Contacts of the helix formed by residues 310 - 327 (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 ASN 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.6 27.7 - - - +
305A THR 2.9 24.2 + - - -
306A ILE* 3.5 5.5 - - - -
307A SER* 2.8 30.9 + - - +
309A GLN* 1.3 78.4 - - - +
311A VAL* 1.3 70.1 + - - +
312A ALA 3.1 3.4 + - - -
313A ALA* 3.2 11.3 + - + +
314A ARG* 2.9 37.0 + - + +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.7 22.4 - - + -
307A SER 2.9 19.8 + - - +
308A ASP* 3.8 19.5 - - + +
309A GLN 3.7 0.2 - - - -
310A ASN* 1.3 81.2 - - - +
312A ALA* 1.3 59.6 + - + +
314A ARG* 4.3 2.5 - - - -
315A SER* 2.7 42.0 + - - +
359A ARG* 3.8 11.4 - - + +
360A LEU* 4.3 4.3 - - + -
363A HIS* 3.5 39.5 - - + +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASP 5.1 1.2 + - - +
309A GLN 5.4 0.4 - - - -
310A ASN 3.2 1.0 - - - -
311A VAL* 1.3 83.3 - - + +
313A ALA* 1.3 56.4 + - - +
315A SER* 3.8 1.2 - - - -
316A ASP* 2.9 29.3 + - - +
363A HIS* 3.6 26.2 + - + +
370A PHE* 4.8 2.6 - - - -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 6.2 1.6 - - - +
310A ASN* 3.2 11.6 + - + +
312A ALA* 1.3 78.4 - - - +
314A ARG* 1.3 66.2 + - + +
316A ASP* 3.3 8.1 + - - +
317A LEU* 3.1 28.5 + - + +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLN* 2.8 47.3 + - - +
285A PHE* 3.4 23.3 - - + -
302A PRO 4.8 0.8 + - - -
304A ARG* 3.4 49.5 - - - +
306A ILE* 3.6 33.2 - - + -
310A ASN* 2.9 33.0 + - + +
311A VAL* 3.9 3.6 - - - +
313A ALA* 1.3 79.0 - - - +
315A SER* 1.3 56.9 + - - +
317A LEU* 3.2 28.5 + - - +
318A LEU* 3.0 23.4 + - - +
360A LEU* 4.1 6.3 - - + -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 2.7 30.4 + - - +
312A ALA 3.8 2.2 - - - -
314A ARG* 1.3 70.0 - - - +
316A ASP* 1.3 68.0 + - - +
318A LEU* 4.4 1.6 - - - +
319A VAL* 2.8 27.9 + - - +
360A LEU* 3.6 16.9 + - - +
363A HIS* 3.3 25.5 - - - +
364A ILE* 3.6 25.5 - - - +
370A PHE* 4.0 7.2 - - - -
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA 2.9 18.6 + - - +
313A ALA* 3.6 8.7 - - - +
314A ARG 3.3 0.2 - - - -
315A SER* 1.3 79.1 - - - +
317A LEU* 1.3 62.3 + - - +
319A VAL* 4.3 0.7 - - - +
320A ASP* 3.2 23.2 + - - +
369A HIS* 5.1 3.3 - - - -
370A PHE* 3.4 24.1 - - + -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 4.3 35.5 - - + +
284A GLN* 4.9 3.6 - - - +
285A PHE* 4.6 3.1 - - + -
313A ALA* 3.1 19.2 + - + +
314A ARG* 3.2 38.8 - - - +
315A SER 3.2 0.2 - - - -
316A ASP* 1.3 76.6 - - + +
318A LEU* 1.3 63.7 + - - +
320A ASP* 3.4 8.9 + - - +
321A GLN* 3.2 24.4 + - - +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A CYS* 4.1 20.6 - - + -
285A PHE* 3.9 32.7 - - + -
314A ARG 3.0 16.4 + - - +
315A SER* 4.0 4.3 - - - +
317A LEU* 1.3 75.5 - - - +
319A VAL* 1.3 66.0 + - + +
321A GLN* 3.1 8.0 + - - +
322A TRP* 3.0 69.7 + - + +
357A TYR* 4.5 9.4 - - + +
360A LEU* 4.0 30.7 - - + -
364A ILE* 4.6 4.0 - - + -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER 2.8 23.0 + - - +
316A ASP 4.3 0.4 - - - +
318A LEU* 1.3 72.7 - - - +
320A ASP* 1.3 57.4 + - - +
322A TRP* 3.2 14.8 + - + +
323A LYS* 2.8 54.7 + - + +
364A ILE* 3.8 37.7 - - + -
370A PHE* 3.7 30.5 - - + -
372A VAL* 4.0 10.5 - - + -
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 2.6 41.5 + - - +
316A ASP 3.2 20.0 + - - +
317A LEU* 3.6 8.9 - - + +
318A LEU 3.2 0.2 - - - -
319A VAL* 1.3 78.4 - - - +
321A GLN* 1.3 68.0 + - - +
323A LYS 3.4 0.2 + - - -
