Contacts of the helix formed by residues 321 - 338 (chain A) in PDB entry 3D14
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 GLU 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A HIS* 3.3 66.0 + - + +
264A ARG* 3.1 41.9 + - - +
265A VAL 5.0 1.1 - - - +
266A ILE* 3.9 20.9 - - + +
294A ALA* 3.5 2.7 - - - +
320A ASP* 1.3 78.4 - - - +
322A LYS* 1.3 60.9 + - + +
323A VAL 3.1 1.3 - - - -
324A ASP* 3.1 14.6 + - - +
325A LEU* 3.8 3.1 - - + +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 4.9 0.2 - - - +
320A ASP* 2.9 20.4 + - - +
321A GLU* 1.3 75.0 - - + +
323A VAL* 1.3 64.4 + - - +
324A ASP 3.2 0.2 - - - -
325A LEU* 3.1 24.9 + - + +
326A TRP 3.2 5.4 + - - -
381A ALA* 3.4 35.0 - - + +
382A SER* 4.6 10.4 + - - +
384A ARG* 2.8 56.2 + - + +
385A LEU 3.2 14.3 + - - -
386A THR* 3.8 17.7 - - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.5 19.3 - - + -
268A ARG* 3.9 19.3 - - + -
310A PRO* 3.7 22.7 - - + +
312A GLU* 3.6 12.3 - - - +
313A MET* 3.8 14.1 - - - -
319A HIS* 3.5 27.4 - - + -
320A ASP 3.2 19.0 + - - +
321A GLU 3.1 1.2 - - - -
322A LYS* 1.3 77.1 - - - +
324A ASP* 1.3 67.8 + - - +
326A TRP* 3.4 4.9 + - - +
327A SER* 3.1 25.2 + - - -
384A ARG* 4.0 1.1 - - - +
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.8 28.8 - - + +
261A HIS* 2.8 30.5 + - + +
266A ILE* 3.4 8.3 - - - +
267A HIS* 3.0 22.6 + - - +
268A ARG* 2.9 28.8 + - - -
270A ILE* 4.1 6.4 - - + +
321A GLU 3.1 8.9 + - - +
323A VAL* 1.3 77.2 - - - +
325A LEU* 1.3 58.5 + - - +
327A SER* 3.8 7.2 + - - -
328A LEU* 3.0 28.1 + - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A HIS* 3.9 11.9 - - + +
321A GLU* 3.8 14.8 - - + +
322A LYS* 3.1 21.6 + - + +
324A ASP* 1.3 76.7 - - - +
326A TRP* 1.3 64.8 + - - +
328A LEU* 3.3 8.9 + - + +
329A GLY 3.1 16.8 + - - -
376A LEU* 3.4 30.5 - - + +
384A ARG* 4.5 9.0 - - + -
385A LEU 3.2 27.1 - - - +
386A THR* 4.0 11.0 - - - +
387A LEU* 3.8 38.6 - - + +
390A VAL* 4.2 3.4 - - + -
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Residues in contact with TRP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASP 5.0 0.8 + - - -
308A TYR 3.6 10.4 + - - -
309A LEU 3.4 12.7 + - - -
310A PRO* 3.5 25.8 - - + -
311A PRO* 3.7 19.7 - - + -
322A LYS 3.2 5.7 + - - -
323A VAL 3.6 8.1 - - - +
325A LEU* 1.3 76.7 - - - +
327A SER* 1.3 64.9 + - - +
329A GLY 3.0 11.4 + - - -
330A VAL* 3.0 28.2 + - + +
342A PHE* 3.5 31.5 - + - -
354A ILE* 4.1 11.0 - - + -
357A VAL* 3.9 21.1 - - + -
376A LEU 3.9 9.4 - - - -
377A LEU* 3.4 35.5 - - + +
378A LYS 3.5 28.7 - - - -
384A ARG* 3.7 26.7 - - - +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG 5.4 4.9 + - - -
270A ILE* 3.8 36.6 + - - +
308A TYR* 2.8 28.7 + - - +
309A LEU* 5.6 1.2 - - - +
310A PRO* 4.8 1.9 - - - +
323A VAL 3.1 14.8 + - - -
324A ASP* 3.9 5.8 + - - -
325A LEU 3.3 0.2 - - - -
326A TRP* 1.3 78.3 - - - +
328A LEU* 1.3 57.4 + - - +
330A VAL* 3.3 6.9 + - - +
331A LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.8 30.6 - - + +
253A LEU* 3.8 32.1 - - + -
254A ALA* 4.5 4.0 - - + -
257A LEU* 4.6 5.4 - - + -
270A ILE* 4.8 2.1 - - + +
324A ASP 3.0 15.4 + - - +
325A LEU* 3.4 13.5 - - + +
326A TRP 3.2 0.2 - - - -
327A SER* 1.3 76.8 - - - +
329A GLY* 1.3 56.2 + - - +
331A LEU* 3.3 8.3 + - + +
332A CYS* 3.0 28.2 + - - +
376A LEU* 4.4 6.3 - - + -
387A LEU* 4.0 27.4 - - + -
390A VAL* 4.2 28.7 - - + -
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU 3.1 6.9 + - - -
326A TRP 3.0 8.8 + - - -
328A LEU* 1.3 72.9 - - - +
330A VAL* 1.3 64.5 + - - +
332A CYS* 3.4 5.9 + - - +
333A TYR* 3.1 22.0 + - - +
373A ILE* 4.0 9.0 - - - +
376A LEU* 3.8 29.1 - - - +
377A LEU* 4.0 10.8 - - - -
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASP 3.6 17.3 - - - +
308A TYR* 3.5 33.2 - - + -
326A TRP* 3.0 39.6 + - + +
327A SER* 3.3 9.4 + - - +
329A GLY* 1.3 74.5 - - - +
331A LEU* 1.3 58.0 + - - +
333A TYR* 3.3 4.0 + - - +
