Contacts of the helix formed by residues 307 - 316 (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 ASP 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A GLY 3.3 6.0 + - - +
306A ASP* 1.3 71.6 - - - +
308A PRO* 1.3 74.2 - - - +
309A TRP* 3.5 15.6 + - - +
310A VAL* 3.0 34.4 + - + +
311A GLN* 3.0 27.8 + - - +
330A PHE* 5.4 0.5 - - - -
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Residues in contact with PRO 308 (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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271A VAL* 5.4 4.7 - - + -
272A ASN 5.0 0.9 - - - +
275A GLN* 3.8 37.7 - - + +
276A LEU* 3.9 25.8 - - + +
279A ALA* 3.6 21.5 - - + -
281A PHE* 3.6 7.5 - - + -
302A TRP* 4.1 14.8 - - + -
306A ASP 3.4 10.7 - - - +
307A ASP* 1.3 88.6 - - - +
309A TRP* 1.3 58.2 + - + +
311A GLN* 3.6 1.2 + - - +
312A HIS* 3.0 27.7 + - - +
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Residues in contact with TRP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN 5.6 1.1 - - - -
278A SER* 3.2 24.5 - - - -
279A ALA* 3.6 27.0 - - + +
307A ASP* 3.3 12.9 + - - +
308A PRO* 1.3 77.1 - - + +
310A VAL* 1.3 67.5 + - - +
312A HIS* 3.3 6.0 + - - +
313A ALA* 3.1 23.7 + - - +
321A TYR* 3.4 24.7 - + - -
322A LEU* 3.4 41.6 - - + +
325A ILE* 3.7 29.8 - - + +
326A LYS* 3.6 28.4 - - + +
330A PHE* 3.9 17.9 - - + -
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Residues in contact with VAL 310 (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* 3.0 34.1 + - + +
309A TRP* 1.3 76.7 - - - +
311A GLN* 1.3 65.7 + - - +
313A ALA* 3.2 1.9 + - - -
314A LYS* 2.8 39.5 + - - +
330A PHE* 4.1 17.3 - - + -
333A GLN* 6.0 0.7 - - - +
334A VAL* 3.7 28.6 - - + +
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Residues in contact with GLN 311 (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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299A LEU* 4.1 3.7 - - + +
302A TRP* 3.8 22.9 - - + -
306A ASP* 3.7 18.2 + - - -
307A ASP 3.0 21.2 + - - +
308A PRO 3.8 3.6 - - - +
310A VAL* 1.3 85.5 - - - +
312A HIS* 1.3 61.3 + - - +
314A LYS* 4.0 17.5 - - - +
315A TRP* 3.0 43.8 + - - +
242B SER* 2.6 45.3 + - - +
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Residues in contact with HIS 312 (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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279A ALA 2.8 29.2 + - - -
281A PHE* 3.5 15.6 - + + -
292A CYS* 3.2 17.2 - - + +
295A CYS* 3.7 0.6 - - - -
308A PRO 3.0 17.9 + - - +
309A TRP* 3.6 12.2 - - - +
310A VAL 3.3 0.2 - - - -
311A GLN* 1.3 76.0 - - - +
313A ALA* 1.3 58.9 + - - +
316A PHE* 2.8 52.9 + + + -
319A CYS* 3.4 11.9 - - + -
321A TYR* 4.5 5.6 - + - -
322A LEU* 3.8 15.0 - - + -
1336A ZN 1.9 38.1 - - - -
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Residues in contact with ALA 313 (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 3.1 16.4 + - - +
310A VAL 3.7 3.8 - - - +
312A HIS* 1.3 74.3 - - - +
314A LYS* 1.3 62.5 + - - +
317A PRO* 3.6 12.0 - - - +
322A LEU* 3.4 19.5 - - + +
330A PHE* 4.1 12.6 - - + -
331A ILE* 4.3 12.3 - - + -
334A VAL* 3.8 20.9 - - + -
335A GLN* 2.8 23.4 + - - +
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Residues in contact with LYS 314 (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* 2.8 24.2 + - - +
311A GLN* 3.5 25.8 - - - +
313A ALA* 1.3 77.2 - - - +
315A TRP* 1.3 75.4 + - + +
317A PRO* 4.1 0.5 - - - +
334A VAL* 3.8 23.9 + - + +
335A GLN* 3.0 20.2 + - - +
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Residues in contact with TRP 315 (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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299A LEU* 3.5 14.8 - - + +
311A GLN* 3.0 37.4 + - - +
314A LYS* 1.3 93.2 - - + +
316A PHE* 1.3 91.0 + - + +
317A PRO* 3.4 8.1 - - - +
242B SER* 3.3 28.3 + - - -
243B MET* 4.1 4.3 - - + -
244B ARG* 3.5 52.5 + - + -
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Residues in contact with PHE 316 (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 PHE* 5.0 2.9 - + - -
295A CYS* 3.8 25.4 - - + -
297A GLY* 3.4 35.9 - - - -
298A GLY 3.6 12.8 - - - -
299A LEU* 3.7 23.3 - - + -
312A HIS* 2.8 35.5 + + + +
315A TRP* 1.3 104.2 - - + +
317A PRO* 1.4 64.0 - - - +
318A ARG* 3.1 5.1 + - - -
319A CYS* 3.2 16.9 + - + +
322A LEU* 3.5 2.9 - - - +
244B ARG* 3.8 32.1 - - + -
246B THR* 4.3 0.7 - - - -
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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