Contacts of the helix formed by residues 294 - 311 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG* 2.9 51.3 + - - +
134D LEU* 5.9 0.6 - - - +
292D ILE 4.2 1.0 + - - -
293D ILE* 1.3 70.8 - - - +
295D THR* 1.3 57.9 + - - +
296D ASN* 3.3 18.2 + - - +
297D GLY* 3.3 20.2 + - - +
298D ALA* 3.0 25.8 + - - +
331D ILE* 5.6 1.6 - - - +
332D ARG* 4.8 30.2 + - + +
500D 5I5 4.8 6.2 - - - +
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Residues in contact with THR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 6.0 3.8 - - - -
132D ARG* 5.1 2.0 - - - +
223D ASN* 5.6 6.5 - - + +
224D GLU* 5.9 3.4 - - - +
267D GLY* 5.0 18.0 - - - +
293D ILE* 3.3 18.5 + - - +
294D ASP* 1.3 73.6 + - - +
296D ASN* 1.3 66.2 + - - +
298D ALA* 3.6 7.2 + - + +
299D GLY* 3.2 20.3 + - - -
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Residues in contact with ASN 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 5.4 5.4 + - - +
37D ASP 5.3 0.5 - - - +
38D GLN* 3.5 36.1 + - - +
132D ARG* 4.8 12.1 - - - +
134D LEU* 4.4 11.3 - - + +
223D ASN* 5.1 7.5 + - - -
226D GLU* 5.5 0.4 + - - -
294D ASP* 3.2 9.9 - - - +
295D THR* 1.3 81.9 + - - +
297D GLY* 1.3 64.9 + - - +
298D ALA 3.1 1.8 - - - -
299D GLY* 3.3 2.6 + - - -
300D ASP* 3.2 26.9 + - - +
500D 5I5 3.4 22.7 - - + -
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Residues in contact with GLY 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 5.4 3.8 - - - -
294D ASP* 3.3 25.5 + - - -
296D ASN* 1.3 77.5 - - - +
298D ALA* 1.3 56.8 + - - +
300D ASP* 3.7 6.4 + - - +
301D ALA* 3.1 27.9 + - - +
330D ILE* 4.6 6.2 - - - +
332D ARG* 6.5 1.1 - - - -
500D 5I5 4.0 6.9 - - - +
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Residues in contact with ALA 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ILE* 5.9 4.5 - - + -
294D ASP 3.0 17.5 + - - +
295D THR* 3.8 9.6 - - + +
296D ASN 3.1 0.6 - - - -
297D GLY* 1.3 75.4 - - - +
299D GLY* 1.3 59.1 + - - +
301D ALA* 3.3 4.6 + - - -
302D PHE* 2.8 32.3 + - - +
327D ALA* 3.7 27.3 - - + +
330D ILE 5.3 1.3 - - - -
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Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D ASN* 5.8 1.6 - - - -
265D THR* 5.1 12.3 - - - -
295D THR 3.2 14.6 + - - -
296D ASN* 3.3 4.6 + - - -
298D ALA* 1.3 74.7 - - - +
300D ASP* 1.3 63.6 + - - +
302D PHE* 3.0 17.7 + - - +
303D VAL* 3.2 17.7 + - - +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D SER* 2.5 32.8 + - - -
68D ASN* 3.3 26.3 + - + +
69D SER* 2.5 34.6 + - - +
166D TYR* 5.5 0.5 + - - -
196D ASN* 5.4 4.0 + - - -
296D ASN 3.2 13.0 + - - +
297D GLY* 3.9 5.3 - - - +
299D GLY* 1.3 73.6 - - - +
301D ALA* 1.3 61.0 + - - +
303D VAL* 4.0 2.5 - - - -
304D GLY 3.2 9.7 + - - -
500D 5I5 3.2 29.0 - - - +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D VAL* 3.6 23.9 - - + +
297D GLY 3.1 18.8 + - - +
298D ALA 3.8 3.4 - - - +
299D GLY 3.3 0.2 - - - -
300D ASP* 1.3 73.2 - - - +
302D PHE* 1.3 66.4 + - - +
304D GLY 3.3 1.0 + - - -
305D GLY 2.9 19.4 + - - -
326D ALA* 3.3 31.8 - - - +
327D ALA* 4.0 5.6 - - - -
330D ILE* 4.2 11.0 - - + +
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Residues in contact with PHE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D PHE* 4.6 4.7 - + - -
263D ILE* 3.8 30.3 - - + -
265D THR* 4.0 20.9 - - + -
271D THR* 4.3 10.1 - - + -
298D ALA 2.8 18.0 + - - +
299D GLY* 3.0 6.9 + - - +
301D ALA* 1.3 77.0 - - - +
303D VAL* 1.3 69.1 + - + +
306D PHE* 2.9 37.5 + + + +
320D ILE* 3.6 34.5 - - + -
323D GLY* 3.1 42.4 - - - +
324D HIS* 3.5 22.9 - + - -
327D ALA* 4.3 4.9 - - + +
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Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER* 3.5 11.0 - - - +
