Contacts of the helix formed by residues 292 - 313 (chain B) in PDB entry 3D0O
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 ASN 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B TRP* 5.7 2.2 - - - +
188B SER* 3.8 18.4 + - - +
198B LYS* 5.8 3.8 - - - +
291B LEU* 1.3 74.2 - - - +
293B ASP* 1.3 66.6 + - - +
294B GLU* 3.2 13.0 + - - +
295B GLU* 2.8 51.8 + - - +
296B GLN* 2.8 22.5 + - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASN* 1.3 75.6 - - - +
294B GLU* 1.3 56.9 + - - +
296B GLN* 3.7 19.0 + - - +
297B SER* 2.9 35.0 + - - +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PRO* 5.9 2.6 - - - +
187B TRP* 5.5 6.6 - - - -
198B LYS* 4.1 18.5 + - - -
292B ASN* 3.2 12.8 + - - +
293B ASP* 1.3 78.9 - - - +
295B GLU* 1.3 62.0 + - + +
297B SER* 3.3 6.3 + - - -
298B LYS* 3.0 63.0 + - + +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.8 15.3 - - + +
185B PRO 4.0 13.9 - - - +
186B VAL* 4.0 8.7 - - - -
187B TRP* 3.0 12.8 + - - +
188B SER* 2.6 48.5 + - - -
291B LEU* 3.5 22.8 - - + +
292B ASN* 2.8 36.1 + - - +
294B GLU* 1.3 79.1 - - + +
296B GLN* 1.3 65.7 + - - +
298B LYS* 3.4 2.0 + - + -
299B PHE* 2.9 27.0 + - - +
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Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 2.8 40.9 + - + +
292B ASN* 2.8 23.9 + - - +
293B ASP* 3.7 16.8 + - - +
295B GLU* 1.3 71.9 - - - +
297B SER* 1.3 65.4 + - - +
299B PHE* 3.3 1.7 + - - +
300B ALA* 3.0 27.3 + - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 2.9 23.2 + - - +
294B GLU* 3.5 7.1 - - - -
296B GLN* 1.3 77.9 - - - +
298B LYS* 1.3 64.2 + - - +
300B ALA* 3.5 4.2 + - - +
301B HIS* 3.1 23.6 + - - +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR 4.5 3.3 - - - +
183B GLU 5.8 0.2 - - - +
184B LEU* 4.0 31.0 - - + +
185B PRO* 5.3 5.4 - - + -
294B GLU* 3.0 53.4 + - + +
295B GLU* 4.0 3.1 - - + +
297B SER* 1.3 75.8 - - - +
299B PHE* 1.3 58.5 + - - +
301B HIS* 3.3 9.5 + - - +
302B SER* 3.0 27.9 + - - -
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ILE* 3.7 26.2 - - + -
177B GLY* 3.8 11.4 - - - -
184B LEU* 3.9 9.1 - - + +
261B LEU* 3.9 10.3 - - + -
265B TYR* 3.7 33.4 - + + -
267B GLU* 4.2 12.3 - - + -
272B ILE* 3.7 21.5 - - + +
273B GLY 3.7 20.4 - - - -
274B VAL* 3.5 24.9 - - + -
291B LEU* 4.2 13.2 - - + -
295B GLU 2.9 21.6 + - - +
296B GLN* 3.9 2.9 - - - +
298B LYS* 1.3 68.9 - - - +
300B ALA* 1.3 69.3 + - - +
302B SER* 3.1 3.6 + - - -
303B ALA* 2.9 19.4 + - - +
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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
----------------------------------------------------------
267B GLU* 3.6 21.2 - - - +
296B GLN 3.0 17.6 + - - +
297B SER* 3.8 4.3 - - - +
299B PHE* 1.3 80.7 - - - +
301B HIS* 1.3 57.2 + - - +
303B ALA* 3.3 2.3 + - - +
304B LYS* 2.9 28.9 + - - +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.7 18.6 + - - -
297B SER 3.1 17.7 + - - +
298B LYS* 3.6 8.7 - - - +
300B ALA* 1.3 73.8 - - - +
302B SER* 1.3 61.4 + - - +
304B LYS* 3.5 14.0 + - + +
305B THR* 2.9 45.6 + - - -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY* 4.3 4.3 - - - -
178B GLU* 2.9 23.8 + - - +
182B THR* 2.3 49.1 + - - +
184B LEU* 4.7 0.2 - - - -
272B ILE* 3.9 8.2 - - - +
298B LYS 3.0 10.1 + - - -
299B PHE* 3.1 9.4 + - - -
301B HIS* 1.3 75.3 - - - +
303B ALA* 1.3 66.4 + - - +
