Contacts of the helix formed by residues 265 - 279 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLN 5.3 0.6 + - - -
96C HIS* 3.6 33.4 + - + +
235C ARG 6.1 0.2 - - - +
263C GLY 4.9 1.6 - - - +
264C PRO* 1.3 74.0 - - - +
266C MET* 1.3 58.8 + - - +
267C HIS* 3.1 14.4 - - + +
268C VAL* 2.8 47.0 + - + +
269C ILE* 3.0 16.7 + - + +
96D HIS* 5.0 7.9 - - + +
97D SER* 6.2 0.7 - - - -
235D ARG* 3.5 44.6 - - + +
265D LEU* 4.3 22.2 - - + -
268D VAL* 5.8 1.8 - - + -
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.7 26.7 + - + +
54C LYS 4.3 11.4 + - - +
56C ALA* 4.3 17.3 - - + +
63C ARG* 4.5 0.9 - - - +
71C VAL* 3.3 50.9 - - + +
74C VAL* 4.3 6.2 - - + +
75C GLU* 4.1 23.6 - - + +
264C PRO* 3.5 19.3 + - - +
265C LEU* 1.3 71.8 - - - +
267C HIS* 1.3 58.7 + - - +
269C ILE* 3.4 22.2 + - + +
270C ALA* 3.1 26.5 + - - +
235D ARG* 5.2 1.0 - - - +
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Residues in contact with HIS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA 3.6 26.6 - - - +
47C GLN* 3.3 22.8 + - + +
49C SER* 3.9 2.0 - - - +
51C LEU* 3.7 12.8 - - + +
52C THR* 3.5 39.2 + - - +
265C LEU* 3.7 31.1 - - + +
266C MET* 1.3 79.0 - - - +
268C VAL* 1.3 77.6 + - + +
270C ALA* 3.6 3.8 - - - +
271C GLY 3.4 13.5 + - - -
47D GLN* 3.4 32.5 + - + -
235D ARG* 4.2 6.2 - - - +
267D HIS* 6.3 0.7 - + - -
268D VAL* 5.4 5.4 - - + -
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLN* 3.9 25.4 - - + +
234C PRO* 3.9 7.9 - - + +
235C ARG 3.6 23.8 - - - +
265C LEU* 2.8 40.8 + - + +
267C HIS* 1.3 91.1 - - + +
269C ILE* 1.3 61.4 + - + +
270C ALA 3.2 0.2 - - - -
271C GLY* 3.1 4.0 + - - -
272C LYS* 2.9 36.6 + - - +
265D LEU* 5.7 2.2 - - + -
267D HIS* 5.5 5.8 - - + -
268D VAL* 6.0 0.9 - - + -
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 4.5 3.8 - - + -
75C GLU* 4.0 22.9 - - + +
78C ALA* 3.8 19.7 - - + +
93C VAL* 3.6 31.2 - - + +
94C GLN* 4.1 11.0 - - + +
264C PRO* 4.0 20.2 - - + -
265C LEU 3.0 13.3 + - - +
266C MET* 3.8 31.9 - - + +
268C VAL* 1.3 74.7 - - + +
270C ALA* 1.3 59.6 + - - +
272C LYS* 3.2 11.9 + - + +
273C ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA* 4.0 12.6 - - + -
51C LEU* 3.7 20.6 - - + -
74C VAL* 3.6 15.2 - - + +
266C MET 3.1 13.4 + - - +
267C HIS* 3.6 10.5 - - - +
268C VAL 3.2 0.2 - - - -
269C ILE* 1.3 75.3 - - - +
271C GLY* 1.3 63.1 + - - +
273C ALA* 3.1 7.3 + - - +
274C VAL* 3.1 17.7 + - - +
15D LEU* 3.6 17.5 - - + +
19D MET* 4.7 4.7 - - + -
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Residues in contact with GLY 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.9 13.1 - - - +
46C ALA* 3.5 18.1 - - - +
47C GLN* 5.2 0.7 - - - -
234C PRO* 3.8 8.0 - - - +
267C HIS 3.4 5.5 + - - -
268C VAL* 3.1 8.0 + - - -
270C ALA* 1.3 81.4 - - - +
272C LYS* 1.3 61.3 + - - +
274C VAL* 3.1 10.0 - - - +
275C ALA* 3.0 24.3 + - - +
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Residues in contact with LYS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA* 4.7 6.1 - - + -
93C VAL* 2.8 37.2 + - + +
94C GLN 4.3 0.6 - - - -
95C PRO 3.1 17.0 + - - -
227C THR* 4.1 20.6 - - + +
234C PRO* 3.6 18.8 - - + +
236C GLY* 3.8 19.5 - - - -
237C GLY 2.9 24.8 + - - +
238C LEU* 5.5 1.1 - - + -
