Contacts of the helix formed by residues 253 - 268 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ASN* 5.7 3.0 + - - -
202C ARG* 4.6 5.2 - - - -
251C THR* 3.3 2.1 + - - -
252C SER* 1.3 81.5 + - - +
254C HIS* 1.3 62.7 + - - +
255C ARG* 3.6 12.9 + - - +
256C ILE* 3.2 18.0 + - - +
257C THR* 2.8 30.5 + - - -
279C SER* 3.8 2.0 - - - -
280C PHE 3.7 9.2 - - - -
281C ASP* 3.2 15.7 - - - -
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Residues in contact with HIS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASN* 2.8 33.5 + - - -
80C VAL* 4.3 14.2 + - + +
81C PHE* 4.3 6.4 + - + -
253C SER* 1.3 77.9 - - - +
255C ARG* 1.3 88.9 + - - +
257C THR* 3.2 3.2 + - - -
258C GLU* 2.9 40.7 + - - +
280C PHE 3.5 1.2 + - - -
281C ASP* 3.0 32.7 + - + -
283C LEU* 3.8 29.8 - - + +
285C TRP* 4.5 3.4 + - + -
286C MET* 3.6 28.7 - - + -
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ASP* 3.6 22.2 + - - -
78C GLU* 3.9 10.1 + - - +
79C ASN* 3.8 33.6 - - - +
80C VAL 4.5 0.8 - - - +
231C ASN* 2.7 44.6 + - - +
253C SER* 3.2 7.2 + - - +
254C HIS* 1.3 108.0 - - + +
256C ILE* 1.3 56.9 + - + +
258C GLU* 3.5 22.2 + - - +
259C GLY 3.3 9.9 + - - -
80D VAL* 5.5 3.4 - - - +
284D PRO* 6.1 1.2 - - - +
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Residues in contact with ILE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ILE* 3.6 37.6 - - + +
191C VAL 3.3 3.1 - - - +
192C GLY* 2.9 30.1 - - - +
231C ASN* 3.0 20.5 - - - +
232C GLY* 5.0 0.4 - - - +
251C THR* 3.9 10.5 - - - -
252C SER* 2.8 29.2 - - - +
253C SER* 3.2 17.7 + - - +
255C ARG* 1.3 77.6 - - + +
257C THR* 1.3 59.0 + - - +
259C GLY* 3.1 1.9 + - - -
260C ALA* 2.9 26.9 + - - +
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C THR* 2.6 23.7 + - - +
253C SER 2.8 9.5 + - - -
254C HIS* 3.4 10.3 - - - -
256C ILE* 1.3 73.3 - - - +
258C GLU* 1.3 65.1 + - - +
260C ALA* 3.2 2.8 + - - +
261C MET* 2.9 27.0 + - + +
277C ILE* 4.2 8.5 - - + -
279C SER* 2.5 28.9 + - - +
285C TRP* 4.1 13.7 - - + -
286C MET* 4.2 3.1 - - + -
293C LEU* 3.9 28.0 - - + -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 4.5 4.9 + - - +
254C HIS* 2.9 32.4 + - - +
255C ARG* 3.5 33.4 + - - +
256C ILE 3.4 0.2 - - - -
257C THR* 1.3 71.7 - - - +
259C GLY* 1.3 58.6 + - - +
261C MET 3.4 0.5 + - - -
262C GLN* 2.9 33.1 + - - +
285C TRP* 4.2 15.8 + - + -
283D LEU* 6.1 0.2 - - - +
284D PRO* 3.5 37.1 - - + +
285D TRP* 4.7 3.1 + - - +
288D PHE* 3.5 35.4 - - + -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 3.8 18.8 - - - -
233C ARG* 3.3 23.6 - - - +
255C ARG 3.3 5.5 + - - -
256C ILE 3.1 8.4 + - - -
258C GLU* 1.3 79.1 - - - +
260C ALA* 1.3 56.3 + - - +
262C GLN* 3.2 15.1 + - - +
263C ALA* 2.9 23.4 + - - +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ILE* 4.9 2.2 - - + -
232C GLY 4.7 0.2 + - - -
236C ALA* 3.9 22.1 - - + +
240C LEU* 5.0 1.2 - - - +
249C LEU* 4.7 10.3 - - + -
251C THR* 3.9 20.9 - - + -
256C ILE* 2.9 15.9 + - + +
257C THR 3.2 3.8 + - - +
