Contacts of the helix formed by residues 265 - 279 (chain B) in PDB entry 1EQB
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 LEU 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS 4.9 7.6 - - - +
97A SER* 6.1 1.1 - - - -
235A ARG* 3.5 44.0 - - + +
265A LEU* 4.3 21.8 - - + -
94B GLN 5.3 0.6 + - - -
96B HIS* 3.6 33.5 + - + +
235B ARG 6.0 0.2 - - - +
263B GLY 4.9 1.3 - - - +
264B PRO* 1.3 74.2 - - - +
266B MET* 1.3 66.8 + - - +
267B HIS* 3.1 13.5 - - + +
268B VAL* 2.8 40.9 + - + +
269B ILE* 3.0 16.9 + - + +
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 5.1 1.0 - - - +
51B LEU* 3.7 26.3 + - + +
54B LYS 4.4 10.5 + - - +
56B ALA* 4.3 17.3 - - + +
63B ARG* 4.6 0.4 - - - +
71B VAL* 3.2 51.4 - - + +
74B VAL* 4.4 6.6 - - + +
75B GLU* 4.1 23.3 - - + +
264B PRO* 3.4 18.9 + - - +
265B LEU* 1.3 72.6 - - - +
267B HIS* 1.3 59.1 + - - +
269B ILE* 3.4 22.2 + - + +
270B ALA* 3.1 25.5 + - - +
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.4 33.4 + - + -
235A ARG* 4.2 6.7 - - + +
267A HIS* 6.4 0.9 - + - -
268A VAL* 5.5 5.4 - - + -
46B ALA 3.6 27.3 - - - +
47B GLN* 3.2 22.6 + - + +
49B SER* 4.0 2.2 - - - +
51B LEU* 3.7 14.2 - - + +
52B THR* 3.5 36.9 + - - +
265B LEU* 3.8 30.2 - - + +
266B MET* 1.3 79.9 - - - +
268B VAL* 1.3 77.6 + - + +
270B ALA* 3.6 4.5 - - - +
271B GLY 3.4 13.5 + - - -
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Residues in contact with VAL 268 (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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265A LEU* 5.8 2.0 - - + -
267A HIS* 5.4 5.4 - - + -
47B GLN* 3.8 25.1 - - + +
234B PRO* 3.9 7.8 - - + +
235B ARG 3.6 23.8 - - - +
236B GLY* 5.2 0.2 - - - -
265B LEU* 2.8 40.4 + - + +
267B HIS* 1.3 91.9 - - + +
269B ILE* 1.3 62.5 + - + +
270B ALA 3.2 0.4 - - - -
271B GLY* 3.1 3.1 + - - -
272B LYS* 2.9 36.5 + - - +
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Residues in contact with ILE 269 (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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74B VAL* 4.5 4.3 - - + -
75B GLU* 4.0 17.7 - - + +
78B ALA* 3.8 19.7 - - + -
93B VAL* 3.6 35.7 - - + +
94B GLN* 4.1 11.4 - - + +
264B PRO* 4.0 20.0 - - + -
265B LEU 3.0 13.9 + - - +
266B MET* 3.8 32.5 - - + +
267B HIS 3.3 0.2 - - - -
268B VAL* 1.3 76.0 - - + +
270B ALA* 1.3 59.6 + - - +
272B LYS* 3.2 10.9 + - + +
273B ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.4 19.6 - - + +
19A MET* 4.6 4.0 - - + -
46B ALA* 4.0 12.6 - - + -
51B LEU* 3.6 29.4 - - + -
74B VAL* 3.6 15.3 - - + -
266B MET 3.1 5.4 + - - +
267B HIS 3.6 11.0 - - - +
269B ILE* 1.3 76.6 - - - +
271B GLY* 1.3 63.9 + - - +
273B ALA* 3.2 5.0 + - - +
274B VAL* 3.1 17.8 + - - +
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Residues in contact with GLY 271 (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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43B VAL* 3.9 12.9 - - - +
46B ALA* 3.5 17.2 - - - +
47B GLN* 5.2 0.4 - - - -
234B PRO* 3.8 9.6 - - - +
267B HIS 3.4 5.7 + - - -
268B VAL* 3.1 8.7 + - - -
270B ALA* 1.3 77.3 - - - +
272B LYS* 1.3 63.2 + - - +
274B VAL* 3.2 10.2 - - - +
275B ALA* 3.0 23.9 + - - +
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Residues in contact with LYS 272 (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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78B ALA* 4.7 6.1 - - + -
93B VAL* 2.8 34.8 + - + +
94B GLN 4.3 0.8 + - - -
95B PRO 3.1 16.8 + - - -
227B THR* 4.1 17.7 - - + +
234B PRO* 3.7 18.6 - - + -
236B GLY* 3.8 20.4 - - - -
237B GLY 2.8 28.7 + - - +
238B LEU* 5.6 0.9 - - + -