268C VAL* 2.9 26.9 + - - +
269C ILE* 3.4 17.3 - - - +
271C GLY* 1.3 74.6 - - - +
273C ALA* 1.3 58.8 + - - +
275C ALA* 3.2 1.8 + - - +
276C LEU* 2.9 40.8 + - + +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL 4.3 4.0 - - - +
77C LEU* 4.3 6.1 - - + -
78C ALA* 3.8 32.3 - - + +
81C ARG* 3.3 24.5 + - - +
269C ILE 2.9 13.0 + - - +
270C ALA 3.1 10.0 + - - +
272C LYS* 1.3 78.1 - - - +
274C VAL* 1.3 59.9 + - - +
276C LEU* 3.7 3.7 + - - +
277C LYS 3.5 9.0 + - - -
15D LEU* 4.3 17.3 - - + -
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 4.0 41.1 - - + +
43C VAL* 3.8 17.5 - - + -
46C ALA* 4.9 0.9 - - + -
270C ALA 3.1 6.6 + - - +
271C GLY* 3.1 23.1 - - - +
273C ALA* 1.3 75.2 - - - +
275C ALA* 1.3 62.9 + - - +
277C LYS* 3.2 3.9 + - - +
278C GLU* 3.1 29.3 + - + +
8D ILE* 4.5 8.5 - - + -
11D TYR* 4.4 10.3 - - + -
12D ASP* 4.2 18.2 - - + +
15D LEU* 3.9 14.8 - - + +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.8 9.2 - - + -
227C THR* 6.1 0.9 - - - -
231C LEU* 4.9 8.4 - - + +
232C ALA 4.9 1.6 - - - +
233C GLY* 3.7 30.7 - - - +
234C PRO* 3.9 2.7 - - + -
271C GLY 3.0 16.6 + - - +
272C LYS* 3.2 3.8 + - - +
274C VAL* 1.3 74.2 - - - +
276C LEU* 1.3 60.8 + - + +
277C LYS 3.1 2.0 - - - -
278C GLU* 3.2 14.6 + - - +
279C ALA* 2.9 28.3 + - - +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA* 3.5 11.9 - - + +
81C ARG* 4.0 14.8 - - + -
82C ALA* 3.5 37.5 - - + +
85C LEU* 3.8 24.0 - - + +
86C PHE* 4.7 6.7 - - + -
93C VAL* 5.4 1.8 - - + -
227C THR* 5.5 4.9 - - + -
231C LEU* 4.2 24.5 - - + -
238C LEU* 4.7 9.9 - - + -
272C LYS* 2.9 27.1 + - + +
273C ALA 4.0 2.2 - - - +
274C VAL 3.3 0.2 - - - -
275C ALA* 1.3 79.1 - - + +
277C LYS* 1.3 60.3 + - - +
279C ALA* 3.7 8.7 + - - +
280C MET* 3.5 23.8 + - - +
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Residues in contact with LYS 277 (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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81C ARG* 3.9 21.5 - - - +
273C ALA 3.5 10.3 + - - +
274C VAL* 3.2 10.9 + - - +
275C ALA 3.1 0.6 - - - -
276C LEU* 1.3 78.7 - - - +
278C GLU* 1.3 64.1 + - - +
279C ALA 3.2 0.2 - - - -
280C MET* 3.0 30.0 + - - +
281C GLU* 3.7 9.1 + - - +
11D TYR* 3.6 49.9 + - + -
12D ASP* 3.8 26.2 - - - +
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Residues in contact with GLU 278 (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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40C SER* 2.9 35.0 + - - -
42C ARG* 2.6 32.9 + - - +
43C VAL* 4.3 3.9 - - - +
232C ALA 5.3 2.6 - - - +
274C VAL* 3.1 17.0 - - + +
275C ALA* 3.2 14.2 + - - +
277C LYS* 1.3 74.4 - - - +
279C ALA* 1.3 57.8 + - - +
280C MET 2.9 9.7 + - - -
281C GLU* 3.1 21.5 + - + +
284C PHE* 3.6 11.6 - - + +
371C ARG* 5.1 9.5 + - - +
6D MET* 4.2 0.6 - - - +
11D TYR* 3.5 21.8 - - + +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.6 35.2 - - + +
209C ALA* 4.9 2.3 - - - +
231C LEU* 4.0 10.3 - - + +
275C ALA 2.9 16.6 + - - +
276C LEU* 3.9 2.0 - - - +
277C LYS 3.2 0.6 - - - -
278C GLU* 1.3 75.7 - - - +
280C MET* 1.3 59.4 + - - +
281C GLU 3.4 1.1 - - - +
284C PHE* 3.0 48.7 - - + +
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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