Contacts of the helix formed by residues 307 - 324 (chain A) in PDB entry 2UVW
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 SER 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A TYR* 3.6 0.8 + - - -
305A GLY 3.9 3.2 + - - -
306A ILE* 1.3 78.8 - - - +
308A LYS* 1.3 64.5 + - - +
309A GLU* 3.0 26.8 + - - +
310A THR* 2.9 37.9 + - - -
311A ALA 2.9 9.7 + - - -
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Residues in contact with LYS 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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269A ILE* 4.4 0.9 - - + -
270A GLU* 3.1 39.8 + - - +
273A TYR* 3.7 52.6 + - + -
307A SER* 1.3 72.2 - - - +
309A GLU* 1.3 74.8 + - - +
311A ALA* 3.0 12.0 + - - +
312A TYR* 3.0 30.2 + - + -
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Residues in contact with GLU 309 (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 SER* 3.0 28.2 + - - +
308A LYS* 1.3 92.4 - - + +
310A THR* 1.3 61.2 + - - +
312A TYR* 3.5 13.3 + - - +
313A SER* 3.7 14.4 + - - -
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Residues in contact with THR 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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302A PHE* 4.3 27.6 - - + -
304A HIS* 5.3 8.8 - - + -
306A ILE* 3.7 17.0 - - + -
307A SER* 2.9 25.8 + - - -
309A GLU* 1.3 76.4 - - - +
311A ALA* 1.3 59.1 + - - +
313A SER* 3.7 6.0 + - - +
314A GLU* 3.0 26.5 + - + +
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Residues in contact with ALA 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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269A ILE* 4.0 8.3 - - + -
273A TYR* 3.8 27.6 - - + +
284A ILE* 3.9 7.2 - - + +
306A ILE* 3.6 5.8 - - + +
307A SER 2.9 10.2 + - - +
308A LYS 3.0 9.4 + - - +
310A THR* 1.3 75.9 - - - +
312A TYR* 1.3 57.1 + - - +
314A GLU* 4.7 0.4 - - - -
315A SER* 2.8 39.1 + - - -
337A PHE* 4.0 17.5 - - + -
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Residues in contact with TYR 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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266A PHE* 3.3 53.6 + + + +
269A ILE* 3.6 24.2 - - + -
270A GLU* 2.6 44.2 + - - +
308A LYS* 3.0 30.8 + - + -
309A GLU* 3.7 10.3 - - - +
310A THR 3.4 0.4 - - - -
311A ALA* 1.3 73.7 - - - +
313A SER* 1.3 59.3 + - - +
315A SER* 2.7 22.5 + - - -
316A VAL* 2.8 18.6 - - - +
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Residues in contact with SER 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 GLU 3.7 9.1 + - - -
310A THR* 3.7 9.9 + - - +
312A TYR* 1.3 75.2 - - - +
314A GLU* 1.3 68.6 + - - +
316A VAL* 3.0 19.6 + - - +
317A LYS* 3.2 31.8 + - - +
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Residues in contact with GLU 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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284A ILE* 4.1 15.9 - - + -
300A ARG* 3.0 41.3 + - - -
302A PHE* 3.6 26.4 - - + -
306A ILE* 6.0 0.4 - - + -
310A THR* 3.0 20.9 + - + +
311A ALA* 4.0 2.9 - - - +
313A SER* 1.3 81.6 + - - +
315A SER* 1.3 62.2 + - - +
317A LYS* 3.3 22.0 + - - +
318A LEU* 3.2 37.1 + - + +
321A LYS* 5.8 0.3 + - - -
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Residues in contact with SER 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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265A LEU* 3.6 15.4 - - - +
266A PHE* 4.3 0.5 - - - -
269A ILE* 3.1 24.0 - - - +
284A ILE* 3.9 8.5 - - - +
286A VAL* 3.5 27.9 - - - +
311A ALA 2.8 17.1 + - - -
312A TYR 2.7 18.9 + - - -
314A GLU* 1.3 74.2 - - - +
316A VAL* 1.3 63.5 + - - +
318A LEU* 4.3 2.5 - - - -
319A LEU* 3.2 22.3 + - - +
335A VAL* 4.8 0.4 - - - -
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Residues in contact with VAL 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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258A LEU* 4.4 17.3 - - + -
262A LYS* 4.6 14.4 - - + +
