Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 1W59
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 THR 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.9 3.6 - - - -
261A ARG* 5.5 0.2 - - - +
294A ASP 3.5 13.5 - - - +
295A LEU* 1.3 79.4 - - - +
297A LEU* 1.3 63.6 + - - +
298A GLU* 3.0 30.3 + - + +
299A GLU* 3.0 31.1 + - + +
300A ALA* 3.5 7.4 + - - +
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Residues in contact with LEU 297 (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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231A LEU* 3.6 46.5 - - + +
232A ILE* 3.9 21.1 - - + -
296A THR* 1.3 73.7 - - - +
298A GLU* 1.3 54.5 + - + +
299A GLU 3.3 0.2 - - - -
300A ALA* 3.4 3.6 + - - +
301A ARG* 2.8 59.7 + - - +
319A TRP* 4.3 13.4 - - + -
321A ALA* 4.8 3.6 - - + -
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Residues in contact with GLU 298 (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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296A THR* 3.0 16.1 - - + +
297A LEU* 1.3 78.1 - - + +
299A GLU* 1.3 60.7 + - + +
301A ARG* 3.2 10.9 + - - +
302A GLU* 2.9 27.2 + - - +
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Residues in contact with GLU 299 (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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261A ARG* 2.6 46.7 + - - +
262A ALA* 3.6 26.1 + - + +
289A VAL* 5.3 1.1 - - + -
295A LEU* 3.3 12.6 - - + +
296A THR* 3.0 42.0 + - + +
298A GLU* 1.3 71.7 - - + +
300A ALA* 1.3 67.0 + - - +
302A GLU* 2.8 18.5 + - - +
303A VAL* 2.9 17.6 + - - +
331A VAL* 4.5 1.1 - - + +
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Residues in contact with ALA 300 (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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289A VAL* 3.5 36.0 - - + +
295A LEU* 5.0 0.6 - - + +
296A THR 3.5 6.7 + - - +
297A LEU* 3.4 9.8 + - - +
299A GLU* 1.3 79.0 - - - +
301A ARG* 1.3 61.6 + - - +
303A VAL* 3.2 4.1 + - - +
304A VAL* 3.1 30.8 + - - +
319A TRP* 4.0 12.6 - - + -
321A ALA* 3.8 19.7 - - + -
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Residues in contact with ARG 301 (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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232A ILE* 4.7 5.3 - - - +
297A LEU* 2.8 40.5 + - - +
298A GLU* 3.3 13.2 - - - +
300A ALA* 1.3 78.3 - - - +
302A GLU* 1.3 55.8 + - - +
304A VAL* 3.7 7.9 + - - +
305A ALA* 3.2 26.9 + - - +
319A TRP* 3.8 30.6 - - - -
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Residues in contact with GLU 302 (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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260A LYS* 5.5 6.8 + - - +
262A ALA* 3.3 24.0 - - + +
263A LYS* 3.0 41.8 + - - +
298A GLU 2.9 11.9 + - - +
299A GLU* 2.8 10.7 + - - +
301A ARG* 1.3 76.5 - - - +
303A VAL* 1.3 55.7 + - - +
305A ALA* 3.7 5.4 + - - +
306A THR* 2.5 35.0 + - - +
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Residues in contact with VAL 303 (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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262A ALA* 3.8 29.4 - - + +
266A VAL* 3.7 19.5 - - + -
287A ILE* 3.9 25.4 - - + -
289A VAL* 4.6 9.0 - - + -
299A GLU 2.9 18.2 + - - +
300A ALA* 3.2 11.2 + - - +
302A GLU* 1.3 76.9 - - - +
304A VAL* 1.3 63.6 - - - +
306A THR* 3.1 9.4 + - - -
307A VAL* 3.1 22.9 + - + +
333A VAL* 4.0 24.7 - - + -
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Residues in contact with VAL 304 (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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287A ILE* 4.0 23.9 - - + +
289A VAL* 5.5 1.6 - - + -
300A ALA 3.1 18.1 + - - +
301A ARG* 3.9 7.2 - - - +
303A VAL* 1.3 77.6 - - + +
305A ALA* 1.3 57.2 + - - +
307A VAL* 3.4 1.4 + - - +
308A SER* 2.8 37.1 + - - -
317A ILE* 4.4 9.4 - - + -
319A TRP* 3.5 55.9 - - + +
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Residues in contact with ALA 305 (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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301A ARG 3.2 17.0 + - - +
302A GLU* 3.9 7.2 - - - +
304A VAL* 1.3 77.6 - - - +
306A THR* 1.3 64.8 + - - +
308A SER* 3.2 7.8 + - - -
309A SER* 3.2 23.9 + - - -
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Residues in contact with THR 306 (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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263A LYS* 4.3 20.8 + - + -
266A VAL* 3.8 28.9 - - + +
267A SER* 5.7 0.4 - - - +
270A LEU* 4.1 10.8 - - + -
302A GLU* 2.5 22.0 + - - +
303A VAL* 3.1 9.1 + - - -
305A ALA* 1.3 77.4 - - - +
307A VAL* 1.3 60.7 + - - +
309A SER* 2.8 22.5 + - - -
310A ARG* 3.8 9.7 - - - +
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Residues in contact with VAL 307 (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 VAL* 3.7 15.7 - - + -
270A LEU* 4.3 13.5 - - + -
285A ALA* 5.0 3.1 - - + -
287A ILE* 3.9 21.3 - - + -
303A VAL* 3.1 14.9 + - + +
304A VAL 3.9 4.3 - - - +
306A THR* 1.3 73.2 - - - +
308A SER* 1.3 66.9 + - - +
310A ARG* 2.9 20.9 + - - +
311A LEU* 3.4 27.1 + - + +
317A ILE* 5.3 0.4 - - + -
335A LEU* 3.7 39.0 - - + -
337A ILE* 5.1 2.0 - - + -
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Residues in contact with SER 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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304A VAL* 2.8 27.0 + - - -
305A ALA* 3.2 8.7 + - - -
307A VAL* 1.3 74.7 - - - +
309A SER* 1.3 59.8 + - - +
310A ARG 3.3 1.0 + - - -
311A LEU* 3.5 17.9 + - - +
312A ASP 4.7 3.6 - - - +
313A PRO* 5.4 2.3 - - - +
317A ILE* 3.9 26.2 - - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA 3.2 8.7 + - - -
306A THR* 2.8 20.8 + - - -
308A SER* 1.3 77.1 - - - +
310A ARG* 1.3 63.3 + - - +
311A LEU 4.3 2.8 - - - +
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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