324A LYS* 2.8 53.8 + - - +
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Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A CYS* 3.6 31.1 - - - +
276A GLY* 3.3 5.4 - - - -
277A PRO* 3.1 14.6 - - - +
278A ASP* 3.0 45.5 + - - +
281A VAL* 3.6 32.5 - - + +
282A CYS* 4.0 0.3 - - - -
317A LEU* 3.2 8.1 + - - +
318A LEU* 3.1 9.0 + - - +
320A ASP* 1.3 88.3 + - - +
322A TRP* 1.3 62.6 + - - +
324A LYS* 3.2 16.4 + - - +
325A LYS* 2.9 20.1 + - - +
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Residues in contact with TRP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.5 5.8 - - + -
83A VAL* 3.8 25.6 - - + -
85A VAL* 4.3 11.9 - - + -
275A CYS* 3.2 21.0 + - - +
318A LEU* 3.0 51.4 + - + +
319A VAL* 3.5 20.6 - - + +
321A GLN* 1.3 75.8 - - - +
323A LYS* 1.3 58.5 + - - +
325A LYS* 3.2 1.8 + - - +
326A ALA* 2.8 25.3 + - - +
334A LEU* 3.4 22.2 - - + +
336A ILE* 3.6 24.8 - - + +
357A TYR* 5.0 4.2 - + - -
361A PHE* 4.4 8.3 - + - -
364A ILE* 4.0 20.6 - - + -
372A VAL* 4.0 11.0 - - + -
374A ALA* 3.7 31.9 - - + -
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Residues in contact with LYS 323 (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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70A TYR* 3.9 42.1 - - + +
72A PRO* 4.8 10.3 + - + +
75A TYR* 4.4 30.8 - - + +
81A LEU* 4.0 14.1 - - + -
319A VAL* 2.8 37.4 + - + +
322A TRP* 1.3 70.4 - - - +
324A LYS* 1.3 65.0 + - - +
326A ALA* 3.4 7.9 + - - +
327A GLU* 3.3 24.8 + - - +
369A HIS 4.7 3.2 + - - -
370A PHE* 2.8 34.1 + - - +
371A ASN* 5.0 1.6 - - - +
372A VAL* 4.0 7.6 - - - -
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.5 47.4 - - + +
70A TYR* 3.7 16.8 - - + -
277A PRO* 3.8 25.4 - - + -
320A ASP* 2.8 48.8 + - - +
321A GLN* 3.6 15.7 - - - +
322A TRP 3.2 0.2 - - - -
323A LYS* 1.3 74.2 - - - +
325A LYS* 1.3 65.8 + - - +
327A GLU* 3.1 18.5 + - - +
328A LEU 4.0 0.7 + - - -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A HIS* 6.1 2.0 + - - -
264A MET* 6.1 2.0 - - - +
265A PRO* 3.9 30.9 - - + +
266A PHE* 3.9 24.2 - - + -
274A THR* 2.8 29.4 + - - +
275A CYS 4.2 3.1 - - - +
276A GLY* 4.2 5.6 - - - -
277A PRO* 4.3 1.0 - - - +
321A GLN 2.9 13.5 + - - +
322A TRP* 3.2 8.3 + - - +
324A LYS* 1.3 74.7 - - - +
326A ALA* 1.3 62.7 + - - +
328A LEU* 3.0 27.4 + - + +
329A TYR* 3.6 11.8 - - + -
334A LEU* 4.1 9.2 - - + -
335A LEU 2.9 24.2 + - - +
336A ILE* 3.7 16.8 - - + -
337A PRO* 3.8 10.5 - - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 4.9 4.6 + - - -
75A TYR* 4.3 12.4 + - + +
81A LEU* 4.0 27.6 - - + -
322A TRP 2.8 16.3 + - - +
323A LYS* 3.7 10.5 - - - +
324A LYS 3.2 0.6 - - - -
325A LYS* 1.3 75.4 - - - +
327A GLU* 1.3 63.1 + - - +
328A LEU 3.1 1.3 + - - -
329A TYR* 3.2 23.3 + - - +
331A THR 4.9 4.9 - - - +
334A LEU* 3.8 14.3 - - + +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.8 12.8 - - + -
69A LYS 3.5 14.2 - - - +
70A TYR* 3.5 36.4 - - + +
71A ASP 4.9 1.1 + - - -
74A LYS* 3.5 34.1 + - - +
75A TYR* 5.4 2.4 - - - -
238A ALA 5.2 0.2 - - - +
241A ARG* 3.6 18.7 + - - +
323A LYS 3.3 8.6 + - - +
324A LYS 3.1 12.9 + - - +
326A ALA* 1.3 78.8 - - - +
328A LEU* 1.3 62.7 + - + +
329A TYR 3.3 1.8 + - - +
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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
------------------------------------------------------------
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