Contacts of the helix formed by residues 315 - 327 (chain J) in PDB entry 3EXG
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 GLN 315 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214J ARG* 5.8 1.8 - - - +
218J HIS* 5.4 7.0 - - - -
310J ASP* 3.2 44.1 + - + +
311J ASN* 5.1 4.5 - - - +
313J ILE* 3.2 18.6 + - - +
314J PRO* 1.3 80.1 + - - +
316J VAL* 1.3 68.1 + - - +
317J LYS* 3.1 19.7 - - + -
318J ASP* 3.0 33.4 + - - +
319J ILE* 3.3 12.7 + - - +
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Residues in contact with VAL 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J HIS* 3.6 46.3 - - + +
221J GLU* 3.9 32.1 - - + +
222J ALA* 3.9 12.3 - - - +
225J VAL* 5.3 3.8 - - + -
314J PRO 4.2 0.2 + - - -
315J GLN* 1.3 75.8 - - - +
317J LYS* 1.3 58.7 + - + +
319J ILE* 3.7 13.4 + - - +
320J ILE* 3.1 27.4 + - + +
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Residues in contact with LYS 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311J ASN* 5.6 5.3 + - - -
315J GLN* 4.3 18.8 - - + -
316J VAL* 1.3 75.2 - - + +
318J ASP* 1.3 77.9 + - - +
320J ILE* 3.6 12.5 - - + +
321J PHE* 3.0 24.3 + - - +
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Residues in contact with ASP 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295J VAL* 4.4 9.0 - - + +
311J ASN* 6.2 0.3 - - - -
313J ILE 4.6 0.2 - - - +
315J GLN* 3.0 30.4 + - - +
317J LYS* 1.3 95.6 + - - +
319J ILE* 1.3 67.2 + - - +
320J ILE 3.0 0.9 - - - -
321J PHE* 4.1 2.3 - - - +
322J ALA* 3.1 25.1 + - - +
351K ALA* 3.0 30.8 - - + +
352K ASN* 3.6 18.6 + - - +
355K ILE* 4.0 14.1 - - - +
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Residues in contact with ILE 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J VAL* 4.8 2.9 - - + -
215J PRO* 5.6 0.4 - - + -
218J HIS* 3.7 42.0 - - + +
219J CYS* 3.9 10.8 - - - +
222J ALA* 3.8 17.0 - - + -
260J VAL* 5.5 1.1 - - + +
262J VAL* 4.1 37.0 - - + -
295J VAL* 4.7 12.7 - - + +
314J PRO* 5.1 5.2 - - + +
315J GLN 3.3 13.1 + - - +
316J VAL* 3.7 8.1 - - - +
318J ASP* 1.3 79.7 - - - +
320J ILE* 1.3 62.5 + - - +
322J ALA* 4.0 1.2 - - - +
323J ILE* 3.1 35.4 + - + +
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Residues in contact with ILE 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J ALA* 3.8 20.2 - - + +
225J VAL* 3.8 39.5 - - + -
226J LEU* 4.6 12.6 - - + -
229J GLU* 6.1 0.2 - - - +
316J VAL* 3.1 20.4 + - + +
317J LYS* 3.8 10.8 - - + +
318J ASP 3.0 0.4 - - - -
319J ILE* 1.3 76.1 - - - +
321J PHE* 1.3 68.8 + - - +
323J ILE* 3.0 16.9 + - - +
324J LYS* 3.0 39.3 + - + +
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Residues in contact with PHE 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317J LYS 3.0 16.4 + - - +
318J ASP* 3.9 8.3 - - - +
319J ILE 3.5 0.2 - - - -
320J ILE* 1.3 81.2 - - - +
322J ALA* 1.3 56.2 + - - +
324J LYS* 3.6 6.1 + - - +
325J LYS* 2.8 52.6 + - + +
352K ASN* 3.9 15.3 - - - +
354K TRP* 3.7 39.5 - + + -
355K ILE* 6.1 1.3 - - + -
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Residues in contact with ALA 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260J VAL* 4.7 1.6 - - + -
293J VAL* 4.1 10.7 - - + +
295J VAL* 3.9 22.4 - - + -
318J ASP 3.1 17.4 + - - +
319J ILE 4.1 1.6 - - - +
320J ILE 3.1 1.2 - - - -
321J PHE* 1.3 75.4 - - - +
323J ILE* 1.3 65.3 + - - +
325J LYS* 3.8 2.4 - - - +
326J THR* 3.0 26.0 + - - -
352K ASN* 4.6 4.5 - - + -
354K TRP* 3.8 26.9 - - + -
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Residues in contact with ILE 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207J ILE* 3.8 26.0 - - + -
209J VAL* 3.5 31.4 - - + -
222J ALA* 5.4 1.6 - - + -
226J LEU* 3.6 35.2 - - + -
233J CYS* 3.9 8.5 - - - -
260J VAL* 4.5 9.2 - - + -
319J ILE* 3.1 27.4 + - + +
320J ILE 3.0 4.5 + - - +
322J ALA* 1.3 74.6 - - - +
324J LYS* 1.3 59.7 + - - +
326J THR* 2.8 21.7 + - - -
327J LEU* 3.2 26.1 + - + +
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Residues in contact with LYS 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J LEU* 4.6 8.7 - - + -
229J GLU* 3.4 36.6 + - - -
320J ILE* 3.0 33.7 + - + +
321J PHE* 3.8 6.1 - - + +
323J ILE* 1.3 76.5 - - - +
325J LYS* 1.3 63.4 + - - +
326J THR 3.0 1.2 + - - -
327J LEU* 3.7 0.6 + - - -
328J ASN* 3.2 15.9 + - - -
329J ILE* 3.3 47.1 + - + +
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Residues in contact with LYS 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321J PHE* 2.8 42.4 + - + +
322J ALA* 3.8 6.5 - - - +
323J ILE 3.2 0.6 - - - -
324J LYS* 1.3 72.8 - - - +
326J THR* 1.3 59.2 + - - +
328J ASN* 3.7 18.2 + - - +
354K TRP* 3.4 57.7 - - + +
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Residues in contact with THR 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLN* 5.8 1.2 - - - +
207J ILE* 4.4 8.3 - - + -
258J HIS* 3.5 38.0 + - + -
259J LEU 4.7 6.5 - - - +
260J VAL* 4.2 0.2 - - - +
290J ALA* 3.6 21.7 - - + +
291J PRO 4.2 10.3 - - - +
293J VAL* 3.6 25.1 - - - +
322J ALA 3.0 12.9 + - - -
323J ILE 2.8 13.9 + - - -
325J LYS* 1.3 69.6 - - - +
327J LEU* 1.3 59.9 + - - +
328J ASN* 2.7 13.5 + - - +
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Residues in contact with LEU 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLN 4.3 9.7 - - - +
56E LYS* 5.8 0.7 - - - +
206J HIS* 3.6 24.7 - - + +
207J ILE* 3.9 12.3 - - + -
231J VAL* 3.8 28.7 - - + -
258J HIS* 3.4 42.4 - - + +
323J ILE* 3.2 26.4 + - + +
326J THR* 1.3 73.3 - - - +
328J ASN* 1.3 56.6 - - - +
329J ILE* 2.5 47.2 + - + +
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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
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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