Contacts of the helix formed by residues 282 - 297 (chain A) in PDB entry 1Q0R
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 VAL 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.8 37.2 - - + -
271A ILE* 4.3 9.9 - - + -
274A MET* 4.0 27.1 - - + -
278A LEU* 4.3 3.1 - - - -
279A PRO* 3.1 28.4 + - + +
281A SER* 1.3 78.9 - - - +
283A HIS* 1.3 64.7 + - + +
284A GLY 3.3 2.9 - - - -
285A PRO* 3.5 6.8 - - + +
286A LEU* 3.0 46.8 + - + +
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Residues in contact with HIS 283 (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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40A PRO* 4.1 3.3 - - + +
42A GLU* 4.2 6.7 + - + +
43A PHE* 3.7 55.3 + + + +
46A ARG* 4.4 13.7 - - - +
201A TRP* 3.6 28.3 - + - -
278A LEU* 2.8 28.4 + - + +
279A PRO 3.1 17.6 + - - -
280A SER* 3.1 21.9 + - - +
282A VAL* 1.3 79.7 - - + +
284A GLY* 1.3 57.3 + - - +
286A LEU* 3.8 2.6 - - + +
287A ALA* 2.9 33.4 + - - +
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Residues in contact with GLY 284 (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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46A ARG* 3.4 28.2 - - - +
280A SER 4.3 2.2 + - - -
283A HIS* 1.3 80.5 - - - +
285A PRO* 1.3 63.3 - - - +
287A ALA* 3.8 4.1 - - - +
288A GLU* 2.9 32.5 + - - +
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Residues in contact with PRO 285 (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 ILE* 4.3 25.8 - - + +
272A PRO* 6.3 0.4 - - + -
281A SER 3.9 14.8 - - - +
282A VAL* 3.5 15.0 - - + +
284A GLY* 1.3 89.3 - - - +
286A LEU* 1.3 60.8 + - - +
288A GLU* 3.4 10.9 + - + +
289A VAL* 3.3 24.3 + - - +
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Residues in contact with LEU 286 (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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43A PHE* 3.9 19.7 - - + -
125A LEU* 4.0 22.4 - - + -
243A ILE* 4.2 13.0 - - + -
271A ILE* 3.8 26.5 - - + -
274A MET* 3.8 10.3 - - + -
278A LEU* 3.8 24.0 - - + -
282A VAL* 3.0 41.8 + - + +
283A HIS* 3.9 4.0 - - + +
285A PRO* 1.3 73.0 - - - +
287A ALA* 1.3 66.6 + - - +
289A VAL* 3.4 4.5 + - - +
290A ILE* 3.0 33.3 + - + +
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Residues in contact with ALA 287 (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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43A PHE* 4.2 2.6 - - + -
46A ARG* 4.1 23.6 - - + +
47A LEU* 3.8 25.6 - - + +
283A HIS 2.9 19.6 + - - +
284A GLY* 3.8 3.1 - - - +
286A LEU* 1.3 76.2 - - - +
288A GLU* 1.3 58.0 + - - +
290A ILE* 3.8 0.7 - - - +
291A LEU* 2.8 45.1 + - + +
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Residues in contact with GLU 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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284A GLY 2.9 17.8 + - - +
285A PRO* 3.7 10.2 - - - +
286A LEU 3.2 0.4 - - - -
287A ALA* 1.3 78.6 - - - +
289A VAL* 1.3 59.5 + - - +
291A LEU* 3.9 5.9 - - - +
292A ALA* 3.1 29.0 + - + +
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Residues in contact with VAL 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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241A LEU* 3.8 12.5 - - + +
243A ILE* 3.7 25.6 - - + -
269A ALA* 3.9 25.6 - - + -
271A ILE* 4.5 9.4 - - + -
285A PRO 3.3 11.0 + - - +
286A LEU* 3.4 13.2 - - - +
288A GLU* 1.3 77.1 - - - +
290A ILE* 1.3 68.1 + - - +
292A ALA* 3.5 6.5 + - + +
293A HIS* 3.1 22.7 + - - +
