Contacts of the helix formed by residues 14 - 27 (chain B) in PDB entry 1ECX
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 ASP 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 3.5 5.3 + - - +
13B VAL* 1.3 76.2 - - - +
15B ASP* 1.3 57.3 + - - +
16B ARG* 2.9 53.8 + - - +
17B VAL* 2.8 41.9 + - + +
18B LEU* 3.0 10.1 + - - -
205B HIS* 3.2 21.9 + - + +
253B ILE* 4.6 6.0 - - - +
355B LYS* 5.0 1.4 + - - +
356B TYR* 2.7 32.5 + - + -
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 3.0 32.2 + - - +
13B VAL 3.4 2.9 + - - +
14B ASP* 1.3 73.8 + - - +
16B ARG* 1.3 62.4 + - + +
18B LEU* 3.6 11.2 + - - +
19B GLU* 3.2 23.9 + - - +
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Residues in contact with ARG 16 (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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14B ASP* 2.9 36.3 + - - +
15B ASP* 1.3 76.2 - - + +
17B VAL* 1.3 67.6 + - - +
19B GLU* 3.5 9.9 + - - +
20B GLU* 3.4 26.4 + - - +
249B ARG* 4.4 17.8 - - - +
253B ILE* 3.5 34.6 - - + +
257B GLU* 3.4 31.9 + - - -
356B TYR* 3.2 12.7 + - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.0 13.0 - - + -
14B ASP* 2.8 33.8 + - + +
16B ARG* 1.3 71.8 - - - +
18B LEU* 1.3 62.5 + - - +
20B GLU* 3.4 5.7 + - - +
21B MET* 3.2 25.4 + - - +
205B HIS 4.1 3.4 - - - +
207B PRO* 4.5 3.4 - - + -
246B GLY* 3.1 36.7 - - - +
249B ARG* 4.4 12.6 - - + -
250B ALA* 3.8 32.5 - - + +
253B ILE* 4.5 4.3 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.8 22.6 - - + +
14B ASP 3.0 6.5 + - - +
15B ASP* 4.0 14.4 - - - +
16B ARG 3.3 0.2 - - - -
17B VAL* 1.3 75.7 - - - +
19B GLU* 1.3 65.2 + - - +
21B MET* 3.2 22.5 + - + -
22B ILE* 3.1 43.0 + - + +
25B TYR* 5.7 4.0 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP 3.2 15.7 + - - +
16B ARG* 3.7 10.1 - - - +
17B VAL 3.3 0.2 - - - -
18B LEU* 1.3 80.3 - - - +
20B GLU* 1.3 66.5 + - - +
22B ILE* 3.4 21.5 + - - +
23B VAL* 3.8 9.5 + - + +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.4 12.9 - - - +
17B VAL 3.4 6.2 + - - +
18B LEU 3.3 0.4 - - - -
19B GLU* 1.3 78.8 - - + +
21B MET* 1.3 67.6 + - - +
23B VAL* 3.2 17.9 + - - +
24B PHE* 3.3 19.0 - - + -
52B LYS* 6.1 0.5 - - - -
245B VAL* 3.8 24.4 - - + +
246B GLY* 5.7 0.2 - - - -
249B ARG* 2.9 44.7 + - + +
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Residues in contact with MET 21 (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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13B VAL* 4.9 2.9 - - - -
17B VAL* 3.2 19.7 + - - +
18B LEU* 3.2 26.8 + - + +
20B GLU* 1.3 78.0 - - - +
22B ILE* 1.3 63.6 + - - +
24B PHE* 2.8 23.0 + - - +
25B TYR* 3.5 34.3 + - + +
207B PRO* 3.6 41.3 - - + -
242B PRO* 3.1 35.3 - - + +
243B GLY* 4.3 2.0 - - - -
245B VAL* 5.3 1.1 - - - -
246B GLY* 3.8 12.6 - - - -
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Residues in contact with ILE 22 (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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18B LEU* 3.1 36.7 + - + +
19B GLU* 3.5 12.8 - - - +
20B GLU 3.3 0.2 - - - -
21B MET* 1.3 76.1 - - - +
23B VAL* 1.3 63.3 + - + +
25B TYR* 3.1 15.9 + - + +
26B ARG* 3.0 47.9 + - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.8 9.6 + - + +
20B GLU* 3.4 17.0 - - - +
21B MET 2.9 0.8 + - - -
22B ILE* 1.3 77.9 - - + +
24B PHE* 1.3 66.7 + - + +
26B ARG* 5.2 1.1 - - - -
27B GLU* 2.9 43.8 + - + +
28B LYS* 3.0 43.6 + - + +
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Residues in contact with PHE 24 (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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20B GLU* 3.3 22.7 - - + -
21B MET* 2.8 9.5 + - - +
23B VAL* 1.3 83.0 - - + +
25B TYR* 1.3 58.5 + - - +
28B LYS* 3.6 37.7 - - + +
29B TYR* 3.3 21.8 - - - +
42B ALA* 5.3 3.1 - - - -
45B HIS* 3.4 53.4 - + + -
241B VAL* 3.7 19.1 - - + -
242B PRO* 3.8 26.6 - - + +
245B VAL* 3.8 28.7 - - + -
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Residues in contact with TYR 25 (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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18B LEU* 5.7 3.8 - - + -
21B MET* 3.5 36.0 + - + +
22B ILE* 3.1 20.1 + - + +
24B PHE* 1.3 78.1 - - - +
26B ARG* 1.3 67.3 + - + +
29B TYR* 3.9 13.2 - - - +
240B ASN* 5.1 5.7 + - - -
242B PRO* 3.4 32.8 - - + +
243B GLY* 5.1 0.3 + - - -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.0 34.8 + - + +
23B VAL* 5.1 0.7 - - - +
25B TYR* 1.3 83.8 - - + +
27B GLU* 1.3 70.5 + - + +
29B TYR* 3.1 19.8 - - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 2.9 27.8 + - + +
26B ARG* 1.3 83.7 - - + +
28B LYS* 1.3 65.8 + - + +
29B TYR* 3.0 24.7 + - - -
38B MET* 3.5 10.9 - - - +
41B GLU* 5.2 0.6 - - - +
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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
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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