Contacts of the helix formed by residues 315 - 327 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351M ALA* 5.3 0.3 - - - +
218P HIS* 5.1 3.8 - - - -
310P ASP* 3.4 33.2 + - + +
311P ASN* 3.9 21.5 + - - +
313P ILE* 3.1 6.4 + - + +
314P PRO* 1.3 75.0 - - - +
316P VAL* 1.3 68.9 + - - +
317P LYS* 3.2 25.7 - - + +
318P ASP* 2.8 39.9 + - - +
319P ILE* 3.1 16.0 + - - +
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Residues in contact with VAL 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P HIS* 3.9 26.4 - - + +
221P GLU* 3.9 31.4 - - + +
222P ALA* 4.2 15.7 - - + +
225P VAL* 5.0 4.5 - - + -
315P GLN* 1.3 68.3 - - - +
317P LYS* 1.3 73.5 + - - +
318P ASP 2.6 1.9 + - - -
319P ILE* 2.7 20.1 + - - -
320P ILE* 2.9 34.4 + - + -
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Residues in contact with LYS 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311P ASN* 5.8 2.3 + - - -
315P GLN* 4.1 26.7 - - + +
316P VAL* 1.3 82.3 - - - +
318P ASP* 1.3 67.9 + - - +
320P ILE* 3.1 10.8 + - - +
321P PHE* 2.9 27.2 + - + +
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Residues in contact with ASP 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351M ALA* 3.5 27.7 - - + +
352M ASN* 3.4 17.3 + - - +
355M ILE* 3.6 16.0 - - - +
295P VAL* 4.2 10.1 - - + +
313P ILE 4.2 0.2 - - - +
315P GLN* 2.8 49.7 + - - +
316P VAL 2.6 4.2 + - - -
317P LYS* 1.3 85.1 - - - +
319P ILE* 1.3 59.0 + - - +
321P PHE* 3.8 4.6 - - - +
322P ALA* 3.1 24.4 + - - +
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Residues in contact with ILE 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209P VAL* 4.7 2.2 - - + -
218P HIS* 4.6 16.4 - - + +
219P CYS* 4.1 15.5 - - - -
222P ALA* 4.2 16.2 - - + -
260P VAL* 5.0 2.2 - - + -
262P VAL* 3.5 46.0 - - + -
295P VAL* 4.7 7.4 - - + -
314P PRO* 4.4 10.8 - - + -
315P GLN 3.1 19.5 - - - +
316P VAL* 2.7 8.4 + - - +
318P ASP* 1.3 69.7 - - + +
320P ILE* 1.3 63.8 + - - +
322P ALA* 4.1 0.9 - - - +
323P ILE* 3.1 41.4 + - + +
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Residues in contact with ILE 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222P ALA* 4.3 8.1 - - + -
225P VAL* 4.0 28.9 - - + -
226P LEU* 4.3 24.5 - - + -
316P VAL* 2.9 38.4 + - + +
317P LYS* 3.4 9.2 - - - +
319P ILE* 1.3 73.3 - - - +
321P PHE* 1.3 68.0 + - - +
323P ILE* 3.4 4.4 + - - +
324P LYS* 3.0 47.3 + - + +
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Residues in contact with PHE 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352M ASN* 3.9 16.6 - - - +
354M TRP* 3.9 26.0 - + + -
317P LYS* 2.9 13.1 + - + +
318P ASP* 3.7 11.0 - - - +
320P ILE* 1.3 78.8 - - - +
322P ALA* 1.3 58.6 + - - +
324P LYS* 3.8 4.4 - - - +
325P LYS* 2.9 61.4 + - + +
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Residues in contact with ALA 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352M ASN* 4.4 2.5 - - + +
354M TRP* 3.8 25.4 - - + -
260P VAL* 4.6 4.3 - - + -
293P VAL* 4.4 10.8 - - + +
295P VAL* 3.7 29.8 - - + -
318P ASP 3.1 8.4 + - - +
319P ILE 3.6 2.0 + - - +
321P PHE* 1.3 76.5 - - - +
323P ILE* 1.3 68.6 + - - +
325P LYS* 3.3 1.9 + - - +
326P THR* 2.8 28.4 + - - -
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Residues in contact with ILE 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P ILE* 4.1 21.1 - - + -
209P VAL* 3.8 24.7 - - + -
222P ALA* 4.9 3.8 - - + -
226P LEU* 3.8 35.0 - - + -
231P VAL* 4.9 1.3 - - + -
233P CYS* 4.1 4.5 - - - -
260P VAL* 4.0 22.2 - - + -
319P ILE* 3.1 35.4 + - + +
320P ILE 3.9 2.7 - - - +
322P ALA* 1.3 74.8 - - - +
324P LYS* 1.3 58.8 + - + +
326P THR* 3.0 5.4 + - - -
327P LEU* 2.9 38.5 + - + +
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Residues in contact with LYS 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226P LEU* 4.3 12.3 - - + -
229P GLU* 3.7 29.0 + - - -
320P ILE* 3.0 36.8 + - + +
321P PHE* 4.0 4.5 - - - +
323P ILE* 1.3 72.8 - - + +
325P LYS* 1.3 64.3 + - - +
328P ASN* 3.1 18.0 + - - -
329P ILE* 3.3 55.5 + - + +
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Residues in contact with LYS 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354M TRP* 3.4 51.2 - - + +
321P PHE* 2.9 48.4 + - + +
322P ALA 3.5 4.5 - - - +
324P LYS* 1.3 78.3 - - - +
326P THR* 1.3 60.4 + - - +
328P ASN* 3.4 11.7 + - - +
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Residues in contact with THR 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354M TRP* 5.1 0.8 - - - -
207P ILE* 4.3 8.5 - - + -
258P HIS* 3.3 39.4 + - + -
259P LEU 4.6 7.0 - - - +
260P VAL* 3.8 2.5 - - - +
290P ALA* 3.6 21.0 - - + +
291P PRO* 3.9 13.0 - - + +
293P VAL* 2.9 25.7 - - - +
322P ALA 2.8 20.5 + - - -
323P ILE 3.0 8.2 + - - -
325P LYS* 1.3 73.8 - - - +
327P LEU* 1.3 59.4 + - - +
328P ASN* 3.2 2.1 + - - +
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Residues in contact with LEU 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P HIS* 3.8 17.3 - - + +
207P ILE* 3.9 20.4 - - + -
231P VAL* 3.6 31.4 - - + -
258P HIS* 3.4 43.5 - - + +
323P ILE* 2.9 20.2 + - + +
326P THR* 1.3 75.2 - - - +
328P ASN* 1.3 68.5 + - - +
329P ILE* 2.8 31.9 + - + +
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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