268B VAL* 2.9 26.5 + - - +
269B ILE* 3.4 17.6 - - + +
271B GLY* 1.3 75.0 - - - +
273B ALA* 1.3 63.4 + - - +
275B ALA* 3.2 2.0 + - - +
276B LEU* 2.9 35.4 + - + +
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Residues in contact with ALA 273 (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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15A LEU* 4.5 8.5 - - + -
74B VAL 4.3 6.7 - - - +
77B LEU* 4.3 9.4 - - + -
78B ALA* 3.8 32.5 - - + +
81B ARG* 3.2 24.4 + - - +
269B ILE 2.9 13.0 + - - +
270B ALA* 3.2 11.6 + - - +
272B LYS* 1.3 79.5 - - - +
274B VAL* 1.3 61.2 + - - +
276B LEU* 3.6 3.5 + - - +
277B LYS 3.5 7.6 + - - -
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.7 4.5 - - + -
11A TYR* 4.3 11.4 - - + -
12A ASP* 4.2 15.5 - - + +
15A LEU* 3.5 19.2 - - + +
42B ARG* 4.0 34.5 - - + +
43B VAL* 3.8 25.1 - - + +
46B ALA* 4.9 1.1 - - + -
270B ALA 3.1 4.4 + - - +
271B GLY* 3.2 23.6 - - - +
273B ALA* 1.3 75.8 - - - +
275B ALA* 1.3 65.2 + - - +
277B LYS* 3.1 12.3 + - + +
278B GLU* 3.1 15.7 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.9 8.3 - - + -
227B THR* 6.1 1.1 - - - -
231B LEU* 4.9 7.2 - - + +
232B ALA 4.9 1.8 - - - +
233B GLY* 3.7 30.7 - - - +
234B PRO* 3.9 2.7 - - + -
271B GLY 3.0 17.3 + - - +
272B LYS* 3.7 3.6 - - - +
274B VAL* 1.3 72.6 - - - +
276B LEU* 1.3 64.1 + - + +
277B LYS 3.0 1.8 - - - -
278B GLU* 3.2 15.6 + - - +
279B ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 276 (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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78B ALA* 3.5 12.3 - - + +
81B ARG* 3.9 14.6 - - + -
82B ALA* 3.5 38.8 - - + +
85B LEU* 3.9 23.4 - - + +
86B PHE* 4.7 6.3 - - + -
93B VAL* 5.4 2.0 - - + -
227B THR* 5.5 4.5 - - + -
231B LEU* 4.2 24.0 - - + -
238B LEU* 4.8 9.4 - - + -
272B LYS* 2.9 26.1 + - + +
273B ALA 4.0 2.7 - - - +
275B ALA* 1.3 78.7 - - + +
277B LYS* 1.3 60.6 + - - +
279B ALA* 3.7 8.9 + - - +
280B MET* 3.5 23.0 + - - +
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Residues in contact with LYS 277 (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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11A TYR* 3.5 44.6 + - + +
12A ASP* 3.5 32.3 - - - +
81B ARG* 3.8 19.3 - - - +
273B ALA 3.5 10.5 + - - +
274B VAL* 3.1 10.7 + - - +
275B ALA 3.0 0.6 - - - -
276B LEU* 1.3 78.3 - - - +
278B GLU* 1.3 64.8 + - - +
279B ALA 3.2 0.4 - - - -
280B MET* 3.1 30.0 + - + +
281B GLU* 3.6 12.0 + - - +
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Residues in contact with GLU 278 (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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6A MET* 5.3 0.7 - - - -
11A TYR* 3.4 23.6 - - + +
40B SER* 2.9 34.1 + - - -
42B ARG* 2.7 34.5 + - - +
43B VAL* 4.4 3.4 - - - +
232B ALA 5.3 3.3 - - - +
274B VAL* 3.2 16.8 - - - +
275B ALA* 3.6 14.8 - - - +
277B LYS* 1.3 74.4 - - - +
279B ALA* 1.3 59.7 + - - +
280B MET 2.9 6.6 + - - -
281B GLU* 3.1 20.8 + - + +
284B PHE* 3.5 11.6 - - + +
371B ARG* 5.0 9.4 + - - +
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Residues in contact with ALA 279 (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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85B LEU* 3.6 35.2 - - + +
209B ALA* 4.9 2.3 - - - +
231B LEU* 4.0 9.9 - - + +
275B ALA 3.0 16.3 + - - +
276B LEU* 3.9 2.9 - - - +
277B LYS 3.2 0.6 - - - -
278B GLU* 1.3 76.0 - - - +
280B MET* 1.3 59.5 + - - +
281B GLU 3.4 1.2 - - - +
284B PHE* 3.0 49.2 - - + +
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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