Contacts of the helix formed by residues 315 - 333 (chain A) in PDB entry 3CMM
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 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ARG* 3.1 60.0 + - + +
313A THR 3.0 1.4 + - - +
314A MET* 1.3 76.1 - - - +
316A ASP* 1.3 64.8 + - - +
317A GLU* 3.3 8.1 + - - +
318A ASP* 3.0 35.8 + - - +
319A ALA* 3.2 22.3 + - - +
352A SER* 4.7 0.9 + - - -
353A TYR* 3.8 4.2 - - - -
407A GLU* 2.7 25.9 + - - +
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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
----------------------------------------------------------
314A MET 3.5 4.8 + - - +
315A ASN* 1.3 74.0 - - - +
317A GLU* 1.3 64.4 + - - +
319A ALA* 3.2 5.0 + - - +
320A ASN* 3.1 29.8 + - - +
353A TYR* 2.6 32.1 + - - -
407A GLU* 4.6 3.0 + - - -
5119A PRO 3.7 20.9 - - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 4.4 13.2 + - - +
315A ASN* 3.3 10.8 + - - +
316A ASP* 1.3 77.7 - - - +
318A ASP* 1.3 67.2 + - - +
320A ASN* 3.2 12.9 + - - +
321A GLU* 3.0 27.2 + - + +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 3.7 25.0 - - + -
306A HIS* 5.2 3.6 - - - -
311A PRO* 3.8 19.4 - - + +
312A ARG* 2.6 63.8 + - - +
315A ASN* 3.0 16.6 + - + +
316A ASP 3.4 0.2 - - - -
317A GLU* 1.3 78.8 - - - +
319A ALA* 1.3 61.1 + - - +
321A GLU* 3.3 7.9 + - - +
322A LEU* 3.1 19.6 + - - +
352A SER* 3.4 6.2 + - - +
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Residues in contact with ALA 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 ASN 3.2 14.0 + - - +
316A ASP* 3.5 8.7 - - - +
318A ASP* 1.3 74.9 - - - +
320A ASN* 1.3 58.7 + - - +
322A LEU* 2.9 5.0 + - - +
323A ILE* 2.9 34.1 + - + +
349A LYS* 4.1 18.2 - - + -
352A SER* 3.2 24.1 + - - +
353A TYR* 4.0 17.3 - - + +
5119A PRO* 5.1 3.1 - - + -
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Residues in contact with ASN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 3.1 20.9 + - - +
317A GLU* 3.5 10.1 - - - +
319A ALA* 1.3 76.8 - - - +
321A GLU* 1.3 62.1 + - - +
323A ILE* 3.4 8.1 + - - +
324A LYS* 3.0 28.9 + - - +
5119A PRO* 3.0 40.0 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 3.6 16.7 - - + -
305A ARG* 3.1 36.8 + - - +
306A HIS* 3.0 37.3 + - - -
317A GLU* 3.0 19.1 + - + +
318A ASP* 3.5 13.2 - - - +
319A ALA 3.2 0.2 - - - -
320A ASN* 1.3 76.9 - - - +
322A LEU* 1.3 57.9 + - - +
324A LYS* 3.2 9.7 + - + +
325A LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLY 5.0 1.1 - - - +
298A ALA* 3.7 15.9 - - + +
299A LEU* 3.7 40.8 - - + +
302A PHE* 4.1 16.4 - - + -
311A PRO* 4.5 2.7 - - + -
318A ASP 3.1 11.4 + - - +
319A ALA 2.9 9.5 + - - +
321A GLU* 1.3 75.4 - - - +
323A ILE* 1.3 60.4 + - - +
325A LEU* 3.0 6.1 + - + +
326A VAL* 2.9 32.7 + - - +
348A ILE* 3.7 22.0 - - + +
351A LEU* 4.5 10.8 - - + -
352A SER* 3.6 32.3 - - - +
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA 2.9 20.1 + - - +
320A ASN* 3.7 7.4 - - - +
321A GLU 3.4 0.2 - - - -
322A LEU* 1.3 75.9 - - - +
324A LYS* 1.3 52.1 + - - +
326A VAL* 3.9 2.1 - - - +
327A THR* 2.5 43.7 + - - +
343A VAL* 4.6 3.8 - - + +
345A GLU* 3.7 57.9 - - + +
348A ILE* 3.8 22.0 - - + -
349A LYS* 4.2 7.4 - - + +
5119A PRO* 4.0 28.0 - - + -
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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
----------------------------------------------------------
305A ARG* 6.3 0.4 - - - +
320A ASN* 3.0 16.7 + - - +
321A GLU* 3.5 12.3 - - + +
