Contacts of the helix formed by residues 358 - 373 (chain A) in PDB entry 1WDR
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 GLY 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A HIS* 3.0 14.3 + - - -
303A TYR* 3.9 9.6 - - - +
304A LYS* 3.9 11.0 - - - -
348A ASP* 3.7 0.9 - - - -
356A LYS 3.9 1.4 + - - -
357A SER* 1.3 72.9 - - - +
359A PRO* 1.3 65.2 - - - +
360A GLN 3.2 3.2 + - - -
361A GLU* 3.3 18.3 + - - +
362A LEU* 2.9 24.8 + - - +
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Residues in contact with PRO 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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300A HIS* 3.7 19.5 - - + -
343A CYS* 4.2 9.2 - - + +
346A MET* 3.7 39.5 - - + +
347A ARG 4.1 6.3 - - - -
348A ASP* 3.0 15.0 - - - +
351A GLN* 4.1 11.2 - - + +
357A SER* 3.1 18.8 - - - +
358A GLY* 1.3 86.9 - - - +
360A GLN* 1.3 61.5 + - - +
362A LEU* 3.7 3.5 - - + +
363A VAL* 2.9 30.3 + - - +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A MET 3.6 19.5 - - - +
347A ARG* 3.3 40.7 + - - +
348A ASP* 2.8 42.2 + - - +
349A SER 4.6 0.9 + - - -
359A PRO* 1.3 78.0 - - - +
361A GLU* 1.3 64.8 + - - +
363A VAL* 3.5 5.9 + - - +
364A GLN* 3.0 27.5 + - - +
393A GLN* 3.8 12.3 + - - +
396A LEU* 5.9 0.8 - - - +
397A ASN* 5.3 2.6 - - - +
485A TRP* 5.6 1.4 + - - -
2003A SO4 5.0 1.7 + - - -
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Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 3.6 24.7 + - + +
304A LYS* 3.9 14.9 + - - -
348A ASP* 2.4 33.6 - - - +
358A GLY* 3.5 8.4 - - - +
360A GLN* 1.3 78.4 - - + +
362A LEU* 1.3 60.5 + - - +
364A GLN* 3.3 20.2 + - - +
365A GLN* 2.9 29.3 + - - +
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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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298A GLY* 4.0 3.4 - - - -
299A ILE 3.7 40.4 - - - +
300A HIS* 3.9 10.5 - - + -
303A TYR* 3.7 26.1 - - + -
325A TYR* 3.6 38.1 - - + +
341A PHE* 3.7 17.5 - - + -
343A CYS* 5.0 2.2 - - - -
358A GLY 2.9 17.0 + - - +
359A PRO* 3.7 4.5 - - + +
361A GLU* 1.3 75.1 - - - +
363A VAL* 1.3 65.6 + - - +
365A GLN* 3.1 3.3 + - - +
366A VAL* 2.9 34.1 + - + +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 3.8 10.8 - - + -
342A SER 3.5 24.9 - - - +
343A CYS* 3.7 22.2 - - + +
344A LEU* 4.1 5.6 - - + +
359A PRO 2.9 21.6 + - - +
360A GLN* 3.8 4.0 - - - +
362A LEU* 1.3 75.0 - - + +
364A GLN* 1.4 65.0 + - - +
366A VAL 3.3 0.2 + - - -
367A LEU* 2.9 45.6 + - + +
397A ASN* 3.5 34.3 - - - +
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Residues in contact with GLN 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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360A GLN 3.0 18.2 + - - +
361A GLU* 3.6 20.0 + - - +
363A VAL* 1.4 77.7 - - - +
365A GLN* 1.3 61.3 + - - +
368A SER* 2.8 31.9 + - - -
482A PRO* 3.5 30.3 - - + +
483A PHE 2.9 18.5 - - - +
484A PRO* 4.3 1.4 - - - +
485A TRP* 3.6 47.4 + - + +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 2.7 28.4 + - - +
318A ASN* 2.9 39.8 + - - -
319A LEU 5.6 0.8 + - - -
323A ASP* 3.1 34.5 + - - +
325A TYR* 3.6 11.1 - - + +
361A GLU 2.9 13.4 + - - +
362A LEU* 3.1 8.4 + - - +
364A GLN* 1.3 80.1 - - - +
366A VAL* 1.3 58.7 + - - +
368A SER* 3.7 3.4 - - - -
369A GLY* 2.9 26.2 + - - -
482A PRO* 5.0 5.6 - - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 5.6 0.4 - - + -
325A TYR* 3.6 42.6 - - + +
339A LEU* 4.0 26.8 - - + +
