Contacts of the helix formed by residues 253 - 268 (chain B) in PDB entry 3EGC
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 SER 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASN* 5.6 3.2 + - - -
202B ARG* 4.6 5.4 - - - -
251B THR 3.4 1.6 - - - -
252B SER* 1.3 82.4 + - - +
254B HIS* 1.3 61.4 + - - +
255B ARG* 3.5 13.7 + - - +
256B ILE* 3.3 19.4 + - - +
257B THR* 2.9 30.1 + - - -
279B SER* 3.7 1.6 - - - -
280B PHE 3.6 9.4 - - - -
281B ASP* 3.2 15.7 - - - -
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Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 2.8 33.7 + - - -
80B VAL* 4.3 11.3 + - + +
81B PHE* 4.5 5.2 + - + -
253B SER* 1.3 74.6 - - - +
255B ARG* 1.3 89.5 + - - +
257B THR* 3.2 3.3 + - - -
258B GLU* 2.9 39.8 + - - +
280B PHE 3.3 1.8 + - - -
281B ASP* 2.9 36.0 + - + -
283B LEU* 3.8 32.2 - - + +
285B TRP* 4.5 3.4 + - + -
286B MET* 3.6 28.5 - - + -
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 5.4 4.4 - - - +
284A PRO* 6.1 1.2 - - - +
76B ASP* 3.6 22.8 + - - -
78B GLU* 3.9 10.1 + - - +
79B ASN* 3.6 35.1 - - - +
80B VAL 4.6 0.6 - - - +
231B ASN* 2.7 43.5 + - - +
253B SER* 3.2 8.0 + - - +
254B HIS* 1.3 105.8 - - + +
256B ILE* 1.3 63.0 + - + +
258B GLU* 3.3 23.9 + - - +
259B GLY 3.2 8.0 + - - -
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 3.5 36.1 - - + +
191B VAL 4.3 2.5 - - - +
192B GLY* 3.2 27.1 - - - +
231B ASN* 3.0 22.6 - - - +
232B GLY* 5.1 0.6 - - - +
251B THR* 3.8 12.8 - - + -
252B SER* 3.0 28.9 - - - +
253B SER* 3.3 22.0 + - - +
255B ARG* 1.3 75.7 - - + +
257B THR* 1.3 60.5 + - - +
259B GLY 3.1 1.0 + - - -
260B ALA* 2.8 26.9 + - - +
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 2.5 32.2 + - - +
253B SER 2.9 10.9 + - - -
254B HIS* 3.2 10.9 + - - -
256B ILE* 1.3 73.5 - - - +
258B GLU* 1.3 66.0 + - - +
260B ALA* 3.4 1.9 + - - +
261B MET* 2.9 26.9 + - + +
277B ILE* 4.3 7.0 - - + -
279B SER* 2.7 21.5 + - - -
285B TRP* 4.0 20.0 - - + -
286B MET* 4.2 7.2 - - + -
293B LEU* 4.2 17.7 - - + -
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 6.2 0.2 - - - +
284A PRO* 3.5 37.1 - - + +
285A TRP* 4.6 4.0 + - - +
288A PHE* 3.3 34.6 - - + -
231B ASN* 4.5 6.5 + - - +
254B HIS* 2.9 29.4 + - - +
255B ARG* 3.3 34.7 + - - +
256B ILE 3.2 0.2 - - - -
257B THR* 1.3 77.9 - - - +
259B GLY* 1.3 57.1 + - - +
261B MET 3.3 0.5 + - - -
262B GLN* 3.0 28.8 + - - +
285B TRP* 4.1 15.3 + - + -
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Residues in contact with GLY 259 (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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231B ASN* 3.5 28.0 + - - -
233B ARG* 3.3 24.7 - - - +
255B ARG 3.2 5.1 + - - -
256B ILE 3.1 7.5 + - - -
258B GLU* 1.3 76.0 - - - +
260B ALA* 1.3 60.0 + - - +
262B GLN* 3.3 6.1 + - - -
263B ALA* 2.9 21.8 + - - +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 5.1 2.2 - - + -
232B GLY 4.6 0.6 + - - -
236B ALA* 3.9 20.0 - - + +
240B LEU* 5.1 0.9 - - - +
249B LEU* 4.9 9.6 - - + -
251B THR* 3.9 20.9 - - + -
256B ILE 2.8 16.6 + - - +
257B THR 3.7 4.5 - - - +
259B GLY* 1.3 73.3 - - - +
261B MET* 1.3 64.2 + - - +
263B ALA* 3.1 3.8 + - - +
264B LEU* 3.0 28.2 + - + +
277B ILE* 4.2 13.5 - - + -
