Contacts of the helix formed by residues 287 - 301 (chain A) in PDB entry 1B70
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 HIS 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASN* 3.7 13.8 + - - -
258A PHE 5.3 0.2 + - - -
259A PRO 3.5 13.1 + - - -
260A PHE* 2.9 31.9 + - - -
261A VAL* 3.6 1.9 + - - +
262A GLU* 4.2 25.8 - - + +
285A MET 3.2 3.7 + - - -
286A VAL* 1.3 77.4 - - - +
288A PRO* 1.3 80.1 - - + +
289A LYS* 3.0 52.5 + - + +
290A VAL* 3.1 23.5 + - + +
291A PHE* 3.4 5.4 + - - -
455B LEU* 3.7 15.3 - - + +
457B GLU* 6.2 0.9 - - + -
458B ASP* 4.7 7.0 - - - -
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Residues in contact with PRO 288 (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 GLU 5.2 2.0 - - - +
286A VAL 3.6 4.9 - - - +
287A HIS* 1.3 100.6 - - + +
289A LYS* 1.3 55.0 + - - +
291A PHE* 3.1 14.6 + - + +
292A GLN* 2.8 42.7 + - - +
455B LEU* 4.1 13.0 - - + -
457B GLU* 3.5 45.1 - - + +
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Residues in contact with LYS 289 (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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136A ALA 4.2 2.1 - - - +
138A ASN* 3.2 42.8 + - + +
287A HIS* 3.0 27.1 + - + +
288A PRO* 1.3 75.0 - - - +
290A VAL* 1.3 58.7 + - - +
292A GLN* 3.5 23.0 - - + +
293A ALA* 3.0 26.0 + - - +
455B LEU* 4.7 13.3 - - + +
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Residues in contact with VAL 290 (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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136A ALA 3.8 11.4 - - - +
137A LEU* 4.1 24.0 - - + -
138A ASN 4.1 3.4 - - - +
183A GLN* 5.4 4.3 - - - +
184A VAL* 4.6 4.3 - - + -
187A MET* 4.5 12.3 - - + -
260A PHE* 3.7 33.2 - - + +
286A VAL* 4.0 13.2 - - + -
287A HIS* 3.1 21.9 + - + +
289A LYS* 1.3 77.5 - - - +
291A PHE* 1.3 67.1 + - - +
293A ALA* 3.1 4.0 + - - +
294A VAL* 3.0 34.8 + - + +
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Residues in contact with PHE 291 (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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187A MET* 3.7 27.1 - - - -
224A VAL* 3.9 17.7 - - + -
286A VAL* 3.7 40.2 - - + -
287A HIS 3.4 6.2 + - - -
288A PRO* 3.1 12.3 + - + +
290A VAL* 1.3 79.8 - - - +
292A GLN* 1.3 62.0 + - - +
294A VAL* 3.1 7.7 + - - +
295A ASP* 3.0 27.0 + - - +
307A TYR* 3.7 41.1 - + + +
310A VAL* 3.9 22.7 - - + -
311A THR* 4.0 16.8 - - - -
312A GLY 4.4 0.7 - - - -
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Residues in contact with GLN 292 (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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288A PRO* 2.8 26.4 + - - +
289A LYS* 3.5 38.4 - - + +
291A PHE* 1.3 77.2 - - - +
293A ALA* 1.3 63.9 + - - +
295A ASP* 3.3 5.4 + - - +
296A ALA* 2.9 24.6 + - - +
455B LEU* 5.9 1.2 - - - +
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Residues in contact with ALA 293 (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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131A PHE* 5.8 6.2 - - + -
135A ASP 5.4 0.4 - - - +
136A ALA* 3.6 30.3 - - + +
184A VAL* 6.1 0.9 - - + -
289A LYS 3.0 12.0 + - - +
290A VAL 3.3 9.0 - - - +
292A GLN* 1.3 79.1 - - - +
294A VAL* 1.3 65.3 + - + +
296A ALA* 3.0 9.3 + - - +
297A TYR* 2.9 23.7 + - - +
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Residues in contact with VAL 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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184A VAL* 4.5 15.0 - - + +
