Contacts of the helix formed by residues 265 - 279 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C HIS* 4.9 7.4 - - + +
97C SER* 6.1 0.9 - - - -
235C ARG* 3.5 43.7 - - + +
265C LEU* 4.3 21.8 - - + -
268C VAL* 5.7 2.0 - - + -
94D GLN 5.3 1.0 + - - -
96D HIS* 3.6 33.9 + - + +
235D ARG 6.0 0.7 - - - +
263D GLY 4.9 1.6 - - - +
264D PRO* 1.3 73.2 - - - +
266D MET* 1.3 59.7 + - - +
267D HIS* 3.1 13.9 - - + +
268D VAL* 2.8 46.7 + - + +
269D ILE* 3.0 17.0 + - - +
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Residues in contact with MET 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ARG* 5.2 1.2 - - - +
51D LEU* 3.7 26.2 + - + +
54D LYS 4.3 14.3 + - - +
56D ALA* 4.3 12.3 - - + -
63D ARG* 4.6 0.4 - - - +
71D VAL* 3.2 51.8 - - + +
74D VAL* 4.3 6.1 - - + +
75D GLU* 4.1 24.2 - - + +
264D PRO* 3.4 19.5 + - - +
265D LEU* 1.3 73.1 - - - +
267D HIS* 1.3 58.0 + - - +
269D ILE* 3.4 21.8 + - + +
270D ALA* 3.1 26.7 + - - +
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Residues in contact with HIS 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLN* 3.4 33.8 + - + -
235C ARG* 4.2 6.2 - - - +
267C HIS* 6.3 0.9 - + - -
268C VAL* 5.5 4.3 - - + -
46D ALA 3.7 27.1 - - - +
47D GLN* 3.2 22.0 + - - +
49D SER* 3.9 2.0 - - - +
51D LEU* 3.7 13.9 - - + +
52D THR* 3.5 37.5 + - - +
265D LEU* 3.8 31.6 - - + +
266D MET* 1.3 78.8 - - - +
268D VAL* 1.3 77.4 + - + +
270D ALA* 3.6 4.0 + - - +
271D GLY 3.4 13.3 + - - -
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C LEU* 5.8 2.2 - - + -
267C HIS* 5.4 5.8 - - + -
268C VAL* 6.0 1.1 - - + -
47D GLN* 3.9 24.2 - - + +
234D PRO* 3.9 7.4 - - + +
235D ARG 3.6 24.0 - - - +
236D GLY* 5.1 0.2 - - - -
265D LEU* 2.8 40.4 + - + +
267D HIS* 1.3 91.0 - - + +
269D ILE* 1.3 62.0 + - + +
270D ALA 3.2 0.4 - - - -
271D GLY* 3.1 3.1 + - - -
272D LYS* 2.9 36.9 + - - +
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 4.5 3.8 - - + -
75D GLU* 4.0 22.0 - - + +
78D ALA* 3.8 20.6 - - + -
93D VAL* 3.5 30.5 - - + +
94D GLN* 4.1 11.9 - - + +
264D PRO* 4.0 20.0 - - + -
265D LEU 3.0 12.8 + - - +
266D MET* 3.8 31.9 - - + +
268D VAL* 1.3 76.9 - - + +
270D ALA* 1.3 58.5 + - - +
272D LYS* 3.2 12.1 + - + +
273D ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.6 16.8 - - + +
19C MET* 4.7 5.2 - - + -
46D ALA* 4.0 12.1 - - + -
51D LEU* 3.7 20.6 - - + -
74D VAL* 3.6 16.2 - - + -
266D MET 3.1 13.2 + - - +
267D HIS* 3.6 10.8 - - - +
269D ILE* 1.3 77.2 - - - +
271D GLY* 1.3 63.0 + - - +
273D ALA* 3.2 6.7 + - - +
274D VAL* 3.1 17.2 + - - +
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Residues in contact with GLY 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 4.0 12.4 - - - +
46D ALA* 3.5 17.9 - - - +
47D GLN* 5.2 0.2 - - - -
234D PRO* 3.8 8.9 - - - +
267D HIS 3.4 6.1 + - - -
268D VAL* 3.1 7.6 + - - -
270D ALA* 1.3 77.5 - - - +
272D LYS* 1.3 63.6 + - - +
274D VAL* 3.1 9.4 - - - +
275D ALA* 3.0 24.6 + - - +
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Residues in contact with LYS 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 4.7 6.3 - - + -
93D VAL* 2.8 37.4 + - + +
