Contacts of the helix formed by residues 292 - 311 (chain B) in PDB entry 3O75
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 GLN 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER* 5.4 0.4 + - - -
291B GLN* 1.3 72.0 - - - +
293B HIS* 1.3 63.8 + - - +
294B GLY 3.3 2.2 - - - -
295B GLN* 3.1 19.3 + - + +
296B ILE* 2.9 28.6 + - - +
320B VAL* 3.8 20.2 - - + +
321B GLY* 2.8 31.4 + - - +
322B ARG 5.1 0.6 - - - -
323B THR* 3.9 18.8 + - - +
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Residues in contact with HIS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B F1X 5.0 0.7 - - - -
75B SER* 3.1 51.8 + - - -
78B ARG* 3.5 42.4 + - + +
79B ILE* 3.9 15.5 - - + +
82B GLN* 4.4 2.0 - - - +
290B ALA* 5.3 4.0 - - + -
291B GLN* 3.4 41.3 + - + +
292B GLN* 1.3 72.1 - - - +
294B GLY* 1.3 62.8 - - - +
296B ILE* 3.4 4.1 + - - +
297B ALA* 3.0 25.6 + - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 5.5 0.6 - - - +
82B GLN* 3.6 27.5 - - - +
292B GLN 3.3 0.4 - - - -
293B HIS* 1.3 80.6 - - - +
295B GLN* 1.3 57.0 + - - +
297B ALA* 3.5 1.4 + - - +
298B ALA* 2.9 30.8 + - - +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 3.1 31.8 + - + +
294B GLY* 1.3 74.2 - - - +
296B ILE* 1.3 59.0 - - - +
298B ALA* 3.6 10.2 - - - +
299B THR* 2.9 56.5 + - - +
302B GLU* 5.5 2.2 + - - -
320B VAL* 4.2 17.7 - - + -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 4.3 9.9 - - + -
147B ILE* 3.9 28.0 - - + -
148B ASP* 5.4 2.2 - - - +
159B VAL* 3.6 23.3 - - + +
160B ILE* 4.7 7.0 - - - +
161B SER* 3.8 20.0 - - - +
291B GLN* 3.4 31.2 - - + +
292B GLN 2.9 21.0 + - - +
293B HIS* 3.7 4.7 - - - +
295B GLN* 1.3 76.9 - - - +
297B ALA* 1.3 58.4 + - - +
300B ALA* 3.0 27.5 + - - +
320B VAL* 4.1 22.4 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 3.9 10.1 - - + +
82B GLN* 3.5 35.7 - - + +
83B LEU* 3.3 30.8 - - + +
293B HIS 3.0 12.5 + - - +
296B ILE* 1.3 75.6 - - - +
298B ALA* 1.3 60.2 + - - +
300B ALA* 4.4 1.3 - - - -
301B LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLY 2.9 20.1 + - - +
295B GLN* 3.6 16.2 - - - +
297B ALA* 1.3 77.8 - - - +
299B THR* 1.3 61.9 + - - +
301B LEU* 4.0 4.4 - - - +
302B GLU* 3.1 29.6 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 4.0 22.7 - - + -
295B GLN* 2.9 33.9 + - - +
296B ILE 4.0 3.4 - - - -
298B ALA* 1.3 75.0 - - - +
300B ALA* 1.3 63.1 + - - +
302B GLU* 3.2 22.9 + - + +
303B LEU* 3.2 30.0 - - + +
318B HIS* 4.3 16.4 - - + +
320B VAL* 4.8 5.7 - - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.4 0.7 - - + -
122B PHE* 3.4 15.3 - - + -
145B ILE* 4.0 4.3 - - + +
147B ILE* 3.7 31.0 - - + -
159B VAL* 3.8 19.5 - - + +
296B ILE 3.0 19.7 + - - +
297B ALA* 3.9 4.3 - - - +
298B ALA 3.3 0.2 - - - -
299B THR* 1.3 73.8 - - - +
301B LEU* 1.3 65.5 + - - +
303B LEU* 3.2 6.8 + - - +
304B ALA 3.2 16.6 + - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.9 26.5 - - + -
83B LEU* 4.3 11.4 - - + +
86B GLY* 3.4 39.3 - - - +
87B ALA* 3.5 6.5 - - + +
90B ARG* 4.4 9.2 - - + -
122B PHE* 4.0 13.6 - - + -
297B ALA 2.9 18.0 + - - +
