 3.0 29.4 + - - +
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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