Contacts of the helix formed by residues 346 - 367 (chain A) in PDB entry 1HXK
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 GLN 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 4.2 0.9 - - - +
288A LYS* 4.1 15.3 - - - +
292A SER 5.6 0.5 - - - +
293A PHE* 3.4 35.4 + - - +
345A LYS* 1.3 90.6 - - + +
347A ASN* 1.3 65.8 + - - +
348A THR* 3.7 14.6 + - - +
349A GLU* 2.9 20.6 + - + +
350A TRP* 3.1 16.0 + - - -
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Residues in contact with ASN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.1 29.9 + - - +
116A ARG* 4.9 11.4 - - - +
117A HIS* 2.9 32.0 + - + +
345A LYS 3.8 1.8 + - - -
346A GLN* 1.3 71.8 - - - +
348A THR* 1.3 65.7 + - + +
350A TRP* 3.1 6.7 + - - +
351A ASP* 3.1 28.2 + - - +
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.4 25.1 - - - -
346A GLN* 3.7 12.1 + - - +
347A ASN* 1.3 79.9 - - + +
349A GLU* 1.3 57.7 + - - +
351A ASP* 3.4 11.3 + - - +
352A VAL* 3.0 29.8 + - - +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 2.8 40.1 + - + +
293A PHE* 3.9 14.8 - - + -
343A ARG* 3.2 22.0 + - - +
344A PHE* 2.7 38.7 + - + -
345A LYS 3.1 9.8 + - - +
346A GLN* 2.9 14.9 + - + +
348A THR* 1.3 79.3 + - - +
350A TRP* 1.3 66.2 + - - +
352A VAL* 3.2 8.1 - - - +
353A GLN* 3.1 35.5 + - + +
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Residues in contact with TRP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 3.8 14.9 - - + +
114A ALA* 3.3 36.3 - - + -
117A HIS* 3.5 42.6 - + + +
118A LEU* 4.3 9.2 - - + -
124A MET* 3.9 36.8 - - + -
125A LYS 4.8 0.2 - - - -
126A PHE* 3.9 28.0 - + + -
344A PHE* 2.8 58.7 + + + -
346A GLN 3.1 24.1 + - - -
347A ASN 3.1 7.7 + - - +
349A GLU* 1.3 75.4 - - - +
351A ASP* 1.3 59.0 + - - +
353A GLN* 4.1 0.9 - - - +
354A ARG* 3.0 36.4 + - + +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 3.6 18.3 + - - -
347A ASN* 3.1 19.9 + - - +
348A THR* 3.6 12.0 - - - +
350A TRP* 1.3 76.4 - - - +
352A VAL* 1.3 58.3 + - - +
354A ARG* 3.6 20.3 + - - +
355A VAL* 2.9 44.2 + - + +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 3.5 23.0 - - + +
288A LYS* 4.3 4.7 - - - +
290A MET* 3.4 33.4 - - + -
293A PHE* 4.5 8.7 - - + -
305A THR* 5.8 0.2 - - - +
348A THR 3.0 16.0 + - - +
349A GLU* 3.2 17.0 - - - +
351A ASP* 1.3 76.5 - - - +
353A GLN* 1.3 69.5 + - + +
355A VAL* 5.1 0.7 - - - -
356A ASN* 2.7 42.3 + - - +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 5.5 0.9 - - + -
271A ILE* 3.8 12.1 - - - +
286A ASP* 3.1 25.8 + - - -
287A PHE* 3.1 30.2 + - - +
288A LYS* 3.9 7.7 - - - +
338A LEU* 4.6 12.1 - - + +
343A ARG* 3.7 12.3 - - - +
344A PHE* 4.0 30.6 - - + -
349A GLU* 3.1 23.0 + - + +
350A TRP 4.2 0.2 - - - +
352A VAL* 1.3 85.4 - - + +
354A ARG* 1.3 62.6 + - - +
357A TYR* 3.1 37.3 + - - +
376A PHE* 5.2 0.9 - - - -
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Residues in contact with ARG 354 (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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117A HIS* 5.2 5.5 + - - -
121A ASN* 3.1 46.1 + - - +
124A MET* 4.2 32.0 - - + +
350A TRP* 3.0 20.6 + - + +
351A ASP* 3.6 21.4 + - - +
353A GLN* 1.3 78.0 - - - +
355A VAL* 1.3 77.2 + - - +
357A TYR* 3.8 0.9 - - - -
358A GLU* 2.8 83.9 + - + +
376A PHE* 3.9 12.0 - - + -
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Residues in contact with VAL 355 (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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351A ASP* 2.9 30.0 + - + +
352A VAL* 4.8 1.6 - - - +
354A ARG* 1.3 97.2 - - - +
356A ASN* 1.3 64.0 + - - +
358A GLU* 3.2 11.7 + - - +
359A ARG* 3.1 61.4 + - + +
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Residues in contact with ASN 356 (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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287A PHE* 3.4 39.6 - - + -
290A MET* 4.8 0.8 - - - +
305A THR* 3.7 8.6 - - - +
306A ILE* 2.8 31.7 + - + +
352A VAL* 2.7 41.8 + - - +
354A ARG 3.4 0.4 - - - -
355A VAL* 1.3 77.2 - - - +
357A TYR* 1.3 64.2 + - - +
359A ARG* 3.3 21.4 + - - +
360A LEU* 3.1 25.7 + - - +
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Residues in contact with TYR 357 (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* 4.4 16.6 - - + -
271A ILE* 4.7 2.3 - - - +
275A CYS* 5.7 2.9 - - - +
285A PHE* 2.7 41.0 + - + +
287A PHE* 3.6 19.1 - + - -
318A LEU* 4.4 20.1 - - + +
322A TRP* 4.9 2.5 - + - -
336A ILE* 5.9 3.2 - - + +
338A LEU* 3.4 33.1 - - + +
353A GLN* 3.1 30.0 + - - +
356A ASN* 1.3 74.8 - - - +
358A GLU* 1.3 60.4 + - - +
360A LEU* 3.1 9.8 + - + +
361A PHE* 2.8 58.8 + + + -
376A PHE* 3.6 22.2 - + + -