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 3.7 48.1 - - + +
257B THR* 2.9 29.4 + - + +
258B GLU 3.7 5.2 - - - +
260B ALA* 1.3 75.3 - - - +
262B GLN* 1.3 62.6 + - - +
264B LEU* 3.5 16.2 + - + +
265B ASN* 3.5 17.5 + - - +
271B TYR* 3.9 33.2 - - + -
277B ILE* 3.8 22.9 - - + -
285B TRP* 4.6 2.9 - - + -
289B LEU* 4.5 15.3 - - + -
293B LEU* 4.7 6.3 - - - -
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Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO* 4.6 10.9 - - - +
288A PHE* 3.8 20.6 - - + -
231B ASN* 2.8 28.8 + - - +
233B ARG* 3.6 25.7 - - - +
258B GLU* 3.0 17.2 + - - +
259B GLY* 3.5 9.4 - - - +
260B ALA 3.2 0.2 - - - -
261B MET* 1.3 75.8 - - - +
263B ALA* 1.3 64.1 + - - +
265B ASN* 3.5 7.6 + - - +
266B VAL* 3.0 27.2 + - + +
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.8 3.3 - - - +
236B ALA* 3.4 30.3 - - + -
237B ILE* 3.5 28.5 - - + +
240B LEU* 4.6 4.7 - - + -
259B GLY 2.9 8.9 + - - +
260B ALA 3.1 9.4 + - - +
262B GLN* 1.3 74.9 - - - +
264B LEU* 1.3 69.3 + - - +
266B VAL* 3.2 1.5 + - - +
267B LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.8 16.2 - - + -
260B ALA 3.0 19.1 + - - +
261B MET* 3.7 21.8 - - + +
262B GLN 3.3 0.2 - - - -
263B ALA* 1.3 75.1 - - - +
265B ASN* 1.3 59.8 + - + +
267B LEU* 2.8 7.1 + - - -
268B GLY 2.8 22.3 + - - -
269B LEU* 2.9 36.0 + - + +
270B ARG 4.8 0.4 - - - +
271B TYR* 3.7 35.7 - - + +
275B VAL* 3.7 34.5 - - + -
277B ILE* 4.3 11.0 - - + -
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Residues in contact with ASN 265 (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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287A ALA 4.6 10.2 - - - +
288A PHE* 4.9 11.3 - - - +
261B MET 3.5 14.3 + - - +
262B GLN* 4.1 7.3 + - - +
263B ALA 3.3 0.2 - - - -
264B LEU* 1.3 76.5 - - + +
266B VAL* 1.3 69.1 + - - +
268B GLY* 3.6 11.7 + - - +
269B LEU 4.6 5.8 - - - +
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Residues in contact with VAL 266 (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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233B ARG* 3.4 26.0 - - - +
237B ILE* 3.7 24.2 - - + -
262B GLN* 3.0 23.6 + - + +
263B ALA 3.5 4.5 - - - +
264B LEU 3.2 0.2 - - - -
265B ASN* 1.3 80.7 - - - +
267B LEU* 1.3 66.9 + - + +
268B GLY 3.3 1.4 + - - -
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Residues in contact with LEU 267 (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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237B ILE* 4.0 23.6 - - + +
240B LEU* 3.6 34.1 - - + +
241B THR* 3.2 33.2 - - + -
263B ALA 3.0 17.0 + - - +
264B LEU 2.8 5.5 + - - +
266B VAL* 1.3 85.8 - - + +
268B GLY* 1.3 59.6 + - - +
269B LEU* 3.3 22.2 + - + +
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Residues in contact with GLY 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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264B LEU 2.8 3.7 + - - -
265B ASN* 3.6 10.1 + - - -
266B VAL 3.3 4.9 + - - -
267B LEU* 1.3 79.1 - - - +
269B LEU* 1.3 65.2 + - - +
270B ARG* 4.7 5.7 - - - +
274B ASP* 4.6 2.1 - - - +
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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