187A MET* 3.6 34.1 - - + -
188A VAL* 3.6 40.0 - - + +
290A VAL* 3.0 23.1 + - + +
291A PHE* 3.2 9.6 - - - +
293A ALA* 1.3 76.5 - - + +
295A ASP* 1.3 66.0 + - - +
297A TYR* 3.1 3.1 + - - +
298A ARG* 2.9 23.1 + - - +
307A TYR* 3.9 14.8 - - + -
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Residues in contact with ASP 295 (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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291A PHE 3.0 10.5 + - - +
292A GLN* 3.8 7.7 - - - +
294A VAL* 1.3 78.8 - - - +
296A ALA* 1.3 62.3 + - - +
298A ARG* 3.0 10.8 + - - +
299A GLU* 2.9 24.8 + - - +
303A LEU 5.2 0.2 - - - +
305A PRO* 3.5 12.1 - - + +
306A ALA 3.0 20.3 + - - -
307A TYR* 3.3 30.4 + - - +
308A ARG* 3.3 42.4 + - - +
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Residues in contact with ALA 296 (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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292A GLN 2.9 13.9 + - - +
293A ALA* 3.3 12.6 - - - +
295A ASP* 1.3 77.7 - - - +
297A TYR* 1.3 60.7 + - - +
299A GLU* 3.3 11.4 - - - +
300A ARG* 3.1 21.3 + - - +
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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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131A PHE* 4.0 31.6 - + + -
132A PHE* 4.2 12.6 - + - -
164A PRO* 3.9 13.9 - - + -
167A GLU* 2.5 35.5 + - - +
169A VAL* 4.2 18.7 - - + +
184A VAL* 6.4 0.7 - - + -
188A VAL* 3.8 24.7 - - + -
293A ALA 2.9 12.3 + - - +
294A VAL* 3.6 7.2 - - - +
296A ALA* 1.3 74.3 - - - +
298A ARG* 1.3 66.8 + - - +
300A ARG* 3.2 35.8 + - + +
301A LEU* 3.0 39.2 + - + +
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Residues in contact with ARG 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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187A MET 3.3 11.5 + - - -
188A VAL* 2.6 48.8 + - + +
189A ALA 4.6 0.4 - - - -
190A HIS 3.3 12.9 + - - +
191A THR* 5.3 3.2 + - - -
294A VAL* 2.9 25.9 + - - +
295A ASP* 3.2 28.8 + - - +
297A TYR* 1.3 74.8 - - - +
299A GLU* 1.3 60.4 + - - +
301A LEU* 2.8 19.8 + - - +
302A GLY 3.0 0.3 + - - -
303A LEU* 2.9 45.1 + - + +
304A PRO* 2.9 32.2 + - - +
306A ALA* 3.7 20.6 - - - +
307A TYR* 4.4 2.0 - - - -
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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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295A ASP 2.9 11.9 + - - +
296A ALA* 3.3 15.7 - - - +
298A ARG* 1.3 71.7 - - - +
300A ARG* 1.3 64.6 + - - +
301A LEU 2.9 4.5 - - - -
302A GLY* 2.7 23.5 + - - -
303A LEU 3.3 15.4 + - - +
305A PRO* 5.8 5.6 - - + -
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Residues in contact with ARG 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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131A PHE* 5.6 4.8 - - - -
296A ALA 3.1 11.7 + - - +
297A TYR* 3.4 39.3 - - + +
298A ARG 3.2 0.2 - - - -
299A GLU* 1.3 89.4 - - + +
301A LEU* 1.3 63.3 + - + +
302A GLY 3.3 0.6 + - - -
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Residues in contact with LEU 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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165A LEU* 3.1 33.5 - - + +
167A GLU* 3.7 37.7 - - + +
188A VAL* 4.4 3.6 - - + -
297A TYR* 3.0 32.9 + - + +
298A ARG 2.8 13.0 + - - +
300A ARG* 1.3 85.4 - - + +
302A GLY* 1.3 56.1 + - - +
303A LEU* 3.4 16.5 + - + +
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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