Contacts of the helix formed by residues 265 - 279 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLN 5.3 1.0 + - - -
96A HIS* 3.6 33.3 + - + +
235A ARG 6.0 0.7 - - - +
263A GLY 4.9 1.1 - - - +
264A PRO* 1.3 73.6 - - - +
266A MET* 1.3 58.7 + - - +
267A HIS* 3.1 13.2 - - + +
268A VAL* 2.8 47.4 + - + +
269A ILE* 3.0 16.0 + - + +
96B HIS* 4.9 8.1 - - + +
97B SER* 6.1 1.3 - - - -
235B ARG* 3.5 44.4 - - + +
265B LEU* 4.3 21.5 - - + -
268B VAL* 5.8 1.6 - - + -
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.6 31.4 + - + +
54A LYS 4.4 10.7 + - - +
56A ALA* 4.3 15.9 - - + -
63A ARG* 4.6 0.4 - - - +
71A VAL* 3.2 52.5 - - + +
74A VAL* 4.3 6.9 - - + +
75A GLU* 4.1 24.0 - - + +
264A PRO* 3.5 18.8 + - - +
265A LEU* 1.3 71.6 - - - +
267A HIS* 1.3 58.4 + - - +
269A ILE* 3.7 22.1 - - + +
270A ALA* 3.1 20.4 + - - +
235B ARG* 5.2 1.0 - - - +
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Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.7 27.5 - - - +
47A GLN* 3.3 22.7 + - - +
49A SER* 3.9 2.2 - - - +
51A LEU* 3.7 13.1 - - + +
52A THR* 3.5 37.9 + - - +
265A LEU* 3.7 31.6 - - + +
266A MET* 1.3 76.2 - - - +
268A VAL* 1.3 79.4 + - + +
270A ALA* 3.6 4.3 + - - +
271A GLY 3.4 13.3 + - - -
47B GLN* 3.5 32.5 + - + -
235B ARG* 4.2 5.8 - - + +
267B HIS* 6.4 0.7 - + - -
268B VAL* 5.4 5.6 - - + -
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Residues in contact with VAL 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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47A GLN* 3.8 25.4 - - + +
234A PRO* 3.9 7.9 - - + +
235A ARG 3.6 23.8 - - - +
236A GLY* 5.2 0.2 - - - -
265A LEU* 2.8 39.5 + - + +
267A HIS* 1.3 91.9 - - + +
269A ILE* 1.3 61.2 + - + +
270A ALA 3.2 0.4 - - - -
271A GLY* 3.0 3.8 + - - -
272A LYS* 2.8 36.2 + - - +
265B LEU* 5.8 2.5 - - + -
267B HIS* 5.5 5.4 - - + -
268B VAL* 6.0 1.1 - - + -
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Residues in contact with ILE 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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74A VAL* 4.5 3.4 - - + -
75A GLU* 4.0 23.3 - - + +
78A ALA* 3.8 19.9 - - + +
93A VAL* 3.6 29.2 - - + +
94A GLN* 4.1 11.2 - - + +
264A PRO* 4.0 20.2 - - + -
265A LEU 3.0 13.2 + - - +
266A MET* 3.7 31.9 - - + +
268A VAL* 1.3 76.0 - - + +
270A ALA* 1.3 60.5 + - - +
272A LYS* 3.2 12.6 + - + +
273A ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 270 (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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46A ALA* 3.9 12.6 - - + -
51A LEU* 3.6 29.2 - - + -
74A VAL* 3.6 15.0 - - + +
266A MET 3.1 5.6 + - - +
267A HIS* 3.6 10.8 - - - +
268A VAL 3.2 0.2 - - - -
269A ILE* 1.3 77.1 - - - +
271A GLY* 1.3 63.5 + - - +
273A ALA* 3.1 2.3 + - - +
274A VAL 3.1 17.2 + - - -
15B LEU* 3.4 21.0 - - + +
19B MET* 4.6 5.6 - - + -
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Residues in contact with GLY 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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43A VAL* 3.9 12.4 - - - +
46A ALA* 3.5 17.6 - - - +
47A GLN* 5.2 0.4 - - - -
234A PRO* 3.8 8.7 - - - +
267A HIS 3.4 5.5 + - - -
268A VAL* 3.0 8.5 + - - -
270A ALA* 1.3 76.6 - - - +
272A LYS* 1.3 64.4 + - - +
274A VAL* 3.2 9.5 - - - +
275A ALA* 3.0 24.6 + - - +
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Residues in contact with LYS 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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78A ALA* 4.7 6.1 - - + -
93A VAL* 2.8 36.4 + - + +
94A GLN 4.4 1.0 + - - -
95A PRO 3.1 16.6 + - - -
227A THR* 4.1 19.1 - - + +
234A PRO* 3.6 17.9 - - + +
236A GLY* 3.8 19.5 - - - -
237A GLY 2.9 25.2 + - - +
238A LEU* 5.7 1.1 - - + -
268A VAL* 2.8 25.9 + - - +
269A ILE* 3.2 18.4 + - - +
271A GLY* 1.3 75.7 - - - +