166D TYR* 3.4 37.2 - - + +
196D ASN* 3.6 25.6 - - - +
221D PHE* 4.1 23.1 - - + -
299D GLY 3.2 14.0 + - - +
300D ASP* 3.8 0.9 - - - +
301D ALA 3.2 0.2 - - - -
302D PHE* 1.3 80.1 - - + +
304D GLY* 1.3 58.4 + - - +
306D PHE* 3.0 5.6 + - - +
307D LEU* 2.6 52.9 + - + +
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Residues in contact with GLY 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER* 3.1 29.6 - - - -
72D VAL* 3.8 9.4 - - - -
73D ALA* 3.3 17.7 - - - +
300D ASP 3.2 9.2 + - - -
301D ALA 3.3 2.9 + - - -
303D VAL* 1.3 78.2 - - - +
305D GLY* 1.3 61.9 + - - +
307D LEU* 4.3 1.6 - - - -
308D SER* 3.0 18.9 + - - -
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Residues in contact with GLY 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D VAL* 3.7 1.6 - - - +
76D MET* 4.3 4.5 - - - -
301D ALA 2.9 13.7 + - - -
302D PHE 3.6 2.7 - - - -
304D GLY* 1.3 77.8 - - - +
306D PHE* 1.3 61.3 + - - +
308D SER* 2.6 25.7 + - - -
309D GLN 3.7 1.2 + - - -
322D ALA* 3.2 28.3 - - - +
323D GLY 3.8 5.6 - - - -
326D ALA* 3.9 6.7 - - - -
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ILE* 4.0 15.7 - - + -
221D PHE* 4.0 21.1 - + + -
261D ILE* 5.4 0.7 - - + -
263D ILE* 2.9 35.4 - - + -
273D MET* 4.2 2.5 - - + -
302D PHE* 2.9 29.8 + + + +
303D VAL 3.5 6.7 - - - +
305D GLY* 1.3 68.9 - - - +
307D LEU* 1.3 69.1 + - + +
309D GLN 3.3 2.6 + - - -
310D LEU* 3.0 43.6 + - + -
316D LEU* 4.0 17.0 - - + -
319D CYS* 3.2 46.4 + - + +
320D ILE* 3.9 13.2 - - + -
323D GLY* 3.7 0.4 - - - -
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.3 20.9 - - + -
69D SER* 4.8 2.0 - - - -
70D ILE* 4.8 4.3 - - + -
73D ALA* 4.1 9.0 - - + -
77D ILE* 5.7 0.2 - - - -
164D VAL* 4.2 24.7 - - + -
166D TYR* 3.7 30.5 - - + -
194D THR* 4.4 4.7 - - + +
221D PHE* 4.3 18.8 - - + -
303D VAL* 2.6 41.2 + - + +
304D GLY* 3.7 8.1 - - - +
306D PHE* 1.3 74.8 - - + +
308D SER* 1.3 64.4 + - - +
309D GLN 3.1 1.2 + - - -
310D LEU* 3.1 13.5 + - + +
311D VAL* 3.1 19.4 + - - +
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ALA* 3.8 11.2 - - - +
76D MET* 3.1 35.1 - - - +
77D ILE* 3.9 18.9 - - - +
304D GLY 3.0 13.8 + - - -
305D GLY 2.6 18.9 + - - -
306D PHE 3.2 0.2 - - - -
307D LEU* 1.3 75.6 - - - +
309D GLN* 1.3 77.1 + - - +
311D VAL* 3.6 15.4 - - - +
312D SER* 4.3 4.2 + - - -
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PHE* 3.7 29.8 - - + -
345A HIS* 4.4 5.7 - - - +
76D MET* 4.8 9.1 + - - +
77D ILE* 6.0 0.6 - - - +
305D GLY 4.0 0.4 - - - +
306D PHE 3.3 1.4 + - - -
307D LEU 3.1 0.4 - - - -
308D SER* 1.3 99.7 + - - +
310D LEU* 1.3 67.8 + - - +
311D VAL 3.0 3.1 - - - -
312D SER* 3.0 15.8 + - - -
313D ASP 3.4 0.2 + - - -
314D LYS* 3.3 47.9 + - + +
318D GLU* 3.9 5.9 - - + +
319D CYS* 3.9 15.7 - - - -
322D ALA* 3.6 22.9 - - + -
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D VAL* 3.5 40.3 - - + +
192D ILE* 4.0 29.1 - - + +
194D THR* 4.8 3.1 - - + -
219D ILE* 4.4 12.1 - - + -
306D PHE* 3.0 39.3 + - + +
307D LEU* 3.6 11.2 - - + +
309D GLN* 1.3 77.4 - - - +
311D VAL* 1.3 57.8 - - - +
313D ASP* 3.0 21.9 + - - +
314D LYS 4.9 4.7 - - - +
316D LEU* 4.8 8.3 - - + -
319D CYS* 3.7 12.0 - - - -
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Residues in contact with VAL 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 4.4 9.8 - - + +
8D ILE* 3.5 57.3 - - + +
9D LEU* 4.1 16.2 - - + -
77D ILE* 4.3 13.9 - - + -
163D ARG* 5.0 4.7 - - - +
164D VAL* 3.7 29.1 - - + +
307D LEU 3.1 9.6 + - - +
308D SER 3.6 15.0 - - - +
309D GLN 3.0 0.4 - - - -
310D LEU* 1.3 80.5 - - - +
312D SER* 1.3 61.1 + - - +
313D ASP* 3.8 1.9 + - - +
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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