265A LEU* 4.6 3.6 - - + -
266A PHE* 3.8 26.5 - - + -
312A TYR 2.8 27.1 - - - +
313A SER* 3.0 10.0 + - - +
315A SER* 1.3 76.2 + - - +
317A LYS* 1.3 65.9 + - + +
319A LEU* 3.3 7.5 + - - +
320A GLN* 2.9 42.6 + - + +
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Residues in contact with LYS 317 (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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300A ARG* 5.2 4.0 - - - +
313A SER* 3.2 28.2 + - - +
314A GLU* 3.3 29.8 + - - +
316A VAL* 1.3 74.2 - - + +
318A LEU* 1.3 54.9 + - + +
320A GLN* 2.8 21.3 + - - +
321A LYS* 2.7 39.5 + - - +
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Residues in contact with LEU 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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284A ILE* 4.1 27.4 - - + +
286A VAL* 3.7 29.2 - - + +
298A ARG* 3.6 38.8 - - + +
299A GLY* 3.9 13.7 - - - +
300A ARG* 4.9 0.7 - - + -
314A GLU* 3.2 32.3 + - - +
315A SER* 3.9 1.8 - - - +
316A VAL 3.4 0.2 - - - -
317A LYS* 1.3 76.8 - - + +
319A LEU* 1.3 57.0 + - - +
321A LYS* 3.2 24.1 + - - +
322A ILE* 2.8 33.7 + - - +
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Residues in contact with LEU 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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258A LEU* 3.6 25.4 - - + -
261A ILE* 3.8 26.2 - - + -
262A LYS* 4.8 6.5 - - + +
265A LEU* 3.9 20.9 - - + -
286A VAL* 4.5 6.7 - - + +
315A SER 3.2 14.5 + - - +
316A VAL* 3.5 8.5 - - - +
317A LYS 3.1 0.8 - - - -
318A LEU* 1.3 76.1 - - - +
320A GLN* 1.3 57.8 + - - +
322A ILE* 3.3 6.8 + - + +
323A LEU* 3.0 31.1 + - + +
330A ILE* 4.0 27.4 - - + -
333A ILE* 4.0 17.0 - - + -
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Residues in contact with GLN 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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258A LEU* 3.5 33.2 - - + +
316A VAL* 2.9 29.0 + - - +
317A LYS* 2.8 24.7 + - - +
319A LEU* 1.3 72.2 - - - +
321A LYS* 1.3 59.1 + - - +
323A LEU* 3.4 10.1 + - + +
324A GLU* 2.9 38.8 + - - +
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Residues in contact with LYS 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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298A ARG* 4.1 24.7 - - + +
299A GLY 5.4 2.4 + - - -
314A GLU* 5.8 0.4 + - - -
317A LYS* 2.7 13.8 + - - +
318A LEU* 3.3 26.9 - - - +
320A GLN* 1.3 75.3 - - - +
322A ILE* 1.3 65.5 + - - +
324A GLU* 3.2 26.0 + - + +
325A GLU* 3.1 43.5 - - - +
8P G 4.7 4.9 + - - +
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Residues in contact with ILE 322 (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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286A VAL* 3.7 41.1 - - + +
288A ALA* 4.0 28.0 - - + -
296A VAL* 4.1 23.1 - - + +
297A SER* 4.4 2.0 - - - -
298A ARG* 3.6 22.0 - - + +
318A LEU 2.8 15.7 + - - +
319A LEU* 3.3 11.2 + - + +
321A LYS* 1.3 75.5 - - - +
323A LEU* 1.3 65.1 + - - +
325A GLU* 3.1 13.8 + - - -
326A ASP* 3.2 20.0 + - + +
330A ILE* 4.4 12.6 - - + -
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Residues in contact with LEU 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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256A ARG* 2.7 78.7 + - - +
258A LEU* 3.9 29.4 - - + +
261A ILE* 4.6 2.5 - - + -
319A LEU* 3.0 30.0 + - + +
320A GLN* 3.7 7.6 - - - +
322A ILE* 1.3 77.6 - - - +
324A GLU* 1.3 56.7 + - - +
325A GLU 3.2 2.0 + - - -
326A ASP 3.2 8.9 + - - +
327A GLU* 5.0 0.2 - - - -
328A ARG 5.2 0.4 - - - +
330A ILE* 4.2 19.3 - - + -
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Residues in contact with GLU 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 GLN* 2.9 31.2 + - - +
321A LYS* 3.2 21.8 + - - +
323A LEU* 1.3 74.5 - - - +
325A GLU* 1.3 71.5 + - + +
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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