Contacts of the helix formed by residues 313 - 326 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276F VAL* 4.4 15.5 - - + -
277F PHE 4.5 3.4 - - - +
278F GLU* 4.2 18.2 - - + +
282F LEU* 4.4 20.0 - - + -
309F LEU* 4.8 1.6 - - + -
310F HIS* 2.9 29.4 + - + +
312F SER* 1.3 89.2 + - - +
314F HIS* 1.3 67.5 + - - +
315F ASP 3.5 1.6 - - - -
316F ALA* 3.3 10.2 + - + +
317F VAL* 3.0 40.5 + - + +
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Residues in contact with HIS 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F LEU* 3.6 26.1 - - + +
310F HIS 2.9 15.6 + - - +
311F GLU* 3.5 16.6 + - - +
313F VAL* 1.3 75.4 - - - +
315F ASP* 1.3 88.0 + - - +
318F VAL* 3.1 42.8 + - + +
386F THR* 4.5 14.5 - - + +
387F GLY 5.7 1.0 + - - -
406F VAL* 3.6 23.8 + - + +
408F LYS* 3.7 43.6 + - + +
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Residues in contact with ASP 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F GLU 4.9 2.1 + - - -
313F VAL 3.5 0.8 - - - -
314F HIS* 1.3 103.3 + - - +
316F ALA* 1.3 61.8 + - - +
318F VAL* 4.1 4.5 - - - +
319F GLU* 3.3 27.1 + - - +
408F LYS* 4.9 5.2 + - - -
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Residues in contact with ALA 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F LEU* 5.6 6.1 - - + -
313F VAL* 3.3 14.1 + - + +
315F ASP* 1.3 80.0 - - - +
317F VAL* 1.3 64.5 + - + +
319F GLU* 3.6 7.9 + - - +
320F ARG* 3.2 33.4 + - - +
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Residues in contact with VAL 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F VAL* 5.1 3.1 - - + -
282F LEU* 4.0 24.2 - - + -
285F VAL* 4.4 14.1 - - + -
286F VAL* 4.6 6.7 - - + -
309F LEU* 3.7 26.2 - - + -
313F VAL* 3.0 39.5 + - + +
314F HIS 3.9 2.5 - - - +
316F ALA* 1.3 74.4 - - + +
318F VAL* 1.3 59.7 + - - +
320F ARG* 3.1 9.8 + - - +
321F ILE* 2.8 51.6 + - + +
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Residues in contact with VAL 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F LEU* 5.7 0.2 - - + -
309F LEU* 3.6 17.5 - - + -
314F HIS* 3.1 33.2 + - + +
315F ASP* 4.1 5.6 - - - +
317F VAL* 1.3 75.1 - - - +
319F GLU* 1.3 58.4 + - - +
321F ILE* 3.3 8.6 + - - +
322F ALA* 2.8 27.2 + - - +
367F VAL* 4.0 33.2 - - + -
384F ILE* 4.8 7.4 - - + +
386F THR* 4.1 6.5 - - + -
406F VAL* 3.8 20.9 - - + -
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Residues in contact with GLU 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F ASP 3.3 18.7 + - - +
316F ALA* 3.7 7.4 - - - +
317F VAL 3.2 0.6 - - - -
318F VAL* 1.3 79.6 - - - +
320F ARG* 1.3 59.0 + - + +
322F ALA* 3.3 9.2 + - + +
323F LYS* 2.9 53.2 + - + +
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Residues in contact with ARG 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E PHE* 4.9 17.3 + - - +
282F LEU* 3.4 42.6 + - - +
283F ASN* 3.0 28.9 + - - +
286F VAL* 3.8 31.1 - - + +
316F ALA* 3.2 21.2 + - - +
317F VAL* 3.1 9.4 + - - +
319F GLU* 1.3 73.8 - - + +
321F ILE* 1.3 66.1 + - - +
323F LYS* 3.3 15.9 + - + +
324F ALA* 3.1 21.3 + - - +
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Residues in contact with ILE 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F VAL* 4.4 17.9 - - + +
289F ALA* 3.8 19.7 - - + -
290F VAL* 4.0 9.6 - - + +
307F LEU* 3.5 32.1 - - + -
317F VAL* 2.8 35.1 + - + +
318F VAL* 3.7 6.7 - - - +
320F ARG* 1.3 74.8 - - - +
322F ALA* 1.3 58.1 + - - +
324F ALA* 3.2 4.9 + - - +
325F TYR* 2.9 52.3 + - + -
384F ILE* 3.7 11.0 - - + -
404F LEU* 5.0 7.0 - - + -
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Residues in contact with ALA 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F VAL 2.8 17.0 + - - +
319F GLU* 3.4 10.8 - - + +
320F ARG 3.2 0.2 - - - -
321F ILE* 1.3 77.6 - - - +
323F LYS* 1.3 61.2 + - - +
325F TYR* 3.3 13.7 + - - +
326F LYS* 3.4 20.1 + - + +
367F VAL* 3.9 25.1 - - + +
368F CYS* 5.1 5.4 - - + +
384F ILE* 4.2 9.1 - - + +
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Residues in contact with LYS 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508E LYS 6.1 0.2 - - - +
319F GLU* 2.9 40.5 + - + +
320F ARG* 3.3 18.8 + - + +
322F ALA* 1.3 75.7 - - - +
324F ALA* 1.3 61.2 + - - +
326F LYS* 3.6 27.7 + - + +
327F GLN* 3.5 18.5 + - - +
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Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E ILE* 4.1 15.6 - - + +
508E LYS 5.3 0.7 - - - -
509E PHE* 3.7 23.8 - - + -
290F VAL* 3.6 24.9 - - + -
320F ARG 3.1 11.7 + - - +
321F ILE* 3.4 8.7 - - - +
323F LYS* 1.3 75.4 - - - +
325F TYR* 1.3 66.0 + - - +
326F LYS 3.1 0.4 - - - -
327F GLN* 2.9 17.1 + - - +
328F VAL* 3.4 13.6 + - - +
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Residues in contact with TYR 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F VAL* 4.5 17.9 - - + -
293F SER* 3.4 26.4 - - - -
294F VAL* 3.7 15.1 - - + +
321F ILE* 2.9 42.6 + - + +
322F ALA* 3.3 12.7 + - - +
324F ALA* 1.3 75.1 - - - +
326F LYS* 1.3 62.4 + - + +
328F VAL* 3.2 23.8 + - - +
330F ILE* 6.1 0.7 - - - +
368F CYS* 3.8 15.0 - - + -
382F PRO* 3.5 51.2 - - + +
383F THR 4.1 2.0 + - - -
384F ILE* 3.7 19.3 - - + +
402F PRO 5.8 0.5 + - - -
404F LEU* 4.0 12.0 - - - +
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Residues in contact with LYS 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322F ALA* 3.4 15.1 + - + +
323F LYS* 3.6 21.5 - - + +
324F ALA 3.1 0.6 - - - -
325F TYR* 1.3 78.1 - - - +
327F GLN* 1.3 62.2 + - + +
328F VAL 3.4 3.3 + - - +
368F 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