94D GLN 4.3 0.6 + - - -
95D PRO 3.1 17.0 + - - -
227D THR* 4.1 20.2 - - + +
234D PRO* 3.6 19.7 - - + +
236D GLY* 3.8 20.2 - - - -
237D GLY 2.8 25.7 + - - +
238D LEU* 5.6 0.9 - - + -
268D VAL* 2.9 25.7 + - - +
269D ILE* 3.2 17.9 + - - +
271D GLY* 1.3 75.1 - - - +
273D ALA* 1.3 57.7 + - - +
275D ALA* 3.3 2.0 + - - +
276D LEU* 2.9 41.4 + - + +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.5 8.7 - - + -
74D VAL 4.3 6.7 - - - +
77D LEU* 4.4 9.2 - - + -
78D ALA* 3.8 31.8 - - + +
81D ARG* 3.2 25.7 + - - +
269D ILE 2.9 12.8 + - - +
270D ALA* 3.4 11.7 - - - +
271D GLY 3.2 0.2 - - - -
272D LYS* 1.3 79.2 - - - +
274D VAL* 1.3 61.1 + - - +
276D LEU* 3.7 3.5 + - - +
277D LYS 3.5 8.5 + - - -
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 4.7 5.8 - - + -
11C TYR* 4.2 21.8 - - + -
12C ASP* 4.4 10.3 - - + +
15C LEU* 3.8 18.6 - - + +
42D ARG* 3.9 31.6 - - + +
43D VAL* 3.8 17.7 - - + -
46D ALA* 4.9 1.1 - - + -
81D ARG* 4.5 2.0 - - - +
270D ALA 3.1 4.8 + - - +
271D GLY* 3.1 23.6 - - - +
273D ALA* 1.3 75.0 - - - +
275D ALA* 1.3 64.2 + - - +
277D LYS* 3.2 6.4 + - + +
278D GLU* 3.1 27.5 + - + +
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 3.9 8.5 - - + -
227D THR* 6.1 1.1 - - - -
231D LEU* 5.0 8.1 - - + +
232D ALA 4.9 1.3 - - - +
233D GLY* 3.7 31.0 - - - +
234D PRO* 3.9 2.7 - - + -
271D GLY 3.0 16.4 + - - +
272D LYS* 3.3 4.5 + - - +
274D VAL* 1.3 72.6 - - - +
276D LEU* 1.3 63.2 + - + +
277D LYS 3.0 2.2 - - - -
278D GLU* 3.2 15.8 + - - +
279D ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 3.5 12.1 - - + +
81D ARG* 4.0 15.0 - - + -
82D ALA* 3.5 38.4 - - + +
85D LEU* 3.8 23.7 - - + +
86D PHE* 4.7 5.8 - - + -
93D VAL* 5.4 2.0 - - + -
227D THR* 5.5 4.7 - - + -
231D LEU* 4.2 25.1 - - + -
238D LEU* 4.8 9.6 - - + -
272D LYS* 2.9 26.9 + - + +
273D ALA 4.0 2.2 - - - +
275D ALA* 1.3 78.0 - - + +
277D LYS* 1.3 59.0 + - - +
279D ALA* 3.7 9.2 + - - +
280D MET* 3.5 24.1 + - - +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.4 43.0 + - + +
12C ASP* 3.7 34.8 - - + +
81D ARG* 3.8 19.0 - - - +
273D ALA 3.5 10.1 + - - +
274D VAL* 3.2 10.7 + - - +
275D ALA 3.0 0.8 - - - -
276D LEU* 1.3 78.7 - - - +
278D GLU* 1.3 64.0 + - - +
279D ALA 3.2 0.2 - - - -
280D MET* 3.0 30.7 + - - +
281D GLU* 3.7 11.1 + - - +
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 5.4 0.4 - - - -
11C TYR* 3.4 23.1 - - + +
40D SER* 2.9 35.6 + - - -
42D ARG* 2.7 33.0 + - - +
43D VAL* 4.3 3.9 - - - +
232D ALA 5.3 3.1 - - - +
274D VAL 3.1 16.5 + - - +
275D ALA* 3.6 14.9 - - - +
277D LYS* 1.3 74.3 - - - +
279D ALA* 1.3 60.0 + - - +
280D MET 2.9 6.4 + - - -
281D GLU* 3.1 22.0 + - + +
284D PHE* 3.6 11.1 - - + +
371D ARG* 5.1 8.2 + - - +
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 3.6 35.7 - - + +
209D ALA* 4.9 1.7 - - - +
210D ALA* 5.9 0.2 - - - -
231D LEU* 4.0 10.3 - - + +
275D ALA 2.9 14.8 + - - +
276D LEU* 3.8 2.7 - - - +
277D LYS 3.2 0.4 - - - -
278D GLU* 1.3 76.3 - - - +
280D MET* 1.3 59.1 + - - +
281D GLU 3.4 1.3 - - - +
284D PHE* 3.0 49.6 - - + +
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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