Contacts of the helix formed by residues 313 - 326 (chain C) in PDB entry 2JG7
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 VAL 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276C VAL* 4.4 16.6 - - + -
277C PHE 4.5 3.4 - - - +
278C GLU* 4.3 18.2 - - + +
282C LEU* 4.4 20.2 - - + -
309C LEU* 4.8 1.8 - - + -
310C HIS* 2.9 28.3 + - + +
312C SER* 1.3 89.2 + - - +
314C HIS* 1.3 66.1 + - - +
315C ASP 3.5 2.0 - - - -
316C ALA* 3.3 10.2 + - + +
317C VAL* 2.9 39.9 + - + +
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Residues in contact with HIS 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU* 3.5 24.8 - - + +
310C HIS 2.9 14.7 + - - +
311C GLU* 3.5 16.4 + - - +
313C VAL* 1.3 76.0 - - - +
315C ASP* 1.3 84.7 + - - +
318C VAL* 3.0 47.9 + - + +
386C THR* 4.5 14.1 - - + +
387C GLY 5.7 1.2 + - - -
406C VAL* 3.6 24.2 + - + +
407C LEU 4.6 0.4 + - - -
408C LYS* 3.6 42.7 + - + +
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Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C GLU 4.9 1.9 + - - -
313C VAL 3.5 0.4 - - - -
314C HIS* 1.3 104.5 + - - +
316C ALA* 1.3 62.5 + - - +
318C VAL* 4.1 3.7 - - - +
319C GLU* 3.3 27.5 + - - +
408C LYS* 4.9 6.9 + - - -
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C LEU* 5.6 6.1 - - + -
312C SER 5.7 0.7 - - - +
313C VAL* 3.3 13.9 + - + +
315C ASP* 1.3 78.9 - - - +
317C VAL* 1.3 64.6 + - + +
319C GLU* 3.6 8.4 + - - +
320C ARG* 3.2 33.8 + - - +
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 5.1 2.7 - - + -
282C LEU* 4.0 30.3 - - + -
285C VAL* 4.4 13.9 - - + -
286C VAL* 4.6 6.5 - - + -
309C LEU* 3.7 25.6 - - + -
313C VAL* 2.9 34.1 + - + +
314C HIS 3.9 2.5 - - - +
316C ALA* 1.3 74.4 - - + +
318C VAL* 1.3 66.6 + - - +
320C ARG* 3.1 8.4 + - - +
321C ILE* 2.9 41.4 + - + +
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C LEU* 5.7 0.4 - - + -
309C LEU* 3.6 16.6 - - + -
314C HIS* 3.0 31.8 + - + +
315C ASP* 4.1 5.8 - - - +
317C VAL* 1.3 75.1 - - - +
319C GLU* 1.3 59.5 + - - +
321C ILE* 3.2 9.8 + - - +
322C ALA* 2.8 27.7 + - - +
367C VAL* 4.0 33.2 - - + -
384C ILE* 4.9 6.4 - - + +
386C THR* 4.1 7.4 - - + -
406C VAL* 3.8 21.3 - - + -
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ASP 3.3 17.2 + - - +
316C ALA* 3.8 7.9 - - - +
317C VAL 3.2 0.4 - - - -
318C VAL* 1.3 80.3 - - - +
320C ARG* 1.3 57.8 + - + +
322C ALA* 3.3 9.7 + - + +
323C LYS* 2.9 51.9 + - + +
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Residues in contact with ARG 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C LEU* 3.4 42.0 + - - +
283C ASN* 3.0 28.3 + - - +
286C VAL* 3.8 30.1 - - + +
316C ALA* 3.2 21.4 + - - +
317C VAL* 3.1 9.0 + - - +
319C GLU* 1.3 76.2 - - + +
321C ILE* 1.3 64.5 + - - +
323C LYS* 3.3 15.9 + - + +
324C ALA* 3.1 21.3 + - - +
509D PHE* 4.9 16.7 + - - +
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Residues in contact with ILE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C VAL* 4.4 18.2 - - + +
289C ALA* 3.8 19.7 - - + -
290C VAL* 4.0 10.1 - - + +
307C LEU* 3.5 31.9 - - + -
317C VAL* 2.9 35.1 + - + +
318C VAL* 3.6 7.0 - - - +
320C ARG* 1.3 75.7 - - - +
322C ALA* 1.3 57.8 + - - +
324C ALA* 3.2 4.9 + - - +
325C TYR* 2.9 53.0 + - + -
384C ILE* 3.8 10.3 - - + -
404C LEU* 5.0 6.3 - - + -
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C VAL 2.8 16.8 + - - +
319C GLU* 3.4 10.3 - - + +
320C ARG 3.2 0.2 - - - -
321C ILE* 1.3 77.9 - - - +
323C LYS* 1.3 61.6 + - - +
325C TYR* 3.3 13.5 + - - +
326C LYS* 3.3 19.3 + - + +
367C VAL* 3.9 25.1 - - + -
368C CYS* 5.1 6.1 - - + +
384C ILE* 4.2 9.1 - - + +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C GLU* 2.9 41.1 + - + +
320C ARG* 3.6 18.2 - - + +
321C ILE 3.3 0.2 - - - -
322C ALA* 1.3 76.6 - - - +
324C ALA* 1.3 61.9 + - - +
326C LYS* 3.6 27.6 + - + +
327C GLN* 3.4 17.8 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C VAL* 4.8 0.2 - - + -
290C VAL* 3.7 25.8 - - + -
320C ARG 3.1 12.2 + - - +
321C ILE 3.4 8.3 - - - +
323C LYS* 1.3 75.5 - - - +
325C TYR* 1.3 59.5 + - - +
326C LYS 3.2 0.4 - - - -
327C GLN* 2.9 30.8 + - - +
328C VAL* 3.4 12.9 + - - +
507D ILE* 4.3 7.0 - - + +
508D LYS 5.5 0.4 - - - -
509D PHE* 3.8 22.4 - - + -
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Residues in contact with TYR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C VAL* 4.5 18.2 - - + -
293C SER* 3.4 25.6 - - - -
294C VAL* 3.7 15.5 - - + +
321C ILE* 2.9 41.9 + - + +
322C ALA 3.5 10.8 - - - +
324C ALA* 1.3 75.7 - - - +
326C LYS* 1.3 62.0 + - + +
328C VAL* 3.2 23.6 + - - +
330C ILE* 6.1 0.5 - - - +
368C CYS* 3.7 16.8 - - - -
382C PRO* 3.5 51.9 - - + +
383C THR 4.1 2.6 + - - -
384C ILE* 3.7 19.4 - - + +
402C PRO 6.2 0.3 - - - -
404C LEU* 4.0 12.2 - - + +
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Residues in contact with LYS 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ALA* 3.3 14.8 + - + +
323C LYS* 3.6 21.1 - - + +
324C ALA 3.2 0.4 - - - -
325C TYR* 1.3 78.4 - - + +
327C GLN* 1.3 60.5 + - + +
328C VAL 3.4 3.4 + - - +
368C CYS* 6.5 1.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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