Contacts of the helix formed by residues 294 - 311 (chain B) in PDB entry 2I6A
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 ASP 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 2.9 53.5 + - - +
134B LEU* 6.0 0.2 - - - +
292B ILE* 3.7 6.5 + - - +
293B ILE* 1.3 67.5 - - - +
295B THR* 1.3 61.3 + - - +
296B ASN* 3.4 14.9 + - - +
297B GLY* 3.0 28.2 + - - -
298B ALA* 2.9 27.0 + - - +
331B ILE* 5.1 3.2 - - + +
332B ARG* 4.8 25.7 + - + +
500B 5I5 4.6 4.5 - - - +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 5.4 8.8 + - - -
132B ARG* 5.0 1.8 - - - +
223B ASN* 6.0 2.7 - - + +
224B GLU* 5.8 4.3 - - - +
267B GLY* 4.6 20.6 - - - +
293B ILE* 2.7 15.7 + - + +
294B ASP* 1.3 69.9 + - - +
296B ASN* 1.3 61.0 + - - +
298B ALA* 2.9 9.3 + - + +
299B GLY* 2.7 33.3 + - - -
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Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 5.3 7.0 + - - +
37B ASP 5.9 0.2 + - - -
38B GLN* 3.2 40.4 - - - +
132B ARG* 4.9 12.6 - - - +
134B LEU* 4.1 11.4 - - + +
223B ASN* 5.1 7.1 + - - -
226B GLU* 5.4 0.2 + - - -
294B ASP* 3.3 9.8 + - - +
295B THR* 1.3 85.5 - - - +
297B GLY* 1.3 63.3 + - - +
299B GLY* 2.9 12.6 + - - -
300B ASP* 3.1 16.3 + - - +
500B 5I5 3.5 22.4 - - + +
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 5.8 2.5 - - - -
294B ASP* 3.0 28.6 + - - -
296B ASN* 1.3 75.4 - - - +
298B ALA* 1.3 61.2 + - - +
300B ASP* 3.3 8.0 + - - +
301B ALA* 3.1 22.6 + - - +
330B ILE 5.0 3.7 - - - +
500B 5I5 3.9 7.5 - - - +
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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
----------------------------------------------------------
293B ILE* 5.3 9.9 - - + -
294B ASP 2.9 17.2 + - - +
295B THR* 2.9 13.0 + - + +
297B GLY* 1.3 71.9 - - - +
299B GLY* 1.3 67.4 + - - +
301B ALA* 3.2 4.0 + - - +
302B PHE* 2.8 25.3 + - - +
327B ALA* 3.8 29.1 - - + +
330B ILE 5.4 1.6 - - - -
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASN* 6.0 0.7 - - - -
265B THR* 5.1 11.4 - - - -
295B THR 2.7 17.7 + - - -
296B ASN* 2.9 5.8 + - - -
298B ALA* 1.3 77.0 - - - +
300B ASP* 1.3 60.4 + - - +
302B PHE* 3.0 19.9 + - - +
303B VAL* 3.3 12.8 + - - +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 2.5 46.0 + - - +
68B ASN* 3.5 27.0 + - + -
69B SER* 2.3 37.3 + - - +
72B VAL* 5.2 0.4 - - - -
166B TYR* 5.3 1.7 + - - -
196B ASN* 5.4 3.3 + - - -
296B ASN 3.1 9.1 + - - +
297B GLY* 3.6 9.9 - - - +
298B ALA 3.3 0.2 - - - -
299B GLY* 1.3 75.2 - - - +
301B ALA* 1.3 61.1 + - - +
303B VAL* 3.7 3.3 + - - -
304B GLY 3.2 7.4 + - - -
500B 5I5 3.5 13.6 - - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.7 21.7 - - + +
297B GLY 3.1 14.1 + - - +
298B ALA* 3.7 3.8 - - - +
300B ASP* 1.3 77.3 - - - +
302B PHE* 1.3 68.3 + - - +
304B GLY 3.3 0.9 + - - -
305B GLY 2.9 20.4 + - - -
326B ALA* 3.0 35.5 - - + +
327B ALA* 4.0 3.4 - - - -
330B ILE* 4.3 13.0 - - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 4.3 3.8 - + - -
263B ILE* 3.6 33.0 - - + -
265B THR* 3.9 20.2 - - + -
271B THR* 4.2 10.8 - - + -
298B ALA 2.8 13.4 + - - +
299B GLY* 3.2 12.6 - - - +
301B ALA* 1.3 79.6 - - - +
303B VAL* 1.3 66.4 + - + +
306B PHE* 2.9 45.6 + + + -
320B ILE* 3.9 17.9 - - + -
323B GLY* 3.1 40.6 + - - +
324B HIS* 3.9 22.2 - + - -
327B ALA* 4.3 6.0 - - + +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 3.4 11.4 - - - +
