Contacts of the helix formed by residues 257 - 276 (chain A) in PDB entry 2BEW
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 3.7 2.8 - - - +
36A VAL 2.7 29.5 + - - -
37A MET* 2.8 34.2 + - - +
254A ASP* 3.0 16.7 + - - +
255A GLY 3.2 0.6 - - - -
256A ASN* 1.3 77.5 - - - +
258A VAL* 1.3 64.3 + - - +
259A PHE* 3.0 17.7 + - - +
260A ALA* 3.1 13.1 + - + -
261A VAL* 3.1 22.5 + - - +
318A ARG* 3.7 13.2 - - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 4.0 13.8 - - + +
60A LEU* 4.5 8.5 - - + +
64A MET* 3.9 18.6 - - + -
94A GLY* 3.6 37.7 - - - +
97A VAL* 4.1 9.9 - - + -
98A GLY* 3.7 10.6 - - - -
256A ASN 3.9 2.0 + - - -
257A ASP* 1.3 71.0 + - - +
259A PHE* 1.3 73.6 + - + +
261A VAL* 3.9 1.1 - - - -
262A TYR* 2.9 28.2 + - - +
315A PRO* 5.1 4.0 + - + +
319A LEU* 3.9 30.3 - - + -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.8 17.5 - - + -
37A MET* 3.8 25.4 - - + -
43A ILE* 4.2 13.9 - - + -
49A ASP* 5.7 1.3 - - - -
50A PRO* 4.0 22.9 - - + -
52A LEU* 4.0 24.7 - - + -
57A VAL* 4.2 15.9 - - + -
60A LEU* 4.4 4.9 - - + -
257A ASP* 3.0 6.5 + - - +
258A VAL* 1.3 86.2 - - + +
260A ALA* 1.3 59.7 + - - +
262A TYR* 3.6 3.1 - - + +
263A ASN* 2.9 34.3 + - - +
319A LEU* 4.5 4.5 - - + -
322A TYR* 3.7 52.9 - + - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.5 40.9 - - + +
36A VAL* 3.6 14.0 - - + +
253A VAL* 3.9 3.7 - - + +
254A ASP 4.1 4.5 - - - +
257A ASP* 3.1 30.8 + - + +
259A PHE* 1.3 73.7 - - - +
261A VAL* 1.3 64.4 + - - +
264A ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 4.2 3.1 - - - +
95A THR* 3.7 19.5 - - - +
98A GLY* 3.7 1.1 - - - -
99A SER* 3.4 26.7 - - - +
218A PHE* 3.9 16.9 - - + -
253A VAL* 4.1 14.4 - - + -
254A ASP 3.8 12.8 - - - +
255A GLY* 3.8 20.4 - - - +
257A ASP 3.1 15.4 + - - +
258A VAL 3.8 7.2 - - - +
260A ALA* 1.3 77.3 - - - +
262A TYR* 1.3 61.3 + - - +
264A ALA* 3.9 1.3 - - - +
265A THR* 2.8 29.5 + - - -
281A ILE* 6.1 0.2 - - - -
283A ALA* 4.8 2.0 - - + -
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 4.1 15.3 - - + -
52A LEU* 3.5 42.1 - - + +
56A LYS* 3.7 9.1 + - - -
60A LEU* 5.9 1.8 - - + -
98A GLY* 3.3 25.1 + - - +
101A ALA* 3.5 31.2 - - + -
102A ALA* 3.6 12.7 - - + +
258A VAL 2.9 19.2 + - - +
259A PHE* 3.6 6.3 - - + +
261A VAL* 1.3 76.6 - - - +
263A ASN* 1.3 70.1 + - - +
265A THR 3.3 0.3 + - - -
266A LYS* 2.8 67.1 + - + +
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Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.0 30.5 + - + +
36A VAL* 3.8 9.5 - - - +
48A GLU* 2.7 30.3 + - - -
50A PRO* 3.3 29.2 - - - +
259A PHE 2.9 18.9 + - - +
262A TYR* 1.3 78.4 - - - +
264A ALA* 1.3 62.9 + - - +
266A LYS* 3.9 4.1 - - - +
267A GLU* 3.1 25.6 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 4.7 2.8 - - + -
251A ILE* 4.2 25.5 - - + +
253A VAL* 3.5 23.8 - - + -
260A ALA 3.1 17.1 + - - +
261A VAL 4.0 2.2 - - - +
263A ASN* 1.3 77.8 - - - +
265A THR* 1.3 58.3 + - - +
267A GLU* 4.0 3.3 - - - +
268A ALA* 2.9 30.5 + - - +
281A ILE* 3.8 8.8 - - + +
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 3.6 40.5 - - - +
102A ALA* 3.7 11.9 - - + -
103A LEU* 4.2 17.0 - - + -
188A ILE* 4.3 9.4 - - + -
216A ILE* 4.0 5.2 - - + +
218A PHE* 3.8 11.3 - - - -
261A VAL 2.8 22.9 + - - -
264A ALA* 1.3 78.6 - - - +
266A LYS* 1.3 57.2 + - - +
268A ALA* 3.8 0.9 - - - +
269A ARG* 2.9 28.6 + - - +
281A ILE* 3.8 11.2 - - + +