298B ALA* 4.0 5.2 - - - +
300B ALA* 1.3 71.8 - - - +
302B GLU* 1.3 68.9 + - - +
303B LEU 3.1 0.3 + - - -
304B ALA* 3.1 1.8 + - + -
305B LEU* 3.0 44.1 + - + +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 6.2 0.9 - - - +
295B GLN* 5.5 2.6 + - - -
298B ALA* 3.1 16.6 + - - +
299B THR* 3.2 27.9 + - - +
301B LEU* 1.3 77.1 - - - +
303B LEU* 1.3 62.0 + - + +
305B LEU* 3.3 6.6 + - - +
306B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.9 17.4 - - + +
157B CYS* 3.2 31.2 - - - -
159B VAL* 3.5 24.0 - - + -
299B THR* 3.2 22.7 - - + +
300B ALA* 3.2 6.2 + - - +
301B LEU 3.1 1.0 - - - -
302B GLU* 1.3 82.7 - - + +
304B ALA* 1.3 58.7 + - - +
306B ALA* 3.4 7.8 + - + +
307B ALA* 3.0 28.2 + - - +
312B ARG 4.8 0.9 - - - +
313B TYR* 5.2 1.4 - - - -
318B HIS* 3.9 18.6 - - + +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 5.1 1.3 - - + -
120B ALA* 3.9 21.5 - - + +
122B PHE* 3.6 34.3 - - + -
143B PRO* 5.3 0.2 - - - -
145B ILE* 3.9 12.7 - - + +
300B ALA 3.2 2.0 + - - -
301B LEU* 3.1 6.7 + - + +
303B LEU* 1.3 78.2 - - - +
305B LEU* 1.3 61.6 + - + +
307B ALA* 3.3 6.1 + - - +
308B ILE* 2.9 33.8 + - + +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.8 3.8 - - + -
90B ARG* 3.5 56.3 - - + +
92B TYR* 3.9 33.2 - - + +
301B LEU* 3.0 41.7 + - + +
302B GLU* 3.7 6.1 - - - +
304B ALA* 1.3 76.2 - - - +
306B ALA* 1.3 56.3 + - - +
308B ILE* 4.3 8.1 - - + -
309B GLU* 2.7 48.8 + - - +
310B GLU* 3.8 1.7 - - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU 2.9 17.4 + - - +
303B LEU* 3.7 9.6 - - + +
305B LEU* 1.3 76.2 - - - +
307B ALA* 1.3 58.8 + - - +
310B GLU* 3.0 40.1 + - - +
311B LYS 3.3 5.2 + - - -
312B ARG* 3.4 32.4 + - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 3.7 30.8 - - + +
303B LEU 3.0 15.2 + - - +
304B ALA* 3.5 9.4 - - - +
306B ALA* 1.3 77.7 - - - +
308B ILE* 1.3 59.6 + - - +
311B LYS* 3.3 19.5 + - - -
312B ARG 3.3 16.0 + - - +
313B TYR* 3.9 17.5 - - + -
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 3.6 28.7 + - + +
64B LEU* 3.8 12.1 - - + -
92B TYR* 3.2 27.6 - - + +
119B ASP* 3.3 39.0 - - + +
120B ALA* 3.6 21.1 - - + -
143B PRO* 4.3 5.4 - - + -
304B ALA 2.9 19.1 + - - +
305B LEU* 3.8 6.3 - - + +
306B ALA 3.2 0.2 - - - -
307B ALA* 1.3 81.7 - - - +
309B GLU* 1.3 66.6 + - + +
310B GLU 3.7 0.2 + - - -
311B LYS* 4.3 2.4 + - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 5.5 1.8 - - - +
62B ARG* 3.5 12.0 + - - +
90B ARG* 3.3 29.2 + - - +
92B TYR* 3.3 31.6 + - - +
305B LEU* 2.7 28.2 + - - +
308B ILE* 1.3 83.9 - - + +
310B GLU* 1.3 71.8 + - - +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU 3.8 1.2 - - - +
306B ALA* 3.0 23.8 + - - +
309B GLU* 1.3 93.9 - - - +
311B LYS* 1.3 71.3 + - - +
312B ARG* 2.7 56.9 + - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA 3.3 2.6 + - - -
307B ALA 3.3 16.6 + - - -
308B ILE 4.3 2.9 + - - +
309B GLU 3.8 0.2 - - - -
310B GLU* 1.3 77.7 - - - +
312B ARG* 1.3 59.1 + - - +
313B TYR* 4.2 1.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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