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Residues in contact with ILE 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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26A LEU* 4.2 13.5 - - + -
43A PHE* 4.2 20.0 - - + -
47A LEU* 3.8 19.7 - - + -
52A LEU* 5.0 0.4 - - + -
99A VAL* 4.4 23.1 - - + -
123A THR* 4.2 12.1 - - + +
125A LEU* 5.7 2.9 - - + -
241A LEU* 4.3 4.9 - - - -
243A ILE* 4.1 22.4 - - + -
286A LEU* 3.0 27.5 + - + +
287A ALA 3.9 2.9 - - - +
289A VAL* 1.3 77.7 - - - +
291A LEU* 1.3 57.1 + - - +
293A HIS* 3.2 3.4 + - - +
294A THR* 2.9 41.7 + - + +
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Residues in contact with LEU 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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46A ARG 4.4 4.0 - - - +
47A LEU* 3.8 19.1 - - + +
50A GLY* 3.8 36.3 - - - +
51A GLY 5.2 0.2 - - - -
52A LEU* 3.6 28.0 - - + -
287A ALA* 2.8 34.0 + - + +
288A GLU* 4.0 4.7 - - - +
290A ILE* 1.3 75.0 - - - +
292A ALA* 1.3 63.4 + - - +
294A THR* 3.2 6.4 + - - +
295A ARG* 3.0 26.5 + - - +
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Residues in contact with ALA 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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267A ARG* 5.6 0.2 - - - -
288A GLU* 3.1 19.4 + - + +
289A VAL* 3.8 7.6 - - + +
291A LEU* 1.3 76.4 - - - +
293A HIS* 1.3 60.7 + - - +
295A ARG* 3.5 7.5 + - - +
296A SER* 3.3 23.0 + - - -
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Residues in contact with HIS 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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121A SER* 4.0 13.3 + - - -
122A LEU 3.1 26.5 - - - -
123A THR* 3.4 11.0 + - - -
239A PRO* 3.4 31.4 - - + +
240A THR 3.5 5.1 + - - -
241A LEU* 3.3 32.6 - - + +
267A ARG* 3.0 33.3 + - - +
289A VAL 3.1 14.0 + - - +
290A ILE 3.2 8.0 + - - +
292A ALA* 1.3 76.2 - - - +
294A THR* 1.3 66.3 + - - +
296A SER* 2.7 22.8 + - - -
297A ALA* 3.2 6.4 + - - +
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Residues in contact with THR 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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26A LEU* 4.1 14.6 - - + -
52A LEU* 4.0 16.8 - - + +
97A HIS* 3.4 58.3 + - + +
121A SER* 4.3 4.3 - - - +
123A THR* 5.5 1.8 - - - +
290A ILE* 2.9 23.0 + - + +
291A LEU* 3.2 19.1 + - - +
293A HIS* 1.3 78.0 - - + +
295A ARG* 1.3 61.6 + - - +
297A ALA* 3.2 9.7 + - - -
298A ALA* 3.6 8.5 + - - +
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Residues in contact with ARG 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 LEU 3.0 19.3 + - - +
292A ALA* 3.7 8.1 - - - +
294A THR* 1.3 78.6 + - - +
296A SER* 1.3 60.6 + - - +
298A ALA* 3.4 21.4 + - - +
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Residues in contact with SER 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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239A PRO* 5.2 3.4 - - - +
267A ARG* 3.1 29.3 + - - -
292A ALA 3.3 9.0 + - - -
293A HIS* 2.7 20.0 + - - -
295A ARG* 1.3 79.5 - - - +
297A ALA* 1.3 56.5 + - - +
298A ALA 3.2 7.5 + - - +
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Residues in contact with ALA 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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97A HIS* 4.1 6.1 + - - +
120A SER* 3.8 20.7 - - - +
121A SER* 3.8 13.2 - - - -
239A PRO* 3.7 29.3 - - + +
293A HIS 3.2 7.8 + - - +
294A THR 3.2 10.3 + - - +
296A SER* 1.3 77.7 + - - +
298A ALA* 1.3 60.5 + - - +
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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