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 5.2 3.4 - - - +
101A ALA 5.0 2.2 + - - -
102A ALA* 3.6 31.5 + - + +
103A LEU 5.7 1.2 + - - -
262A TYR* 2.8 50.7 + - + +
263A ASN* 3.9 4.9 - - - +
265A THR* 1.3 76.0 - - - +
267A GLU* 1.3 59.1 + - - +
269A ARG* 3.5 5.8 + - + +
270A ARG* 3.1 27.5 + - + +
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASN 3.1 17.4 + - - +
264A ALA* 4.0 3.6 - - - +
266A LYS* 1.3 76.9 - - - +
268A ALA* 1.3 64.4 + - - +
270A ARG* 2.7 47.7 + - - +
271A ARG* 3.1 42.0 + - - +
279A PHE* 6.2 0.7 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 4.1 9.6 - - + -
251A ILE* 6.3 0.4 - - + -
264A ALA 2.9 19.6 + - - +
265A THR 3.9 3.1 - - - +
267A GLU* 1.3 78.6 - - - +
269A ARG* 1.3 51.5 + - - +
272A ALA* 2.8 37.9 + - - +
279A PHE* 3.7 38.2 - - + -
281A ILE* 4.1 16.4 - - + -
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 4.2 17.7 - - - +
103A LEU* 4.7 4.0 - - + -
104A ASP* 3.8 19.7 + - - +
107A ASP* 2.8 41.1 + - - +
184A ASN 3.2 24.5 + - - -
185A ARG* 3.8 4.4 - - - +
186A VAL* 3.7 14.6 - - + +
216A ILE* 3.7 14.3 - - + +
265A THR 2.9 19.6 + - - +
266A LYS* 3.7 7.9 - - - +
267A GLU 3.3 0.2 - - - -
268A ALA* 1.3 75.0 - - - +
270A ARG* 1.3 67.3 + - - +
272A ALA* 4.6 0.2 - - - -
273A VAL* 3.0 51.8 + - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LYS* 3.1 17.9 + - + +
267A GLU* 2.7 44.4 + - - +
269A ARG* 1.3 80.1 - - - +
271A ARG* 1.3 73.2 + - - +
273A VAL* 4.2 2.9 - - - +
274A ALA* 3.2 31.7 + - + +
275A GLU* 5.8 0.2 + - - -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A MET* 3.4 34.0 - - - +
267A GLU* 3.1 37.2 + - - +
270A ARG* 1.3 96.1 - - - +
272A ALA* 1.3 66.2 + - - +
274A ALA* 4.5 2.5 - - - +
275A GLU* 2.9 64.8 + - - +
277A GLN* 3.9 5.9 - - - +
279A PHE* 3.4 25.2 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.5 9.9 - - + -
214A PRO* 3.4 9.6 - - + +
215A ILE 4.2 19.3 - - - +
216A ILE* 4.7 1.6 - - + -
268A ALA 2.8 23.5 + - - +
269A ARG 4.0 2.9 - - - +
271A ARG* 1.3 73.5 - - - +
273A VAL* 1.3 58.4 - - - +
276A ASN* 2.9 30.0 + - - -
277A GLN 3.3 24.0 - - - +
279A PHE* 3.6 6.8 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASN* 3.8 45.6 - - + +
185A ARG 4.0 4.7 - - - +
186A VAL* 2.2 46.4 - - + -
214A PRO* 4.3 5.4 - - + -
269A ARG* 3.0 29.6 + - - +
270A ARG 4.3 2.0 - - - +
272A ALA* 1.3 74.5 - - - +
274A ALA* 1.3 66.1 + - - +
275A GLU 3.6 0.2 + - - -
276A ASN* 4.1 12.0 + - - +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ARG* 3.2 25.5 + - + +
271A ARG* 4.0 3.1 - - - +
273A VAL* 1.3 78.7 - - - +
275A GLU* 1.3 69.0 + - + +
276A ASN* 3.6 2.0 + - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 5.7 0.5 - - - +
270A ARG* 5.6 0.7 + - - -
271A ARG* 2.9 54.2 + - - +
274A ALA* 1.3 85.6 - - + +
276A ASN* 1.3 70.8 + - - +
277A GLN* 2.4 46.8 + - + +
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Residues in contact with ASN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS* 3.6 26.7 - - + +
212A GLU* 3.1 44.5 - - + +
213A CYS 4.1 1.3 - - - -
214A PRO* 3.6 31.3 - - - +
272A ALA 2.9 9.2 + - - -
273A VAL 4.1 10.1 + - - +
274A ALA 3.6 2.4 - - - +
275A GLU* 1.3 79.6 - - - +
277A GLN* 1.3 60.1 + - - +
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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
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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