Contacts of the helix formed by residues 310 - 328 (chain A) in PDB entry 1A16
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 ILE 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A TYR* 3.5 25.6 + - + +
309A SER* 1.3 72.3 - - - +
311A LEU* 1.3 56.8 + - - +
313A VAL* 3.3 2.3 + - - +
314A THR* 2.7 45.4 + - - +
352A LEU* 4.9 1.6 - - + +
353A SER* 3.7 37.0 - - - +
354A HIS* 5.0 0.7 - - - -
355A TRP* 4.6 15.9 - - + -
366A TYR* 4.2 23.8 - - + -
370A ARG* 3.5 28.2 + - + +
372A ARG 4.7 0.6 + - - -
374A LEU* 4.4 7.0 - - + +
380A LEU* 4.2 14.6 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER* 3.2 5.6 - - - +
310A ILE* 1.3 77.4 - - - +
312A GLU* 1.3 62.4 + - - +
314A THR* 3.2 18.9 + - + -
315A GLY* 3.3 10.2 + - - -
369A ASP* 3.4 38.1 - - + +
370A ARG 3.1 11.1 + - - +
371A SER* 3.7 22.2 - - - -
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 5.1 5.2 + - - -
307A GLY 4.5 2.1 - - - +
308A THR* 2.7 34.1 + - - +
309A SER* 3.1 19.3 + - - +
311A LEU* 1.3 81.0 - - - +
313A VAL* 1.3 62.0 + - - +
315A GLY* 3.2 12.0 + - - -
316A GLU* 3.6 12.9 + - + +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER* 3.4 38.4 - - - +
303A LEU* 4.1 24.2 - - + -
304A TYR* 3.7 30.5 - - + -
308A THR* 3.9 15.0 - - + +
309A SER 3.0 19.1 + - - +
310A ILE 4.0 0.9 - - - +
312A GLU* 1.3 76.0 - - + +
314A THR* 1.3 61.4 + - - +
316A GLU* 3.1 17.2 + - - +
317A VAL* 3.2 11.5 + - + +
352A LEU* 3.8 7.6 - - + -
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Residues in contact with THR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 2.7 30.7 + - - +
311A LEU* 3.5 13.0 - - + -
312A GLU 3.2 0.2 - - - -
313A VAL* 1.3 74.1 - - - +
315A GLY* 1.3 58.6 + - - +
317A VAL* 3.2 4.7 + - + +
318A VAL* 2.9 46.6 + - + +
344A HIS* 6.1 0.2 - - - +
348A PHE* 5.0 9.9 - - + -
351A GLY* 6.3 0.4 - - - -
352A LEU* 3.7 31.5 + - + +
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU 3.3 8.0 + - - -
312A GLU 3.2 9.4 + - - -
314A THR* 1.3 76.7 - - - +
316A GLU* 1.3 62.4 + - - +
318A VAL* 3.5 7.9 + - - +
319A ARG* 3.2 22.9 + - - +
339A ILE* 5.6 1.0 - - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 4.5 12.6 - - + +
303A LEU* 3.6 37.0 - - + +
312A GLU* 3.6 13.7 + - + +
313A VAL* 3.1 10.2 + - + +
315A GLY* 1.3 78.4 - - - +
317A VAL* 1.3 61.4 + - + +
319A ARG* 3.4 15.2 + - - +
320A ILE* 3.1 28.6 + - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER* 3.4 31.0 - - - +
299A THR* 6.0 0.7 - - + -
300A SER* 3.2 27.6 - - - +
313A VAL* 3.2 11.4 + - + +
314A THR* 3.2 9.1 + - - +
316A GLU* 1.3 75.2 - - + +
318A VAL* 1.3 58.5 + - - +
320A ILE* 3.1 10.0 + - + +
321A MET* 2.8 49.2 + - + +
348A PHE* 4.5 6.3 - - + -
352A LEU* 3.8 17.7 - - + -
384A PRO* 4.3 4.5 - - + -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A THR* 2.9 34.9 + - + +
315A GLY* 3.8 8.1 - - - +
317A VAL* 1.3 76.8 - - + +
319A ARG* 1.3 56.9 + - - +
321A MET* 3.7 6.9 - - - +
322A VAL* 2.9 37.5 + - + +
339A ILE* 4.2 22.0 - - + +
342A ASN* 5.7 0.4 - - - +
344A HIS* 3.6 46.4 - - + +
348A PHE* 5.2 4.7 - - + -
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Residues in contact with ARG 319 (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 GLY 3.2 11.4 + - - +
316A GLU* 3.7 17.3 + - - +
318A VAL* 1.3 75.9 - - - +
320A ILE* 1.3 63.7 + - + +
322A VAL* 4.1 0.7 - - - +
323A SER* 2.7 41.8 + - - +
335A VAL* 4.3 8.3 - - + +
336A ASP* 2.9 33.3 + - - -
339A ILE* 3.7 32.2 - - + +