334A GLU* 2.9 26.0 + - - +
340A PRO* 3.9 3.4 - - + -
341A PRO* 3.8 22.4 - - + +
342A PHE* 4.6 7.4 - - + -
377A LEU* 3.7 10.1 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 4.6 2.5 - - + -
253A LEU* 3.7 15.0 - - + -
270A ILE* 3.4 29.8 - - + -
271A LYS* 4.2 3.1 - - - -
272A PRO* 3.7 39.9 - - + -
275A LEU* 3.6 19.1 - - + -
308A TYR* 4.6 5.6 - - + -
327A SER 3.0 12.5 + - - +
328A LEU* 3.5 13.2 - - + +
330A VAL* 1.3 74.7 - - - +
332A CYS* 1.3 59.7 + - - +
334A GLU* 3.7 3.9 - - + +
335A PHE* 2.8 60.5 + - + -
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Residues in contact with CYS 332 (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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246A THR* 4.0 20.9 - - - -
250A ILE* 4.0 16.7 - - + +
328A LEU 3.0 16.9 + - - +
329A GLY* 3.4 7.4 + - - +
331A LEU* 1.3 74.0 - - - +
333A TYR* 1.3 63.2 + - - +
335A PHE* 3.5 2.0 + - - +
336A LEU* 3.3 30.6 + - - +
369A ALA 5.3 0.9 - - - -
372A LEU* 4.0 25.6 - - + -
373A ILE* 3.9 22.7 - - + -
376A LEU* 5.5 1.6 - - + -
395A TRP* 4.1 11.2 - - - -
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Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLY 3.1 13.2 + - - +
330A VAL 3.5 8.1 - - - +
332A CYS* 1.3 76.7 - - - +
334A GLU* 1.3 56.7 + - - +
336A LEU* 3.2 3.4 + - - -
337A VAL* 2.9 56.7 + - + +
339A MET* 3.2 25.6 - - + -
340A PRO 4.0 0.7 - - - -
341A PRO* 3.5 38.8 + - + +
359A PHE* 3.9 11.7 - + - -
360A THR 2.7 29.3 + - - -
361A PHE* 3.7 32.8 - + - -
362A PRO* 3.7 10.4 - - + +
373A ILE* 3.8 15.3 - - + +
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Residues in contact with GLU 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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232A TYR* 6.0 1.9 - - - -
235A LEU* 3.4 27.1 - - + +
272A PRO* 3.5 12.1 - - - +
308A TYR* 2.4 40.1 + - - -
330A VAL 2.9 16.6 + - - +
331A LEU* 3.8 6.0 - - + +
333A TYR* 1.3 74.9 - - - +
335A PHE* 1.3 60.2 + - + +
338A GLY* 2.7 31.5 + - - +
339A MET* 3.6 22.0 - - - -
340A PRO* 3.8 20.5 - - + +
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Residues in contact with PHE 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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231A VAL* 3.7 29.2 - - + -
235A LEU* 4.1 8.9 - - + +
240A ARG* 3.7 3.1 - - - -
241A PHE* 2.7 54.6 + + + +
246A THR* 3.4 28.9 - - + +
249A TYR* 3.8 29.2 - + + -
250A ILE* 4.2 15.7 - - + -
253A LEU* 5.4 0.7 - - + -
272A PRO* 4.8 5.6 - - + -
275A LEU* 4.0 10.8 - - + -
283A LEU* 5.0 1.6 - - + -
331A LEU* 2.8 55.7 + - + +
332A CYS 3.7 4.9 - - - +
333A TYR 3.3 0.2 - - - -
334A GLU* 1.3 76.2 - - + +
336A LEU* 1.3 56.1 + - - +
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Residues in contact with LEU 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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240A ARG* 3.5 16.7 - - - +
241A PHE 3.8 12.7 - - - +
243A GLU* 4.1 25.4 - - + +
246A THR* 3.4 25.6 - - + +
332A CYS* 3.3 17.9 + - - +
333A TYR* 3.2 4.3 + - - +
335A PHE* 1.3 77.6 - - - +
337A VAL* 1.3 65.0 + - + +
364A PHE* 3.3 17.9 - - + -
365A VAL* 4.4 11.9 - - + -
369A ALA* 3.6 31.4 - - + -
373A ILE* 4.3 11.4 - - + -
395A TRP* 4.2 8.7 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 3.4 24.9 + - - +
333A TYR* 2.9 52.0 + - + +
336A LEU* 1.3 81.6 - - + +
338A GLY* 1.3 59.9 + - - +
339A MET* 4.0 15.3 - - + +
362A PRO* 3.8 35.7 - - + -
364A PHE* 4.1 4.9 - - + -
365A VAL* 3.8 13.7 - - + -
373A ILE* 6.4 0.4 - - + -
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Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.5 6.7 - - - +
239A SER 3.3 26.2 - - - +
240A ARG* 4.3 1.0 - - - +
334A GLU* 2.7 28.2 + - - +
336A LEU 3.7 0.8 - - - -
337A VAL* 1.3 74.3 - - - +
339A MET* 1.3 62.8 + - - +
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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