273A ALA* 1.3 64.2 - - - +
275A ALA* 3.2 2.6 + - - +
276A LEU* 2.9 35.0 + - + +
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Residues in contact with ALA 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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74A VAL 4.3 2.9 - - - +
77A LEU* 4.3 6.3 - - + -
78A ALA* 3.7 32.3 - - + +
81A ARG* 3.3 23.5 + - - +
269A ILE 2.9 12.8 + - - +
270A ALA 3.4 9.6 - - - +
272A LYS* 1.3 79.0 - - - +
274A VAL* 1.3 61.2 + - - +
276A LEU* 3.6 3.1 + - - +
277A LYS 3.5 8.1 + - - -
15B LEU* 4.1 17.9 - - + -
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Residues in contact with VAL 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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42A ARG* 3.9 42.8 - - + +
43A VAL* 3.7 17.7 - - + -
46A ALA* 4.9 1.1 - - + -
270A ALA 3.1 7.4 + - - +
271A GLY* 3.2 22.2 - - - +
273A ALA* 1.3 74.2 - - - +
275A ALA* 1.3 63.1 + - - +
277A LYS* 3.2 4.2 + - - +
278A GLU* 3.1 24.5 + - + +
8B ILE* 4.9 4.5 - - + -
11B TYR* 4.3 11.4 - - + -
12B ASP* 4.3 15.9 - - + +
15B LEU* 3.6 18.1 - - + +
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Residues in contact with ALA 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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43A VAL* 3.8 8.7 - - + -
227A THR* 6.1 0.9 - - - -
231A LEU* 4.9 8.1 - - + +
232A ALA 4.9 1.6 - - - +
233A GLY* 3.7 31.2 - - - +
234A PRO* 3.9 2.9 - - + -
271A GLY 3.0 16.5 + - - +
272A LYS* 3.7 3.4 - - - +
274A VAL* 1.3 74.1 - - - +
276A LEU* 1.3 63.4 + - + +
277A LYS 3.1 1.8 - - - -
278A GLU* 3.2 14.6 + - - +
279A ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 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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78A ALA* 3.5 15.7 - - + +
81A ARG* 4.0 12.8 - - + -
82A ALA* 3.5 34.1 - - + +
85A LEU* 3.9 23.5 - - + +
86A PHE* 4.7 6.5 - - + -
93A VAL* 5.4 2.2 - - + -
227A THR* 5.5 4.5 - - + -
231A LEU* 4.2 24.5 - - + -
238A LEU* 4.7 9.6 - - + -
272A LYS* 2.9 26.1 + - + +
273A ALA 4.0 4.9 - - - +
274A VAL 3.3 0.2 - - - -
275A ALA* 1.3 78.0 - - + +
277A LYS* 1.3 59.7 + - - +
279A ALA* 3.7 7.9 + - - +
280A MET* 3.4 23.8 + - - +
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Residues in contact with LYS 277 (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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81A ARG* 3.8 18.8 - - - +
273A ALA 3.5 11.1 + - - +
274A VAL* 3.2 10.5 + - - +
275A ALA 3.1 0.4 - - - -
276A LEU* 1.3 79.0 - - - +
278A GLU* 1.3 64.6 + - - +
279A ALA 3.2 0.2 - - - -
280A MET* 3.0 30.8 + - + +
281A GLU* 3.7 9.6 + - - +
11B TYR* 3.5 49.3 + - + -
12B ASP* 3.7 26.7 - - - +
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Residues in contact with GLU 278 (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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40A SER* 2.9 35.9 + - - -
42A ARG* 2.7 34.3 + - - +
43A VAL* 4.4 3.0 - - - +
232A ALA 5.3 2.6 - - - +
274A VAL* 3.1 17.6 + - + +
275A ALA* 3.2 15.1 + - - +
277A LYS* 1.3 73.3 - - - +
279A ALA* 1.3 57.3 + - - +
280A MET 2.9 9.5 + - - -
281A GLU* 3.2 21.2 + - + +
284A PHE* 3.5 12.3 - - + +
371A ARG* 5.1 9.6 + - - +
6B MET* 5.4 0.7 - - - -
11B TYR* 3.4 24.7 - - + +
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Residues in contact with ALA 279 (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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85A LEU* 3.6 35.5 - - + +
209A ALA* 4.8 2.4 - - - +
231A LEU* 4.0 10.3 - - + +
275A ALA 3.0 16.5 + - - +
276A LEU* 3.9 2.0 - - - +
277A LYS 3.2 0.6 - - - -
278A GLU* 1.3 75.3 - - - +
280A MET* 1.3 59.1 + - - +
281A GLU 3.4 1.2 - - - +
284A PHE* 3.0 48.5 - - + +
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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