Contacts of the helix formed by residues 315 - 333 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ARG* 3.2 64.0 + - + +
313C THR 3.2 0.2 - - - -
314C MET* 1.3 75.6 - - - +
316C ASP* 1.3 55.2 + - - +
317C GLU* 3.3 8.3 + - - +
318C ASP* 3.0 28.4 + - + +
319C ALA* 2.8 34.5 + - - +
352C SER* 4.7 0.9 + - - -
353C TYR* 3.6 6.6 - - - -
407C GLU* 2.9 30.2 + - - +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C MET 3.6 4.6 + - - +
315C ASN* 1.3 72.9 - - - +
317C GLU* 1.3 55.4 + - - +
319C ALA* 3.0 6.6 + - - +
320C ASN* 2.8 41.8 + - - +
353C TYR* 2.6 30.0 + - - -
407C GLU* 5.0 2.4 + - - -
5129C PRO* 3.4 28.0 - - - +
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Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ARG* 2.8 28.2 + - - +
315C ASN* 3.3 8.6 + - - +
316C ASP* 1.3 78.1 - - - +
318C ASP* 1.3 66.0 + - - +
320C ASN* 3.4 9.0 + - - +
321C GLU* 3.0 23.7 + - - +
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Residues in contact with ASP 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PHE* 3.4 31.4 - - + -
306C HIS* 5.4 2.1 + - - -
310C LEU 4.8 0.3 - - - +
311C PRO* 3.6 13.1 - - + +
312C ARG* 2.7 66.2 + - - +
315C ASN* 3.0 14.0 + - + +
317C GLU* 1.3 77.3 - - - +
319C ALA* 1.3 57.6 + - - +
321C GLU* 3.1 8.5 + - - +
322C LEU* 2.9 26.5 + - - +
352C SER* 3.7 5.9 + - - +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ASN 2.8 21.0 + - - +
316C ASP 3.4 5.4 - - - +
318C ASP* 1.3 72.5 - - - +
320C ASN* 1.3 62.4 + - - +
322C LEU* 3.1 4.5 + - - +
323C ILE* 3.1 29.3 + - - +
349C LYS* 4.4 7.5 - - + -
352C SER* 3.3 21.4 + - - +
353C TYR* 3.7 21.5 - - + -
5129C PRO* 4.1 13.2 - - + -
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Residues in contact with ASN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASP* 2.8 26.6 + - - +
317C GLU* 3.6 6.9 - - - +
319C ALA* 1.3 71.2 - - - +
321C GLU* 1.3 56.8 + - - +
323C ILE* 3.4 9.3 + - - +
324C LYS* 3.0 28.9 + - - +
5129C PRO* 3.1 40.9 + - - +
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Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PHE* 3.3 17.8 - - + -
305C ARG* 2.8 37.6 + - - +
306C HIS* 2.9 37.0 + - - -
317C GLU* 3.0 15.0 + - + +
318C ASP* 3.1 13.6 + - - +
320C ASN* 1.3 75.8 - - - +
322C LEU* 1.3 57.4 + - - +
324C LYS* 3.4 7.6 - - + +
325C LEU* 3.0 27.0 + - + +
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLY 4.8 0.9 - - - +
298C ALA* 3.6 38.4 - - + +
299C LEU* 3.8 23.1 - - + +
302C PHE* 4.1 14.5 - - + -
311C PRO* 4.5 1.6 - - + -
318C ASP 2.9 12.2 + - - +
319C ALA 3.1 8.5 + - - +
321C GLU* 1.3 72.3 - - - +
323C ILE* 1.3 59.6 + - - +
325C LEU* 3.0 7.1 + - + +
326C VAL* 2.9 32.4 + - + +
348C ILE* 3.9 18.8 - - + +
351C LEU* 4.3 11.2 - - + -
352C SER* 3.7 36.6 - - - +
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Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ALA 3.1 17.3 + - - +
320C ASN* 3.8 8.5 - - - +
321C GLU 3.4 0.2 - - - -
322C LEU* 1.3 74.7 - - - +
324C LYS* 1.3 54.3 + - - +
326C VAL* 3.5 2.9 + - - +
327C THR* 2.6 42.7 + - - +
343C VAL* 4.9 2.4 - - + +
345C GLU* 3.8 57.0 - - + +
348C ILE* 3.8 22.2 - - + -
349C LYS* 4.2 5.6 - - + +
5129C PRO* 3.7 32.1 - - + -
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Residues in contact with LYS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ARG* 5.9 5.4 - - - +