341A PHE* 3.6 50.0 - - + -
362A LEU* 2.9 22.4 + - + +
363A VAL 4.1 0.2 - - - +
365A GLN* 1.3 73.1 - - + +
367A LEU* 1.3 68.3 + - + +
369A GLY* 3.2 2.8 + - - -
370A GLY* 3.0 19.1 + - - -
377A VAL* 4.9 1.9 - - + +
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Residues in contact with LEU 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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341A PHE* 4.3 18.8 - - + -
344A LEU* 4.8 1.1 - - + -
363A VAL* 2.9 42.8 + - + +
366A VAL* 1.3 76.0 - - - +
368A SER* 1.3 63.8 + - - +
370A GLY* 3.2 2.8 + - - -
371A TRP* 3.0 45.2 + - + -
377A VAL* 3.7 30.8 - - + +
397A ASN* 3.8 12.8 - - + +
413A MET* 3.8 33.4 - - + -
485A TRP* 3.9 13.7 - - + -
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLN 2.8 22.7 + - - -
365A GLN* 3.7 3.6 - - - -
367A LEU* 1.3 78.4 - - - +
369A GLY* 1.3 57.0 - - - +
371A TRP* 3.3 2.9 + - - -
372A ARG* 2.8 30.8 + - - +
480A THR* 6.2 0.7 - - - -
481A LEU 5.1 0.9 - - - -
482A PRO* 3.6 12.1 - - - +
483A PHE* 3.0 49.3 + - - -
485A TRP* 3.8 8.8 - - - -
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Residues in contact with GLY 369 (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 ASP* 5.4 2.5 - - - -
325A TYR* 6.6 0.2 - - - -
326A ARG* 3.8 28.2 - - - +
329A ALA* 4.3 3.4 - - - -
365A GLN 2.9 15.3 + - - -
366A VAL* 3.2 3.5 + - - -
368A SER* 1.3 76.9 - - - +
370A GLY* 1.3 62.1 + - - +
372A ARG* 3.3 3.0 + - - +
373A GLU* 3.0 30.0 + - - +
480A THR* 5.7 2.7 - - - -
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Residues in contact with GLY 370 (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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329A ALA* 3.9 9.9 - - - +
339A LEU* 5.3 1.3 - - - -
366A VAL 3.0 11.8 + - - -
367A LEU 3.2 2.9 + - - -
369A GLY* 1.3 76.9 - - - +
371A TRP* 1.3 60.2 + - - +
373A GLU 3.2 1.9 + - - -
374A ASP 3.1 5.0 + - - -
375A ILE* 3.0 49.4 + - - +
377A VAL* 3.8 10.8 - - - -
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Residues in contact with TRP 371 (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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367A LEU* 3.0 41.2 + - + +
370A GLY* 1.3 75.2 - - - +
372A ARG* 1.3 61.7 + - - +
374A ASP* 3.0 14.9 + - - +
375A ILE 3.8 15.5 - - - +
376A ARG* 5.5 0.4 - - - +
377A VAL* 4.0 17.6 - - + +
397A ASN 4.4 1.1 - - - -
400A PRO* 3.7 29.4 - - + -
411A LEU* 3.8 30.3 - - + -
412A SER 3.5 37.7 + - - +
413A MET* 3.8 11.0 - - + -
483A PHE* 3.8 26.5 - + + -
485A TRP* 3.8 22.0 - + - -
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Residues in contact with ARG 372 (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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326A ARG* 4.1 22.9 - - - +
368A SER 2.8 21.3 + - - +
369A GLY* 3.6 8.5 - - - +
370A GLY 3.3 0.2 - - - -
371A TRP* 1.3 74.4 - - - +
373A GLU* 1.3 59.6 + - - +
374A ASP* 3.3 2.3 + - - +
480A THR* 3.7 20.1 - - + +
481A LEU 4.7 4.2 + - - -
483A PHE* 4.2 13.1 - - + -
2000A SO4 3.0 26.4 + - - +
2004A SO4 3.0 41.8 + - - -
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 2.8 53.2 + - + +
329A ALA* 4.1 13.0 - - + +
330A ARG* 2.8 49.6 + - - +
333A SER* 4.4 8.4 + - - -
369A GLY 3.0 20.1 + - - +
370A GLY 3.2 4.4 + - - +
372A ARG* 1.3 76.6 - - - +
374A ASP* 1.3 69.5 + - - +
375A ILE* 3.3 8.0 + - + +
2000A SO4 3.9 0.9 + - - -
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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