Contacts of the helix formed by residues 290 - 306 (chain A) in PDB entry 1W6J
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 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PRO 3.2 5.9 + - - -
289A HIS* 1.3 74.4 - - - +
291A TRP* 1.3 65.7 + - - +
292A LEU* 3.3 7.7 + - - +
293A LEU* 3.1 14.6 + - - +
294A ARG* 3.0 22.5 + - - +
514A LEU* 2.6 50.9 + - - -
516A ASN 5.4 0.6 + - - -
1736A BOG 3.4 12.1 - - - -
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 1.3 74.8 - - - +
292A LEU* 1.3 102.4 + - + +
294A ARG* 3.4 4.9 - - - +
295A VAL* 3.3 33.5 + - + +
514A LEU* 4.6 22.0 - - + +
1736A BOG 2.8 67.6 + - + +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 3.1 8.2 + - - +
291A TRP* 1.3 114.5 - - + +
293A LEU* 1.3 60.4 + - - +
295A VAL* 3.3 8.3 + - + +
296A VAL* 2.9 42.7 + - + +
511A LEU* 5.1 2.0 - - + +
514A LEU* 3.9 30.7 - - + -
515A LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A HIS* 3.7 22.2 - - + +
290A SER* 3.1 14.6 + - - +
292A LEU* 1.3 73.4 - - - +
294A ARG* 1.3 60.5 + - - +
296A VAL* 4.2 7.4 - - + -
297A TYR* 2.8 56.7 + - + +
514A LEU 3.7 14.1 + - - +
515A LEU* 3.7 24.7 - - + +
516A ASN 3.4 25.8 - - - +
517A PRO* 3.6 18.2 - - + -
1735A C14 4.2 13.9 - - + -
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Residues in contact with ARG 294 (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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278A ASN* 3.5 44.6 + - - +
288A PRO* 5.7 1.2 - - - +
289A HIS* 3.8 29.8 + - + +
290A SER 3.0 18.0 + - - +
291A TRP 3.4 8.7 - - - +
293A LEU* 1.3 74.9 - - - +
295A VAL* 1.3 58.5 + - + +
297A TYR* 3.9 2.6 - - - +
298A ALA* 3.0 29.0 + - - +
1736A BOG 2.9 54.4 + - + +
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TRP* 3.3 19.3 + - + +
292A LEU* 3.7 13.2 - - + +
293A LEU 3.3 0.2 - - - -
294A ARG* 1.3 73.8 - - - +
296A VAL* 1.3 68.4 + - + +
298A ALA* 3.4 8.0 + - - +
299A LEU* 3.2 38.3 + - + +
1736A BOG 4.1 38.4 - - + -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 2.9 32.7 + - + +
293A LEU* 3.8 16.2 - - + +
295A VAL* 1.3 79.0 - - + +
297A TYR* 1.3 58.3 + - + +
299A LEU* 3.3 8.3 + - - +
300A LEU* 2.8 50.2 + - + +
515A LEU* 4.3 13.5 - - + -
1735A C14 4.0 27.6 - - + -
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Residues in contact with TYR 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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209A ASN* 3.9 29.0 + - + +
210A THR* 3.5 34.3 + - + -
211A LEU* 5.4 5.5 - - - +
212A PHE* 6.1 0.2 - - + -
237A TYR* 5.7 0.5 - - - -
278A ASN* 5.7 1.6 - - - +
289A HIS* 3.7 30.5 - + - -
293A LEU* 2.8 44.4 + - + +
294A ARG* 4.1 3.1 - - - +
296A VAL* 1.3 72.6 - - - +
298A ALA* 1.3 66.0 + - - +
300A LEU* 4.3 8.3 - - + +
301A ASN* 2.9 37.4 + - - +
517A PRO* 3.3 23.1 - - + +
1735A C14 4.2 20.4 - - + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG 3.0 18.2 + - - +
295A VAL* 3.5 9.4 - - - +
297A TYR* 1.3 77.3 - - - +
299A LEU* 1.3 62.9 + - + +
301A ASN* 4.2 4.4 - - - +
302A LEU* 3.4 17.8 + - - +
1734A BOG 4.5 0.3 + - - -
1737A BOG 4.0 37.6 - - + +
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Residues in contact with LEU 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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295A VAL* 3.2 29.0 + - + +
296A VAL* 3.7 8.5 - - - +