166B TYR* 3.7 27.1 - - + +
196B ASN* 3.6 25.1 - - - +
221B PHE* 4.1 23.8 - - + -
299B GLY 3.3 14.7 + - - +
300B ASP* 4.7 1.1 - - - +
301B ALA 3.3 0.2 - - - -
302B PHE* 1.3 83.3 - - + +
304B GLY* 1.3 55.5 + - - +
306B PHE* 3.1 4.8 + - - +
307B LEU* 2.8 60.9 + - + +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 3.1 30.0 + - - -
72B VAL* 4.1 4.5 - - - -
73B ALA* 3.4 15.4 - - - -
300B ASP 3.2 9.5 + - - -
301B ALA 3.3 2.6 + - - -
303B VAL* 1.3 76.9 - - - +
305B GLY* 1.3 56.7 + - - +
307B LEU* 3.7 2.6 - - - +
308B SER* 2.8 30.1 + - - -
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.9 2.4 - - - +
76B MET* 4.3 6.1 - - - -
301B ALA 2.9 13.1 + - - -
302B PHE 3.6 3.4 - - - -
304B GLY* 1.3 74.4 - - - +
306B PHE* 1.3 62.3 + - - +
308B SER* 2.8 25.2 + - - -
309B GLN 3.6 1.0 + - - -
322B ALA* 3.2 29.8 - - - +
323B GLY 3.7 6.5 - - - -
326B ALA* 3.9 5.4 - - - -
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 4.0 16.6 - - + -
221B PHE* 3.7 23.3 - + + -
263B ILE* 2.9 38.1 - - + -
302B PHE* 2.9 24.3 + + + +
303B VAL* 3.1 12.3 + - - +
305B GLY* 1.3 75.7 - - - +
307B LEU* 1.3 65.8 + - + +
309B GLN* 3.2 4.2 + - - -
310B LEU* 3.2 43.2 + - + -
316B LEU* 4.0 20.0 - - + -
319B CYS* 3.5 42.6 - - + +
320B ILE* 4.0 7.2 - - + -
323B GLY* 3.8 1.0 - - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.3 25.6 - - + -
69B SER* 4.7 5.4 - - - +
70B ILE* 4.9 2.5 - - + -
73B ALA* 5.1 0.9 - - - -
164B VAL* 4.2 16.2 - - + +
166B TYR* 3.7 26.5 - - + -
194B THR* 3.9 20.9 - - - +
221B PHE* 4.4 11.9 - - + -
303B VAL* 2.8 48.3 + - + +
304B GLY* 3.7 8.5 - - - +
306B PHE* 1.3 77.3 - - + +
308B SER* 1.3 61.7 + - - +
310B LEU* 3.7 8.6 - - + +
311B VAL* 3.1 31.2 + - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 3.7 12.7 - - - +
76B MET* 3.4 30.8 - - - +
77B ILE* 4.3 17.6 - - - +
304B GLY 2.8 20.6 + - - -
305B GLY 2.8 15.1 + - - -
307B LEU* 1.3 72.3 - - - +
309B GLN* 1.3 77.4 + - - +
311B VAL* 3.7 13.9 - - - +
312B SER* 4.5 3.1 + - - -
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 4.5 7.3 + - - +
305B GLY 3.9 0.4 - - - +
306B PHE 3.2 5.7 + - - +
307B LEU 3.2 0.2 - - - -
308B SER* 1.3 97.4 + - - +
310B LEU* 1.3 55.4 + - - +
311B VAL 2.9 4.7 - - - -
312B SER* 2.8 31.8 + - - -
314B LYS* 3.4 46.0 + - + +
318B GLU* 3.9 12.0 - - - +
319B CYS* 4.0 11.0 - - - -
322B ALA* 3.4 26.5 - - + +
344C PHE* 3.5 31.4 - - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 3.7 39.4 - - + +
192B ILE* 4.1 31.6 - - + +
194B THR* 4.6 4.0 - - + -
219B ILE* 4.3 14.4 - - + -
306B PHE* 3.2 37.9 + - + +
307B LEU* 3.7 9.2 - - + +
309B GLN* 1.3 77.4 - - - +
311B VAL* 1.3 59.2 + - - +
312B SER 3.1 1.3 - - - -
313B ASP* 3.3 16.3 + - - +
314B LYS 4.6 5.2 - - - +
316B LEU* 5.1 6.7 - - + -
319B CYS* 3.9 12.5 - - - -
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Residues in contact with VAL 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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4B VAL* 4.5 6.9 - - + +
8B ILE* 3.3 61.3 - - + +
9B LEU* 4.0 16.6 - - + -
77B ILE* 4.4 12.3 - - + -
163B ARG* 4.9 4.6 - - - +
164B VAL* 3.8 23.1 - - + -
307B LEU 3.1 16.0 + - - +
308B SER* 3.7 16.2 - - - +
310B LEU* 1.3 77.9 - - - +
312B SER* 1.3 62.9 + - - +
313B ASP* 3.6 2.9 + - - +
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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