Contacts of the helix formed by residues 317 - 331 (chain A) in PDB entry 2X14
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 GLY 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A ASP* 3.0 27.6 + - - -
286A PHE* 4.2 6.7 - - - -
287A VAL* 4.9 4.3 - - - -
316A CYS* 1.3 75.9 - - - +
318A PRO* 1.3 76.9 - - - +
320A SER* 3.3 2.6 + - - -
321A SER* 3.1 23.9 + - - -
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Residues in contact with PRO 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASP* 3.3 10.1 - - - +
287A VAL* 6.3 0.2 - - + -
317A GLY* 1.3 82.8 - - - +
319A GLU* 1.3 65.8 + - + +
321A SER* 3.2 9.5 + - - -
322A LYS* 3.0 26.9 + - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A VAL* 3.7 19.1 - - + -
285A ASP* 2.9 18.6 + - + +
318A PRO* 1.3 84.0 - - + +
320A SER* 1.3 61.9 + - - +
322A LYS* 3.4 20.3 + - - +
323A LYS* 3.2 27.0 + - - +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PRO* 3.3 12.2 - - - +
284A VAL* 2.7 32.0 + - - +
285A ASP* 2.7 25.5 + - - -
316A CYS* 3.6 19.7 - - - -
317A GLY 3.6 4.5 - - - -
318A PRO 3.3 0.2 - - - -
319A GLU* 1.3 74.5 - - - +
321A SER* 1.3 59.7 + - - +
323A LYS* 3.1 7.0 + - - +
324A TYR* 2.8 38.9 + - - -
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A CYS* 3.7 12.3 - - - -
317A GLY 3.1 15.5 + - - -
318A PRO* 3.2 12.7 + - - +
320A SER* 1.3 77.1 - - - +
322A LYS* 1.3 56.6 + - - +
324A TYR* 3.5 9.8 + - - +
325A ALA* 2.9 29.6 + - - +
350A ARG* 5.3 0.3 - - - +
351A GLY* 3.9 14.9 + - - -
354A ALA* 4.1 17.6 - - - +
355A LEU 6.0 0.2 - - - -
358A GLU* 5.4 0.9 - - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A PRO 3.0 12.2 + - - +
319A GLU* 3.6 24.0 - - - +
320A SER 3.2 0.2 - - - -
321A SER* 1.3 76.6 - - - +
323A LYS* 1.3 56.8 + - + +
325A ALA* 3.3 7.9 + - + +
326A GLU* 3.0 52.2 + - + +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR* 4.1 22.7 + - + +
282A LEU 5.2 4.0 - - - +
284A VAL* 4.6 25.4 - - + -
319A GLU* 3.2 14.8 + - - +
320A SER* 3.1 11.2 + - - +
322A LYS* 1.3 74.8 - - + +
324A TYR* 1.3 63.5 + - + +
326A GLU* 3.4 27.0 + - - +
327A ALA* 3.2 20.8 + - - +
330A ARG* 5.1 0.9 + - - -
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Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ILE* 3.6 37.7 - - + +
237A GLY* 3.7 12.9 - - - -
238A GLY 4.6 1.4 + - - -
281A THR* 3.8 20.6 - - + -
283A PRO* 3.3 44.4 - - + +
316A CYS* 3.8 26.5 - - - +
320A SER* 2.8 27.7 + - - +
321A SER* 3.7 7.4 - - - +
323A LYS* 1.3 71.4 - - + +
325A ALA* 1.3 63.0 + - - +
327A ALA* 3.2 5.0 + - - +
328A VAL* 3.0 27.7 + - - +
340A VAL* 4.0 18.6 - - + -
351A GLY 5.4 0.4 - - - -
355A LEU* 4.3 26.9 - - + -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A SER 2.9 18.1 + - - +
322A LYS* 3.3 8.9 + - + +
324A TYR* 1.3 76.4 - - - +
326A GLU* 1.3 57.4 + - - +
328A VAL* 3.4 5.0 + - - +
329A THR* 2.9 33.2 + - - +
355A LEU* 5.3 0.2 - - - +
358A GLU* 3.5 41.0 - - + +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LYS* 3.0 47.0 + - + +
323A LYS* 3.5 32.4 + - - +
325A ALA* 1.3 76.2 - - - +
327A ALA* 1.3 61.9 + - - +
329A THR* 3.3 8.2 + - - -
330A ARG* 3.2 43.6 + - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.0 11.2 - - + +
233A GLU* 3.8 13.6 - - - +
235A ILE* 4.1 22.4 - - + -
281A THR* 4.3 5.8 - - - +
323A LYS 3.2 8.7 + - - +
324A TYR 3.2 8.6 + - - +
326A GLU* 1.3 74.4 - - - +
328A VAL* 1.3 65.4 + - - +
330A ARG* 3.2 28.2 + - - +
331A ALA* 3.2 20.1 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.0 20.0 - - + -
211A ILE* 4.2 6.5 - - + -
235A ILE* 4.8 0.4 - - + -
324A TYR 3.0 18.5 + - - +
325A ALA* 3.6 9.4 - - - +
327A ALA* 1.3 72.1 - - - +
329A THR* 1.3 66.5 + - - +
331A ALA* 3.1 11.1 + - - +
334A ILE* 3.9 10.3 - - + -
355A LEU* 3.7 26.0 - - + -
358A GLU* 3.7 31.9 - - + +
359A VAL* 4.3 2.5 - - + +
362A ALA* 3.8 15.2 - - + +
365A ARG* 3.0 16.3 + - - -
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ALA* 2.9 17.1 + - - +
326A GLU* 3.3 11.3 + - - -
328A VAL* 1.3 77.9 - - - +
330A ARG* 1.3 59.5 + - + +
331A ALA 4.0 0.2 - - - +
332A LYS* 5.5 2.1 - - - -
358A GLU* 4.9 5.0 + - - -
365A ARG* 3.1 22.6 + - - +
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 3.3 26.2 - - + +
233A GLU* 2.8 44.4 + - - +
279A LYS* 3.2 31.6 - - - +
281A THR* 4.4 3.0 + - - -
323A LYS 5.1 0.8 + - - -
326A GLU* 3.2 36.5 + - - +
327A ALA* 3.5 19.8 - - - +
328A VAL 3.2 0.4 - - - -
329A THR* 1.3 79.1 - - + +
331A ALA* 1.3 60.8 + - - +
332A LYS* 4.6 5.4 - - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 3.6 8.1 - - - +
209A LEU* 3.9 12.3 - - + -
233A GLU* 5.8 0.4 - - - -
327A ALA 3.2 11.5 + - - +
328A VAL 3.1 13.6 + - - +
330A ARG* 1.3 77.6 - - - +
332A LYS* 1.3 54.7 + - - +
333A GLN 3.9 7.0 - - - +
334A ILE* 3.6 30.5 - - + -
365A ARG* 2.7 39.5 + - - -
367A CYS* 3.6 1.9 - - - -
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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