Contacts of the strand formed by residues 333 - 341 (chain A) in PDB entry 1QWN
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 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 5.0 0.2 - - - -
82A LYS* 3.3 11.4 - - + +
84A PHE* 3.7 15.0 - - + -
329A TYR* 5.6 4.5 - - - +
331A THR* 3.1 22.7 + - - +
332A ASN* 1.3 90.7 - - - +
334A LEU* 1.3 61.1 + - - +
382A TYR* 3.4 37.9 + - + +
385A ALA* 3.6 45.3 - - + +
386A VAL* 4.1 4.3 - - + -
389A ALA* 4.7 2.5 - - + -
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Residues in contact with LEU 334 (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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81A LEU* 4.2 14.6 - - + -
82A LYS 2.8 14.9 + - - +
83A VAL* 3.6 10.1 - - + +
84A PHE* 2.9 31.0 + - - +
322A TRP* 3.4 36.8 - - + +
325A LYS* 4.1 18.4 - - + +
326A ALA* 3.8 26.9 - - + +
329A TYR* 4.8 11.7 - - + -
333A VAL* 1.3 73.3 - - - +
335A LEU* 1.3 63.4 - - - +
336A ILE* 3.7 27.5 + - + -
382A TYR* 3.7 4.2 - - - -
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Residues in contact with LEU 335 (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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84A PHE 3.9 1.3 - - - +
86A VAL* 3.6 33.7 - - + -
201A TRP* 4.8 1.8 - - + -
225A LEU* 3.4 32.8 - - + -
262A HIS* 3.9 20.4 + - + +
264A MET* 5.3 1.1 - - + -
325A LYS* 2.9 24.1 + - - +
334A LEU* 1.3 75.3 - - - +
336A ILE* 1.3 63.9 + - - +
337A PRO* 3.8 16.8 - - + -
379A LEU* 4.4 9.9 - - + -
382A TYR* 3.4 46.8 + - + +
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Residues in contact with ILE 336 (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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83A VAL* 3.6 25.8 - - + -
84A PHE 2.8 13.4 + - - +
85A VAL* 3.2 17.7 - - + +
86A VAL 2.9 23.2 + - - -
274A THR 3.6 19.5 - - - +
275A CYS* 3.9 9.2 - - + +
322A TRP* 3.6 33.4 - - + +
325A LYS* 3.7 10.1 - - + -
334A LEU* 3.7 14.4 - - + -
335A LEU* 1.3 84.1 - - - +
337A PRO* 1.3 71.8 - - - +
338A LEU* 3.5 3.3 + - + -
357A TYR* 6.0 3.4 - - + +
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Residues in contact with PRO 337 (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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86A VAL* 3.6 11.2 - - + +
88A HIS* 3.8 20.4 - - + +
201A TRP* 3.9 18.8 - - + -
264A MET* 4.2 20.6 - - + -
269A TYR* 4.9 0.4 - - + +
271A ILE* 5.0 0.3 - - - +
274A THR* 3.2 33.7 + - + -
325A LYS* 3.8 12.6 - - - +
335A LEU* 3.6 24.2 - - + +
336A ILE* 1.3 94.9 - - - +
338A LEU* 1.3 61.4 + - - +
339A GLY 4.0 0.7 - - - -
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Residues in contact with LEU 338 (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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85A VAL* 3.8 25.4 - - + -
86A VAL 2.8 12.4 + - - +
87A PRO* 3.2 13.3 - - + +
88A HIS* 3.0 21.7 + - - -
124A MET* 5.9 0.9 - - + -
271A ILE* 3.8 28.9 - - + -
285A PHE 4.2 0.7 - - - +
336A ILE* 5.8 2.7 - - + -
337A PRO* 1.3 76.1 - - - +
339A GLY* 1.3 57.1 + - - +
344A PHE* 3.4 21.6 - - + -
353A GLN* 4.7 10.5 - - + +
357A TYR* 3.3 50.9 - - + +
376A PHE* 4.7 4.7 - - + -
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Residues in contact with GLY 339 (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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88A HIS* 3.2 29.4 + - - -
269A TYR 3.4 16.6 - - - +
270A ASP* 3.6 6.6 - - - -
271A ILE* 3.5 18.9 + - - +
274A THR* 5.4 0.2 + - - -
337A PRO 4.0 0.6 - - - -
338A LEU* 1.3 75.1 - - - +
340A ASP* 1.3 64.0 + - - +
343A ARG* 4.3 2.9 - - - -
344A PHE* 4.4 5.4 - - - -
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Residues in contact with ASP 340 (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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88A HIS* 3.8 3.2 + - - -
89A SER* 3.6 1.6 - - - -
90A HIS* 3.0 21.8 + - - -
269A TYR* 3.9 9.3 - - - -
270A ASP* 3.4 23.7 - - + +
271A ILE* 4.8 1.5 + - + +
286A ASP* 5.1 0.2 - - - +
289A ARG* 4.0 14.0 + - - -
339A GLY* 1.3 74.4 - - - +
341A ASP* 1.3 81.7 + - - +
342A PHE 3.3 0.5 + - - -
343A ARG* 3.4 39.1 + - + +
2004A TRS 2.7 31.4 + - - -
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Residues in contact with ASP 341 (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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90A HIS* 3.4 14.3 - - - +
92A ASP* 4.5 2.5 - - - +
95A TRP* 4.2 8.5 - - - -
269A TYR* 2.6 28.6 + - - -
340A ASP* 1.3 82.6 + - - +
342A PHE* 1.3 77.9 + - + +
343A ARG* 3.0 9.0 + - - +
2003A GUL 3.7 9.5 + - - -
2004A TRS 2.7 36.2 + - - +
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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