305B THR* 3.2 3.6 + - - -
306B LEU* 3.1 24.8 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 3.5 37.7 - - + +
270B VAL* 4.5 11.4 - - + -
272B ILE* 3.6 17.6 - - + +
299B PHE* 2.9 16.7 + - + +
300B ALA 3.7 0.9 - - - +
302B SER* 1.3 75.1 - - - +
304B LYS* 1.3 66.1 + - - +
306B LEU* 3.1 7.7 + - - +
307B LYS* 2.8 28.6 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 5.1 1.0 + - - -
300B ALA 2.9 18.0 + - - +
301B HIS* 3.6 15.3 - - + +
303B ALA* 1.3 77.4 - - - +
305B THR* 1.3 56.4 + - - +
307B LYS* 3.7 7.1 - - - +
308B ASP* 2.6 69.5 + - - +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 5.9 4.7 - - - +
178B GLU* 4.6 13.0 - - - +
182B THR* 3.9 18.5 + - - +
301B HIS* 2.9 36.1 + - - -
302B SER* 3.2 6.9 + - - -
304B LYS* 1.3 78.4 - - - +
306B LEU* 1.3 61.6 + - - +
308B ASP* 3.8 7.3 - - - +
309B ILE* 3.2 37.7 + - + +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 6.2 0.9 - - + -
127B ASP* 3.9 15.7 - - + -
128B ILE* 3.8 23.7 - - + +
178B GLU* 4.0 35.0 - - + +
270B VAL* 3.8 11.2 - - + -
271B TYR 3.5 22.0 - - - +
272B ILE* 3.6 29.8 - - + -
302B SER 3.1 10.8 + - - +
303B ALA 3.5 6.1 - - - +
305B THR* 1.3 75.7 - - + +
307B LYS* 1.3 62.4 + - - +
309B ILE* 3.4 9.4 + - + +
310B MET* 3.1 33.2 + - + +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 4.5 12.3 + - - +
268B GLU* 3.0 38.2 + - - +
269B ASP* 3.9 16.5 - - - +
270B VAL* 3.7 23.3 - - + -
303B ALA 2.8 20.0 + - - +
304B LYS* 3.9 6.3 - - - +
306B LEU* 1.3 77.0 - - - +
308B ASP* 1.3 61.5 + - - +
310B MET* 3.5 8.3 + - + +
311B ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B LYS* 2.6 62.6 + - - +
305B THR* 3.8 6.7 - - - +
307B LYS* 1.3 75.3 - - - +
309B ILE* 1.3 62.4 + - + +
311B ALA* 3.2 8.0 + - - +
312B GLU* 3.0 31.0 + - + +
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ARG* 5.5 20.0 - - + +
93B LEU* 3.9 7.0 - - + +
96B VAL* 3.8 29.6 - - + -
128B ILE* 3.8 22.4 - - + -
178B GLU* 5.4 5.2 - - - +
305B THR* 3.2 29.9 + - + +
306B LEU* 3.6 13.9 - - + +
308B ASP* 1.3 78.5 - - + +
310B MET* 1.3 65.1 + - - +
312B GLU* 3.2 20.6 + - - +
313B ALA* 3.1 20.3 + - - +
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Residues in contact with MET 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP 5.5 0.7 - - - +
128B ILE* 3.1 37.0 - - + +
131B TYR* 3.7 40.6 - - + -
269B ASP 4.6 2.5 - - - +
270B VAL* 3.6 30.3 - - + -
271B TYR 4.7 2.9 - - - +
306B LEU* 3.1 29.0 + - + +
307B LYS* 3.9 9.9 - - + +
309B ILE* 1.3 76.4 - - - +
311B ALA* 1.3 63.9 + - - +
313B ALA* 3.1 27.2 + - - +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B LYS 2.9 19.3 + - - +
308B ASP* 3.2 8.5 + - - +
310B MET* 1.3 75.8 - - - +
312B GLU* 1.3 64.0 + - - +
313B ALA 3.8 4.3 - - - -
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.2 40.9 - - + +
308B ASP* 3.0 19.6 + - + +
309B ILE* 3.2 24.5 + - - +
311B ALA* 1.3 76.5 - - - +
313B ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.8 14.0 - - + +
96B VAL* 4.2 7.2 - - + -
97B SER* 4.6 7.6 - - - +
100B LEU* 3.9 27.6 - - + -
309B ILE 3.1 8.9 + - - +
310B MET* 3.1 21.5 - - - +
311B ALA 3.8 4.3 - - - -
312B GLU* 1.3 85.4 - - - +
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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
------------------------------------------------------------
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