Contacts of the helix formed by residues 319 - 335 (chain A) in PDB entry 2UVL
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 CYS 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A CYS* 3.9 4.7 - - - -
295A CYS* 3.7 20.1 - - + +
312A HIS* 3.4 6.5 - - - +
316A PHE* 3.2 16.7 + - - +
317A PRO 3.3 0.6 - - - -
318A ARG* 1.3 75.2 - - - +
320A GLU* 1.3 58.7 + - - +
321A TYR* 3.3 22.6 + - - -
322A LEU* 3.3 14.1 + - + +
323A ILE* 3.0 28.6 + - - +
1336A ZN 2.4 35.9 - - - -
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Residues in contact with GLU 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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244A ARG* 4.7 9.5 + - - +
246A THR* 3.9 31.2 - - + +
294A CYS* 4.1 13.5 - - - -
318A ARG 3.1 7.1 + - - +
319A CYS* 1.3 73.6 - - - +
321A TYR* 1.3 57.2 + - - +
323A ILE* 3.8 26.2 - - - +
324A ARG* 3.0 28.6 + - - +
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Residues in contact with TYR 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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253A GLN 5.7 1.3 - - - -
258A ARG* 3.5 16.1 + - - -
278A SER* 2.7 17.9 + - - -
279A ALA 3.9 9.2 - - - -
280A GLY* 3.6 20.2 - - - -
292A CYS* 4.9 0.2 - - - -
293A PHE* 3.6 26.5 - + + -
294A CYS* 3.5 28.0 - - + -
309A TRP* 3.4 20.5 - + - -
312A HIS* 4.5 4.0 - + - -
319A CYS* 3.2 5.1 - - - -
320A GLU* 1.3 76.6 - - - +
322A LEU* 1.3 68.7 + - - +
324A ARG* 3.1 28.7 + - - +
325A ILE* 3.0 49.0 + - + +
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Residues in contact with LEU 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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309A TRP* 3.4 43.5 - - + +
312A HIS* 3.7 15.9 - - + +
313A ALA* 3.4 35.4 - - + +
316A PHE 3.5 18.8 - - - +
317A PRO* 4.2 2.5 - - + +
319A CYS* 3.3 16.8 + - + +
321A TYR* 1.3 81.1 - - - +
323A ILE* 1.3 57.4 + - - +
326A LYS* 2.9 44.8 + - + +
327A GLY 3.6 0.3 + - - -
330A PHE* 4.6 1.6 - - + -
331A ILE* 3.9 19.8 - - + +
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Residues in contact with ILE 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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317A PRO 4.2 3.4 - - - +
318A ARG* 3.7 20.4 - - - +
319A CYS 3.0 19.0 + - - +
320A GLU* 3.8 26.2 - - - +
322A LEU* 1.3 73.1 - - - +
324A ARG* 1.3 63.8 + - - +
327A GLY* 2.8 29.7 + - - +
328A GLN* 4.0 36.6 - - + +
331A ILE* 3.5 24.2 - - + -
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Residues in contact with ARG 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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253A GLN 5.7 1.6 + - - -
293A PHE* 4.9 5.7 - - - -
320A GLU 3.0 19.7 + - - +
321A TYR* 3.1 34.4 + - - +
323A ILE* 1.3 78.8 - - - +
325A ILE* 1.3 76.4 + - + +
327A GLY 4.9 0.2 + - - -
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Residues in contact with ILE 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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309A TRP* 3.7 27.4 - - + +
321A TYR* 3.0 43.0 + - + +
324A ARG* 1.3 106.9 - - + +
326A LYS* 1.3 68.5 + - + +
327A GLY 3.6 0.2 - - - -
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A TRP* 3.6 53.3 - - + +
322A LEU* 2.9 15.2 + - + +
325A ILE* 1.3 84.6 - - + +
327A GLY* 1.3 64.7 + - - +
329A GLU* 5.8 0.2 - - - +
330A PHE* 3.2 64.6 + - + +
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Residues in contact with GLY 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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322A LEU 3.6 1.0 + - - -
323A ILE* 2.8 21.2 + - - -
324A ARG 4.9 0.2 + - - -
325A ILE 3.6 0.4 - - - -
326A LYS* 1.3 83.8 - - - +
328A GLN* 1.3 65.8 + - - -
329A GLU* 3.3 3.1 - - - -
330A PHE 3.2 7.1 + - - -
331A ILE* 3.4 18.1 + - - +
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Residues in contact with GLN 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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323A ILE* 4.0 40.2 - - + +
327A GLY* 1.3 69.4 - - - -
329A GLU* 1.3 60.6 + - - +
331A ILE* 3.3 9.4 + - + +
332A ARG* 2.8 60.6 + - + +
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A LYS 5.8 0.4 - - - +
327A GLY* 3.3 1.2 - - - -
328A GLN* 1.3 78.8 - - - +
330A PHE* 1.3 62.5 + - - +
332A ARG* 3.3 26.0 + - - +
333A GLN* 3.0 23.4 + - - +
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Residues in contact with PHE 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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307A ASP* 5.4 0.9 - - - -
309A TRP* 3.9 24.7 - - + -
310A VAL* 4.1 17.3 - - + -
313A ALA* 4.1 10.3 - - + -
322A LEU* 4.6 1.3 - - + -
326A LYS* 3.2 67.0 + - + +
327A GLY 3.2 3.1 + - - +
329A GLU* 1.3 77.5 - - - +
331A ILE* 1.3 70.6 + - + +
333A GLN* 3.3 27.2 + - - +
334A VAL* 3.1 32.0 + - + +
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Residues in contact with ILE 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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313A ALA* 4.3 11.4 - - + -
317A PRO* 3.5 44.0 - - + +
322A LEU* 3.9 26.0 - - + +
323A ILE* 3.5 35.0 - - + -
327A GLY 3.5 15.0 - - - +
328A GLN* 3.3 11.6 + - + +
330A PHE* 1.3 77.8 - - + +
332A ARG* 1.3 63.4 + - + +
334A VAL* 3.1 3.6 + - - +
335A GLN* 2.8 31.9 + - + +
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Residues in contact with ARG 332 (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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328A GLN* 2.8 43.2 + - + +
329A GLU* 3.6 34.6 + - - +
331A ILE* 1.3 77.0 - - + +
333A GLN* 1.3 62.3 + - - +
335A GLN* 3.2 22.6 + - - +
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Residues in contact with GLN 333 (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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310A VAL* 6.0 0.4 - - - +
329A GLU 3.0 13.4 + - - +
330A PHE* 3.3 26.2 + - - +
332A ARG* 1.3 79.2 - - - +
334A VAL* 1.3 84.4 + - - +
335A GLN 3.3 5.7 - - - +
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Residues in contact with VAL 334 (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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310A VAL* 3.7 42.2 - - + +
313A ALA* 3.8 7.9 - - + -
314A LYS* 3.8 32.5 + - + +
330A PHE* 3.1 39.4 + - + +
331A ILE 3.1 5.6 + - - +
333A GLN* 1.3 91.0 - - - +
335A GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 335 (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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313A ALA 2.8 26.2 + - - +
314A LYS* 3.0 22.0 + - - +
317A PRO* 3.5 27.1 - - + +
331A ILE* 2.8 24.0 + - + +
332A ARG* 3.2 19.6 - - - +
333A GLN 3.3 5.9 - - - +
334A VAL* 1.3 78.1 - - - +
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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