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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
----------------------------------------------------------
121A ASN* 4.7 2.4 + - - +
123A GLU* 6.0 2.3 - - - +
354A ARG* 2.8 66.5 + - + +
355A VAL* 3.5 9.3 - - - +
357A TYR* 1.3 77.7 - - - +
359A ARG* 1.3 57.4 + - + +
361A PHE* 3.4 9.6 + - + +
362A GLU* 3.0 30.2 + - - +
376A PHE* 4.2 12.0 - - + -
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Residues in contact with ARG 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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305A THR* 3.6 12.1 - - - +
306A ILE* 2.9 44.7 + - + -
307A SER* 4.8 4.0 - - - +
308A ASP* 5.8 3.4 - - - +
311A VAL* 3.7 5.8 - - + +
355A VAL* 3.1 39.2 + - + +
356A ASN* 3.4 24.5 + - - +
357A TYR 3.2 0.2 - - - -
358A GLU* 1.3 78.5 - - + +
360A LEU* 1.3 60.0 + - - +
362A GLU* 3.6 7.7 + - - +
363A HIS* 3.2 23.2 + - - +
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Residues in contact with LEU 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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285A PHE* 3.9 17.9 - - + -
287A PHE* 4.3 5.4 - - + -
306A ILE* 4.0 26.9 - - + -
311A VAL* 4.4 7.0 - - + -
314A ARG* 4.1 4.5 - - + -
315A SER* 3.6 33.0 - - - +
318A LEU* 3.9 23.8 - - + -
356A ASN 3.1 14.2 + - - +
357A TYR* 3.1 22.1 + - + +
359A ARG* 1.3 77.0 - - - +
361A PHE* 1.3 61.0 + - + +
363A HIS* 3.4 1.4 + - - +
364A ILE* 2.9 43.6 + - + +
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Residues in contact with PHE 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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85A VAL* 3.6 37.7 - - + -
322A TRP* 4.2 8.5 - + - -
357A TYR* 2.8 38.4 + + + +
358A GLU* 3.7 10.1 - - + +
360A LEU* 1.3 75.7 - - + +
362A GLU* 1.3 65.5 + - - +
364A ILE* 4.6 1.8 - - + -
365A ASN* 2.9 36.7 + - - +
374A ALA* 3.7 32.3 - - + +
375A GLN* 4.0 10.5 - - - -
376A PHE* 3.7 43.5 - + - -
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Residues in contact with GLU 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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358A GLU 3.0 17.7 + - - +
359A ARG* 3.8 7.7 - - - +
360A LEU 3.3 0.2 - - - -
361A PHE* 1.3 77.7 - - - +
363A HIS* 1.3 60.0 + - - +
365A ASN* 4.2 2.2 - - - +
366A SER* 2.9 27.9 + - - +
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Residues in contact with HIS 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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311A VAL* 3.4 40.2 - - + +
312A ALA* 3.3 28.1 - - + +
315A SER* 3.3 28.0 - - - -
359A ARG 3.2 5.0 + - - +
360A LEU 3.8 1.6 - - - +
362A GLU* 1.3 76.7 - - - +
364A ILE* 1.3 65.7 + - - +
366A SER* 2.8 19.6 + - - -
367A GLN* 3.0 47.9 + - + +
369A HIS* 5.4 1.2 + - - -
370A PHE* 4.2 6.6 - + - -
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Residues in contact with ILE 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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315A SER* 3.5 28.7 - - - +
318A LEU* 4.8 4.3 - - + -
319A VAL* 3.6 26.2 - - + -
322A TRP* 3.8 22.2 - - + -
360A LEU* 2.9 34.3 + - + +
361A PHE* 4.1 3.4 - - + +
363A HIS* 1.3 71.7 - - - +
365A ASN* 1.3 66.6 + - - +
367A GLN* 3.2 21.3 + - - +
370A PHE* 3.9 14.3 - - + +
372A VAL* 3.8 37.4 - - + +
374A ALA* 5.1 0.9 - - + -
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Residues in contact with ASN 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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80A LYS* 5.7 2.9 + - - -
361A PHE* 2.9 29.5 + - - +
362A GLU* 4.5 2.5 - - - +
364A ILE* 1.3 74.9 - - - +
366A SER* 1.3 57.6 + - - +
367A GLN 3.4 1.4 - - - -
368A ALA* 5.3 0.7 + - - -
372A VAL 3.5 10.0 - - - +
373A GLN* 3.2 33.8 - - - +
374A ALA* 2.8 51.9 + - - +
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Residues in contact with SER 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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362A GLU* 2.9 17.4 + - - +
363A HIS* 2.8 21.9 + - - -
365A ASN* 1.3 76.9 - - - +
367A GLN* 1.3 71.4 + - - +
368A ALA* 3.5 5.5 + - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A HIS* 3.0 51.3 + - + +
364A ILE 3.2 10.1 + - - +
365A ASN 5.0 1.1 - - - -
366A SER* 1.3 87.2 + - - +
368A ALA* 1.3 66.4 + - - +
369A HIS* 3.2 26.5 + - - +
370A PHE* 3.0 29.6 + - + +
371A ASN 4.0 1.0 + - - -
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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
------------------------------------------------------------
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