320C ASN 3.0 17.7 + - - +
321C GLU* 3.4 10.5 - - + +
322C LEU 3.2 0.2 - - - -
323C ILE* 1.3 78.2 - - - +
325C LEU* 1.3 57.5 + - + +
327C THR* 3.2 9.5 + - + -
328C ASP* 2.8 59.3 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ALA* 3.3 35.2 - - + +
301C GLN* 3.5 26.7 + - + +
302C PHE* 3.5 29.2 - - + +
305C ARG* 3.5 36.3 - - - +
321C GLU 3.0 17.8 + - - +
322C LEU* 3.0 12.4 + - + +
324C LYS* 1.3 77.6 - - + +
326C VAL* 1.3 59.1 - - - +
328C ASP* 3.4 14.1 - - - +
329C LEU* 3.2 26.0 + - - +
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLN* 5.2 2.9 - - - +
294C LEU* 4.0 22.2 - - + +
295C GLY* 4.0 13.5 - - - -
298C ALA* 3.6 19.5 - - + -
322C LEU 2.9 17.9 + - - +
323C ILE 3.9 3.6 - - - +
325C LEU* 1.3 72.3 - - - +
327C THR* 1.3 67.0 + - - +
329C LEU* 3.0 17.5 + - - +
330C SER* 3.1 11.4 + - - -
337C LEU* 5.5 0.4 - - + -
343C VAL* 3.6 30.7 - - + -
348C ILE* 3.8 26.2 - - + -
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Residues in contact with THR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C ILE* 2.6 31.6 + - - +
324C LYS* 3.2 12.0 + - + -
326C VAL* 1.3 74.0 - - - +
328C ASP* 1.3 66.2 - - - +
330C SER* 3.0 12.2 + - - +
331C VAL* 3.0 34.7 + - + +
343C VAL* 3.9 16.4 - - + +
345C GLU* 4.8 3.6 + - - -
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Residues in contact with ASP 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C GLN* 5.5 2.9 - - - +
305C ARG* 5.2 5.0 + - - -
324C LYS* 2.8 43.8 + - - +
325C LEU* 3.4 19.3 - - - +
327C THR* 1.3 77.7 - - - +
329C LEU* 1.3 64.9 + - + +
331C VAL* 3.4 7.9 + - - +
332C GLN* 3.2 33.0 + - + +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 4.0 40.6 - - + +
297C GLN* 4.3 13.2 - - + +
298C ALA* 4.1 11.9 - - + +
301C GLN* 3.4 34.1 - - - +
325C LEU 3.2 13.9 + - - +
326C VAL* 3.0 9.5 + - - +
328C ASP* 1.3 79.9 - - + +
330C SER* 1.3 58.3 + - - +
332C GLN* 3.5 15.9 + - - +
333C GLN* 3.0 48.4 + - - +
336C VAL* 4.6 0.7 - - - +
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Residues in contact with SER 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 3.9 7.6 - - - -
326C VAL 3.1 8.9 + - - -
327C THR* 3.0 12.9 + - - +
329C LEU* 1.3 73.7 - - - +
331C VAL* 1.3 67.1 + - - +
332C GLN 3.2 0.9 - - - -
333C GLN 3.6 17.7 - - - +
334C PRO* 3.6 13.6 - - - +
337C LEU* 3.7 29.6 - - - +
341C VAL 5.7 0.7 - - - -
343C VAL* 3.7 14.6 - - - +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C THR* 3.0 33.4 + - + +
328C ASP* 3.4 8.5 + - - +
330C SER* 1.3 80.6 - - - +
332C GLN* 1.3 61.5 - - + +
334C PRO* 3.9 12.1 - - - +
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Residues in contact with GLN 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ASP* 3.2 21.7 + - + +
329C LEU* 3.8 20.3 - - - +
330C SER 3.2 0.2 - - - -
331C VAL* 1.3 83.2 - - + +
333C GLN* 1.3 69.0 + - + +
334C PRO* 3.6 6.7 - - - +
335C GLU* 4.8 0.3 - - - +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU 4.8 4.9 - - - +
274C SER* 4.3 12.9 - - - +
294C LEU* 4.8 3.8 - - - +
297C GLN* 5.6 6.7 + - - +
329C LEU* 3.0 36.7 + - - +
330C SER* 3.6 8.8 - - - +
332C GLN* 1.3 87.8 - - + +
334C PRO* 1.3 60.2 - - - +
335C GLU* 3.0 19.1 - - + +
336C VAL* 2.8 47.9 - - + +
337C LEU 4.6 0.3 + - - -
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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