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.8 18.0 - - + +
295A GLU* 3.8 33.9 - - + +
296A SER* 3.5 26.0 - - - +
299A THR* 3.4 40.6 - - + +
316A GLU 3.1 17.4 + - - +
317A VAL* 3.1 7.4 + - - +
319A ARG* 1.3 78.1 - - + +
321A MET* 1.3 62.0 + - - +
323A SER* 3.5 5.7 - - - -
324A GLY* 3.1 18.4 + - - -
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Residues in contact with MET 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 3.7 15.4 - - + +
293A VAL* 5.3 2.7 - - - -
296A SER* 3.7 10.3 - - - +
317A VAL* 2.8 43.7 + - + +
318A VAL* 3.7 6.5 - - - +
320A ILE* 1.3 68.8 - - - +
322A VAL* 1.3 61.0 + - - +
324A GLY* 3.1 3.1 + - - -
325A LEU* 2.8 36.1 + - + +
344A HIS* 4.7 10.1 - - + -
348A PHE* 3.3 37.0 - - + -
384A PRO* 3.7 20.4 - - + -
385A GLY 3.5 26.2 - - - +
386A LEU* 4.3 15.3 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 2.9 27.7 + - + +
319A ARG 4.2 1.1 - - - +
321A MET* 1.3 70.8 - - - +
323A SER* 1.3 63.2 + - - +
325A LEU* 3.3 1.5 + - - +
326A VAL* 2.9 24.5 + - + +
331A LEU* 4.2 14.1 - - + -
335A VAL* 3.9 20.0 - - + +
338A LEU* 3.7 35.2 - - + -
339A ILE* 3.8 24.2 - - + +
344A HIS* 4.1 24.0 - - + +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 2.7 29.4 + - - +
320A ILE* 3.5 6.5 - - - -
322A VAL* 1.3 79.4 - - - +
324A GLY* 1.3 57.4 + - - +
326A VAL* 3.7 2.9 - - - +
327A LYS* 3.1 28.5 + - - +
335A VAL* 4.0 24.6 - - - +
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Residues in contact with GLY 324 (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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292A ILE* 3.5 26.0 - - - -
320A ILE 3.1 10.8 + - - -
321A MET 3.6 0.7 - - - -
323A SER* 1.3 77.9 - - - +
325A LEU* 1.3 57.6 + - - +
327A LYS* 3.4 9.5 + - - +
328A LEU* 3.0 34.9 + - - +
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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
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289A ILE* 4.8 1.8 - - + -
292A ILE* 4.2 6.1 - - + -
321A MET* 2.8 23.3 + - + +
322A VAL 3.9 1.8 - - - +
324A GLY* 1.3 74.3 - - - +
326A VAL* 1.3 63.2 + - - +
328A LEU* 3.6 0.8 + - - -
329A GLY 3.2 1.9 + - - -
330A ILE* 2.8 59.8 + - + -
331A LEU* 2.9 30.5 + - + -
344A HIS* 4.8 8.1 - - + -
347A PHE* 3.5 37.0 - - + -
386A LEU* 4.1 29.4 - - + -
388A ILE* 5.5 2.2 - - + -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 2.9 23.8 + - + +
323A SER 3.7 4.5 - - - +
325A LEU* 1.3 75.0 - - - +
327A LYS* 1.3 66.2 + - - +
329A GLY* 3.1 14.0 + - - -
331A LEU* 3.5 19.5 - - + +
333A GLY 4.2 15.7 - - - +
335A VAL* 4.5 13.9 - - + -
338A LEU* 3.3 34.5 - - + -
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Residues in contact with LYS 327 (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 SER 3.1 17.5 + - - +
324A GLY* 3.7 8.5 - - - +
325A LEU 3.4 0.2 - - - -
326A VAL* 1.3 79.9 - - - +
328A LEU* 1.3 72.9 + - + +
329A GLY 3.6 0.2 + - - -
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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
----------------------------------------------------------
288A GLU* 3.7 46.9 - - + +
289A ILE* 3.9 20.2 - - + -
292A ILE* 3.7 16.6 - - + -
324A GLY 3.0 16.4 + - - +
325A LEU 4.2 3.8 - - - +
326A VAL 3.2 0.4 - - - -
327A LYS* 1.3 95.1 - - + +
329A GLY* 1.3 58.6 + - - +
330A ILE* 3.4 10.3 + - + -
395A PRO* 4.3 3.8 - - - +
398A TYR* 3.7 36.0 + - + +
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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