259C GLY* 1.3 73.3 - - - +
261C MET* 1.3 62.9 + - - +
263C ALA* 3.4 1.9 + - - +
264C LEU* 3.1 30.1 + - + +
277C ILE* 4.3 12.6 - - + -
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Residues in contact with MET 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C THR* 2.9 28.1 + - + +
258C GLU 3.5 7.6 - - - +
260C ALA* 1.3 72.6 - - - +
262C GLN* 1.4 61.3 + - - +
264C LEU* 3.5 17.0 + - + +
265C ASN* 3.6 17.3 + - - +
271C TYR* 4.0 32.5 - - + -
277C ILE* 3.9 22.0 - - - -
285C TRP* 4.6 3.6 - - + -
289C LEU* 4.3 18.8 - - + -
293C LEU* 4.8 6.1 - - - -
288D PHE* 3.8 48.9 - - + +
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Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ASN* 2.9 27.2 + - - +
233C ARG* 3.5 25.4 - - - +
258C GLU* 2.9 22.3 + - - +
259C GLY* 3.2 11.6 + - - +
261C MET* 1.4 72.5 - - - +
263C ALA* 1.3 61.3 + - - +
265C ASN* 3.7 7.3 + - - +
266C VAL* 3.1 33.1 + - + +
284D PRO* 4.8 7.4 - - - +
288D PHE* 4.1 18.3 - - + -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ARG* 3.8 2.4 - - - +
236C ALA* 3.6 22.0 - - + -
237C ILE* 3.6 32.5 - - + +
240C LEU* 4.6 4.3 - - + -
259C GLY 2.9 13.2 + - - +
260C ALA 3.5 9.0 - - - +
261C MET 3.3 0.2 - - - -
262C GLN* 1.3 75.5 - - - +
264C LEU* 1.3 65.5 + - - +
266C VAL* 3.2 1.9 + - - +
267C LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C LEU* 3.9 15.0 - - + -
249C LEU* 6.2 0.4 - - + -
260C ALA 3.1 17.9 + - - +
261C MET* 3.7 13.7 - - + +
262C GLN 3.3 0.2 - - - -
263C ALA* 1.3 78.0 - - - +
265C ASN* 1.3 60.3 + - + +
267C LEU* 3.0 4.4 + - - +
268C GLY 2.7 23.2 + - - -
269C LEU* 2.7 37.0 + - + +
270C ARG 4.8 0.4 - - - +
271C TYR* 3.7 34.5 - - + +
275C VAL* 3.7 34.5 - - + -
277C ILE* 4.2 19.1 - - + -
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C MET 3.6 13.0 + - - +
262C GLN* 3.9 8.5 + - - +
264C LEU* 1.3 76.5 - - + +
266C VAL* 1.3 69.0 + - - +
267C LEU 3.2 0.2 - - - -
268C GLY* 3.7 10.7 + - - +
269C LEU 4.5 5.6 - - - +
287D ALA 4.7 9.5 - - - +
288D PHE* 5.0 10.4 - - - +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ARG* 3.4 25.1 - - - +
237C ILE* 3.6 24.5 - - + -
262C GLN* 3.1 26.6 + - + +
263C ALA 3.5 5.4 - - - +
265C ASN* 1.3 80.4 - - - +
267C LEU* 1.3 69.6 + - + +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 4.0 21.5 - - + +
240C LEU* 3.6 31.9 - - + +
241C THR* 3.2 35.9 - - + -
263C ALA 2.9 19.6 + - - +
264C LEU 3.6 2.9 - - - +
266C VAL* 1.3 86.8 - - + +
268C GLY* 1.3 61.9 + - - +
269C LEU* 3.5 18.7 + - + +
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Residues in contact with GLY 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU 2.7 4.0 + - - -
265C ASN* 3.7 9.7 + - - -
266C VAL 3.3 4.2 + - - -
267C LEU* 1.3 79.4 - - - +
269C LEU* 1.3 64.6 + - - +
270C ARG* 4.9 4.7 + - - +
274C ASP* 4.6 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
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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