322A LEU 3.2 0.2 - - - -
323A ILE* 1.3 74.7 - - + +
325A LEU* 1.3 64.6 - - + +
327A THR* 3.7 5.9 - - - -
328A ASP* 3.0 38.5 + - - +
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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
----------------------------------------------------------
298A ALA* 3.6 31.4 - - + +
301A GLN* 3.7 25.0 + - + +
302A PHE* 3.9 29.4 - - + +
305A ARG* 3.5 40.2 - - - +
321A GLU 3.0 18.1 + - - +
322A LEU* 3.0 10.7 + - + +
324A LYS* 1.3 77.7 - - + +
326A VAL* 1.3 62.5 + - - +
328A ASP* 3.3 11.7 + - + +
329A LEU* 3.0 29.5 + - - +
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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
----------------------------------------------------------
291A GLN* 4.9 3.1 - - - +
294A LEU* 4.0 21.1 - - + +
295A GLY* 3.9 14.8 - - - -
298A ALA* 3.6 18.8 - - + -
322A LEU* 2.9 19.1 + - + +
323A ILE 4.0 3.4 - - - +
325A LEU* 1.3 73.4 - - - +
327A THR* 1.3 64.1 + - - +
329A LEU* 3.2 11.2 + - - +
330A SER* 3.0 20.3 + - - -
337A LEU* 5.2 1.8 - - + -
343A VAL* 3.9 25.8 - - + -
348A ILE* 3.7 28.5 - - + -
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Residues in contact with THR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 2.5 33.3 + - - +
324A LYS* 3.7 9.3 - - + -
326A VAL* 1.3 76.1 - - - +
328A ASP* 1.3 60.9 + - - +
330A SER* 2.7 22.7 + - - +
331A VAL* 2.9 27.5 + - + +
343A VAL* 4.0 13.8 - - + +
345A GLU* 5.2 2.1 + - - -
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 6.1 0.7 - - - +
305A ARG* 5.9 0.5 + - - -
324A LYS* 3.0 30.2 + - - +
325A LEU* 3.6 11.5 - - + +
327A THR* 1.3 78.1 - - - +
329A LEU* 1.3 67.3 + - + +
331A VAL* 3.3 8.9 + - - +
332A GLN* 3.1 45.8 + - - +
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Residues in contact with LEU 329 (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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294A LEU* 3.7 43.1 - - + +
297A GLN* 4.5 11.7 - - + +
298A ALA* 4.1 8.7 - - + +
301A GLN* 3.9 31.9 - - - +
325A LEU 3.0 22.6 + - - +
326A VAL* 3.2 12.5 + - - +
328A ASP* 1.3 77.0 - - + +
330A SER* 1.3 57.5 + - - +
332A GLN* 3.3 13.0 + - - +
333A GLN* 2.8 49.3 + - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 4.0 5.1 - - - +
326A VAL 3.0 11.3 + - - -
327A THR* 2.7 25.1 + - - +
329A LEU* 1.3 72.8 - - - +
331A VAL* 1.3 65.7 + - - +
333A GLN 3.0 26.2 - - - +
334A PRO* 3.1 10.0 - - - +
337A LEU* 3.9 28.7 - - - -
341A VAL 5.6 2.2 - - - -
343A VAL* 3.5 8.5 - - - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 2.9 30.9 + - + +
328A ASP* 3.3 9.6 + - - +
330A SER* 1.3 77.4 - - - +
332A GLN* 1.3 65.9 + - + +
334A PRO* 3.8 12.4 - - - +
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Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 3.1 42.2 + - - +
329A LEU* 3.6 16.6 + - - +
331A VAL* 1.3 80.9 - - + +
333A GLN* 1.3 69.8 + - + +
334A PRO* 3.6 5.9 - - - +
335A GLU* 4.6 0.7 - - - +
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Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU 4.7 1.9 - - - +
274A SER* 4.1 23.2 - - - +
294A LEU* 5.0 4.6 - - - +
297A GLN* 5.6 4.6 + - - +
329A LEU* 2.8 44.2 + - - +
330A SER* 3.0 11.6 - - - +
332A GLN* 1.3 84.1 - - + +
334A PRO* 1.4 62.7 - - - +
335A GLU* 3.1 21.8 - - + +
336A VAL* 2.8 52.8 - - + +
337A LEU 4.5 0.2 + - - -
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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