Contacts of the helix formed by residues 319 - 330 (chain A) in PDB entry 1X0X
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 PHE 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.5 31.2 - - + +
237A ALA* 4.1 4.7 - - + -
238A PHE* 3.6 27.6 - + + -
241A LEU* 4.3 20.0 - - + -
310A LEU* 3.6 43.3 - - + -
315A LEU* 5.1 0.9 - - + -
316A VAL 3.4 4.0 + - - -
318A LYS* 1.3 91.4 - - + +
320A PRO* 1.3 55.6 - - - +
321A LEU 3.5 2.2 - - - -
322A PHE* 3.2 26.7 + + + -
323A MET* 2.7 38.6 + - - +
349A MET* 3.7 22.4 - - + -
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Residues in contact with PRO 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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234A GLU* 3.2 11.4 - - - +
316A VAL 5.5 0.7 - - - +
317A ASP 4.3 12.0 - - - +
318A LYS 3.2 9.2 - - - +
319A PHE* 1.3 86.5 - - - +
321A LEU* 1.3 55.1 + - - +
323A MET* 3.6 4.4 - - + +
324A ALA* 2.7 37.4 + - - +
341A CYS* 4.0 16.2 - - + +
345A HIS* 4.3 10.8 - - + +
346A PRO* 4.3 24.2 - - + -
349A MET* 5.2 0.2 - - + -
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Residues in contact with LEU 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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207A VAL* 4.7 16.4 - - - +
227A VAL* 4.5 14.1 - - + +
230A LEU* 4.1 15.9 - - + -
231A GLY* 4.5 15.0 - - - +
234A GLU* 2.9 23.6 + - - +
320A PRO* 1.3 70.6 - - - +
322A PHE* 1.3 72.9 + - + +
324A ALA* 3.2 2.8 + - - +
325A VAL* 3.1 28.4 + - + +
338A PHE* 4.0 19.1 - - + -
341A CYS* 3.7 10.0 - - - -
342A LEU* 3.4 33.2 - - + -
345A HIS* 4.2 6.1 - - + -
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Residues in contact with PHE 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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203A LEU* 4.2 13.2 - - + -
206A VAL* 3.9 20.6 - - + +
207A VAL* 4.1 24.9 - - + -
231A GLY* 4.4 1.8 - - - -
234A GLU* 3.0 46.1 + - + -
235A MET* 3.8 20.4 - - + -
238A PHE* 4.0 15.3 - + + -
303A ALA* 4.6 0.7 - - - +
306A LEU* 3.8 23.1 - - + -
310A LEU* 5.2 2.0 - - + -
319A PHE* 3.2 27.3 + + + +
321A LEU* 1.3 77.0 - - + +
323A MET* 1.3 82.5 + - + +
325A VAL* 3.0 15.1 + - - +
326A TYR* 3.1 9.7 + - - +
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Residues in contact with MET 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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303A ALA 4.1 8.3 - - - +
306A LEU* 4.2 4.3 - - + -
307A TYR* 3.8 42.0 - - - +
310A LEU* 4.1 14.4 - - + -
316A VAL* 3.3 43.5 - - + +
319A PHE 2.7 24.2 + - - +
320A PRO* 3.9 4.5 - - + +
322A PHE* 1.3 91.5 - - + +
324A ALA* 1.3 56.9 + - - +
326A TYR* 3.2 8.2 + - + +
327A LYS* 2.8 51.6 + - - +
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Residues in contact with ALA 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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320A PRO 2.7 22.4 + - - +
321A LEU 3.5 5.8 - - - +
322A PHE 3.2 0.4 - - - -
323A MET* 1.3 70.4 - - - +
325A VAL* 1.3 64.9 + - - +
327A LYS* 4.7 3.3 - - - +
328A VAL* 3.1 30.7 + - + +
333A GLN* 4.1 12.6 - - - +
338A PHE* 3.8 14.9 - - + -
341A CYS* 3.6 27.1 - - + -
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Residues in contact with VAL 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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206A VAL* 3.7 31.2 - - + +
209A VAL* 3.7 33.4 - - + -
210A GLY* 4.1 6.7 - - - +
213A PHE* 4.3 6.7 - - + -
299A GLY 5.4 0.2 - - - +
300A PRO* 5.5 0.2 - - + -
303A ALA* 4.3 7.0 - - + -
321A LEU* 3.1 24.0 + - + +
322A PHE 3.0 7.8 + - - +
324A ALA* 1.3 78.3 - - - +
326A TYR* 1.3 63.4 + - - +
328A VAL* 3.4 1.6 + - - +
329A CYS* 3.0 29.0 + - - -
338A PHE* 3.9 15.7 - - + -
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Residues in contact with TYR 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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303A ALA* 4.1 14.1 - - + +
304A ARG* 3.8 34.6 - - + +
307A TYR* 3.6 49.3 - + + -
322A PHE 3.1 11.7 + - - +
323A MET* 3.2 17.0 + - + +
325A VAL* 1.3 78.4 - - - +
327A LYS* 1.3 68.0 + - + +
329A CYS* 4.7 0.2 - - - -
330A TYR* 2.9 64.5 + + + +
331A GLU* 3.7 26.3 + - + +
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Residues in contact with LYS 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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307A TYR* 6.0 2.7 - - - -
316A VAL* 5.5 8.3 - - - +
320A PRO 5.8 0.2 + - - -
323A MET* 2.8 42.9 + - + +
324A ALA* 4.9 1.6 - - - +
326A TYR* 1.3 79.0 - - + +
328A VAL* 1.3 60.1 + - - +
331A GLU* 2.8 61.2 + - - +
332A GLY 3.1 9.0 + - - -
333A GLN* 3.3 31.4 + - + +
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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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213A PHE* 3.5 29.4 - - + -
277A PHE* 3.3 36.1 - - + -
324A ALA* 3.1 20.4 + - + +
327A LYS* 1.3 78.0 - - - +
329A CYS* 1.3 60.6 + - - +
332A GLY* 4.3 6.9 + - - -
333A GLN* 3.6 38.9 - - + +
334A PRO 4.2 0.7 - - - +
335A VAL* 4.2 21.5 - - - +
338A PHE* 4.8 9.9 - - + +
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Residues in contact with CYS 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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209A VAL* 4.1 7.4 - - - -
213A PHE* 4.0 17.7 - - - -
277A PHE* 4.5 9.6 - - - -
284A ILE* 3.2 38.0 - - + +
300A PRO* 4.0 14.1 - - - -
325A VAL* 3.0 23.4 + - - +
326A TYR* 4.7 0.4 - - - -
328A VAL* 1.3 80.5 - - - +
330A TYR* 1.3 84.5 + - + +
332A GLY 5.1 0.2 - - - -
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Residues in contact with TYR 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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284A ILE* 5.6 4.9 - - + +
300A PRO* 3.4 40.4 - - + +
301A GLU* 3.4 1.7 + - - +
303A ALA* 5.3 0.4 - - + -
304A ARG* 3.3 45.4 + - + -
326A TYR* 2.9 47.0 + + + +
329A CYS* 1.3 99.7 - - + +
331A GLU* 1.3 62.0 + - - +
332A GLY 3.5 2.2 + - - -
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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