297A TYR 3.2 0.2 - - - -
298A ALA* 1.3 80.7 - - + +
300A LEU* 1.3 62.9 + - + +
302A LEU* 3.2 14.7 + - + +
303A TYR* 3.0 24.8 + - - +
1737A BOG 5.0 14.6 - - + -
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Residues in contact with LEU 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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210A THR* 3.5 16.2 - - + +
212A PHE* 3.7 47.3 - - + -
296A VAL* 2.8 43.4 + - + +
297A TYR* 4.2 11.7 - - + +
299A LEU* 1.3 72.9 - - + +
301A ASN* 1.3 61.5 + - - +
302A LEU 3.1 0.4 - - - -
303A TYR* 3.4 10.7 + - + +
304A GLU* 2.9 27.2 + - - +
1735A C14 3.7 27.6 - - + -
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Residues in contact with ASN 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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208A LEU 4.5 0.3 - - - +
209A ASN* 2.8 30.1 + - - -
210A THR* 2.9 32.4 + - - +
244A TYR* 5.2 0.3 + - - -
277A ARG* 3.7 31.9 + - - +
297A TYR* 2.9 26.2 + - - +
298A ALA* 4.2 4.1 - - - +
300A LEU* 1.3 75.2 - - - +
302A LEU* 1.3 61.6 + - - +
304A GLU* 3.3 7.6 - - - +
305A HIS 3.3 12.6 + - - -
1734A BOG 2.9 24.7 + - - +
1737A BOG 6.2 2.0 - - + -
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Residues in contact with LEU 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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298A ALA 3.4 10.8 + - - +
299A LEU* 3.2 19.0 + - + +
300A LEU 3.1 0.2 - - - -
301A ASN* 1.3 76.9 - - - +
303A TYR* 1.3 64.7 + - - +
305A HIS* 3.1 13.0 + - + +
306A HIS* 3.2 53.3 + - + +
1734A BOG 3.4 32.9 + - + +
1737A BOG 4.5 23.6 - - + -
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Residues in contact with TYR 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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212A PHE* 4.2 21.5 - + - -
214A GLU* 4.1 25.8 - - + +
299A LEU 3.0 12.6 + - - +
300A LEU* 3.7 14.6 - - + +
302A LEU* 1.3 76.7 - - - +
304A GLU* 1.3 54.5 + - - +
306A HIS* 3.0 11.6 + - + +
307A HIS* 2.7 58.4 + - + +
308A SER* 3.2 29.7 + - - -
311A LEU* 4.3 12.3 - - - +
312A ARG* 4.9 1.1 - - - -
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Residues in contact with GLU 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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206A GLU* 5.5 2.2 - - - +
210A THR* 2.7 24.4 + - - +
212A PHE* 5.7 0.5 - - - -
244A TYR* 3.1 24.5 + - - +
247A ARG* 3.3 19.9 + - - +
277A ARG* 5.9 4.0 - - - +
300A LEU 2.9 14.4 + - - +
301A ASN* 3.3 16.2 - - - +
302A LEU 3.2 0.4 - - - -
303A TYR* 1.3 77.6 - - - +
305A HIS* 1.3 60.1 + - - +
307A HIS* 2.9 35.0 - - - -
312A ARG* 2.8 41.1 + - - -
1734A BOG 5.5 2.0 - - - +
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Residues in contact with HIS 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 ASN 3.3 1.6 + - - -
302A LEU* 3.1 11.7 + - - +
304A GLU* 1.3 81.8 - - - +
306A HIS* 1.3 85.1 + + + +
307A HIS* 3.7 3.6 + - - -
1734A BOG 2.7 55.8 + - - +
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Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.2 43.8 + - + +
303A TYR* 3.0 15.7 + - + +
305A HIS* 1.3 99.2 - + - +
307A HIS* 1.3 64.1 + - - +
308A SER 3.6 1.2 + - - -
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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