Contacts of the helix formed by residues 6 - 20 (chain B) in PDB entry 2X0G
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 GLU 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLU* 1.3 64.1 + - - +
8B GLN* 3.0 33.4 + - - +
9B ILE* 3.2 51.8 + - + +
10B ALA* 4.0 4.9 + - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A TYR* 5.3 4.7 + - - -
222A LYS* 2.8 34.2 + - - -
6B GLU* 1.3 74.4 - - - +
8B GLN* 1.3 74.3 + - + +
9B ILE 3.3 0.7 - - - -
10B ALA* 3.1 23.9 - - - +
11B GLU* 3.6 11.4 + - - +
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Residues in contact with GLN 8 (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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6B GLU* 3.0 38.0 + - - +
7B GLU* 1.3 90.1 + - + +
9B ILE* 1.3 65.4 + - - +
11B GLU* 2.9 25.3 + - - +
12B PHE* 2.9 37.5 + - + -
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Residues in contact with ILE 9 (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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53A ARG* 3.1 44.9 - - + +
6B GLU* 3.2 53.8 - - + +
8B GLN* 1.3 78.4 - - - +
10B ALA* 1.3 53.7 + - - +
11B GLU 3.1 0.2 + - - -
12B PHE* 3.2 7.8 + - - +
13B LYS* 2.8 66.8 + - + +
65B PHE* 5.3 1.6 - - + -
69B LEU* 4.8 9.0 - - + -
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Residues in contact with ALA 10 (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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23A GLN* 3.3 22.5 + - - +
6B GLU 4.0 3.4 + - - +
7B GLU* 3.1 20.5 + - - +
8B GLN 3.2 0.2 - - - -
9B ILE* 1.3 79.3 - - - +
11B GLU* 1.3 59.7 + - + +
13B LYS* 4.3 9.4 - - - +
14B GLU* 3.5 11.3 + - - +
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Residues in contact with GLU 11 (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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310A ARG* 5.1 5.6 + - - +
314A LEU* 3.7 10.0 - - + +
317A ARG* 4.7 16.8 + - - -
318A LEU* 5.7 0.9 - - - -
7B GLU* 3.9 14.0 - - - +
8B GLN* 2.9 16.3 + - - +
10B ALA* 1.3 72.6 - - + +
12B PHE* 1.3 70.8 + - + +
13B LYS 3.2 1.8 - - - -
14B GLU* 3.0 36.2 - - - +
15B ALA* 3.2 11.5 + - - +
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Residues in contact with PHE 12 (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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318A LEU* 3.4 36.3 - - + -
8B GLN* 2.9 44.0 + - + +
9B ILE* 3.9 6.3 - - - +
11B GLU* 1.3 83.6 - - + +
13B LYS* 1.3 61.0 + - - +
15B ALA* 4.6 2.2 - - - -
16B PHE* 3.2 21.3 + - - +
65B PHE* 3.6 9.9 - - + -
68B PHE* 3.4 25.3 - + + -
69B LEU* 5.3 14.8 - - + -
71B MET 3.9 13.2 - - - -
72B MET* 4.0 29.8 - - + -
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Residues in contact with LYS 13 (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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23A GLN* 3.3 15.9 - - - +
24A PHE* 3.8 23.7 - - + -
47A ARG* 5.2 6.5 - - - +
53A ARG* 3.2 28.4 + - + +
55A GLY 5.4 2.3 + - - -
9B ILE* 2.8 43.7 + - + +
10B ALA* 3.8 6.0 - - - +
12B PHE* 1.3 75.6 - - - +
14B GLU* 1.3 60.9 + - - +
16B PHE* 3.8 2.1 - - - +
17B SER* 2.9 24.9 + - - -
65B PHE* 3.5 26.0 - - + -
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Residues in contact with GLU 14 (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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23A GLN* 3.2 36.8 + - + +
310A ARG* 2.9 33.8 + - - -
314A LEU* 3.3 22.2 - - + +
10B ALA 3.5 9.1 + - - +
11B GLU* 3.0 26.7 - - - +
13B LYS* 1.3 75.0 - - - +
15B ALA* 1.3 67.7 + - - +
17B SER* 3.4 13.6 + - - -
18B LEU* 3.6 6.9 + - - +
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Residues in contact with ALA 15 (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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314A LEU* 3.7 21.1 - - + -
315A CYS* 5.9 0.7 - - - -
318A LEU* 3.0 37.9 - - + -
11B GLU 3.2 12.4 + - - +
12B PHE 4.0 2.9 - - - +
13B LYS 3.4 0.2 - - - -
14B GLU* 1.3 74.3 - - - +
16B PHE* 1.3 67.2 + - - +
17B SER 2.9 1.7 + - - -
18B LEU* 2.9 15.3 + - - +
19B PHE* 3.1 21.5 + - + -
68B PHE* 4.0 2.7 - - + -
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Residues in contact with PHE 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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24A PHE* 5.2 6.3 - + - -
54A ARG* 4.3 14.4 - - - -
12B PHE 3.2 16.0 + - - +
13B LYS 3.8 4.3 - - - +
15B ALA* 1.3 78.3 - - - +
17B SER* 1.3 57.4 + - - +
19B PHE* 3.4 3.1 + - - +
20B ASP* 2.8 55.7 + - + +
25B GLY 3.5 24.2 - - - -
26B THR* 4.5 1.3 - - - -
27B ILE* 4.1 8.5 - - + -
63B ILE 3.9 11.0 - - - -
64B ASP 3.5 23.6 - - - -
65B PHE* 3.5 34.3 - + + -
68B PHE* 3.3 39.3 - + + -
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Residues in contact with SER 17 (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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22A GLY 4.8 3.6 - - - -
23A GLN* 2.4 36.3 + - - +
24A PHE* 3.7 9.4 - - - -
13B LYS 2.9 17.0 + - - -
14B GLU 3.4 9.0 + - - -
15B ALA 2.9 4.6 + - - -
16B PHE* 1.3 78.0 - - - +
18B LEU* 1.3 58.3 + - - -
20B ASP* 3.1 26.8 - - - +
21B LYS* 4.4 1.6 - - - -
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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
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21A SER* 6.0 1.1 - - - +
311A LEU* 4.1 14.4 - - + -
315A CYS* 4.2 16.8 - - - -
14B GLU 3.6 5.7 + - - +
15B ALA* 2.9 10.9 + - - +
17B SER* 1.3 74.1 - - - +
19B PHE* 1.3 67.2 + - - +
21B LYS* 3.8 15.3 + - + +
35B VAL* 3.9 12.8 - - + +
111B ASN 4.2 9.6 - - - +
112B LEU* 3.0 48.9 - - + +
113B GLY* 4.3 6.1 - - - +
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Residues in contact with PHE 19 (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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315A CYS* 4.0 34.8 - - + -
318A LEU* 4.3 21.3 - - + -
319A SER* 4.3 11.2 - - - -
15B ALA* 3.1 33.0 + - + -
16B PHE 3.7 4.5 - - - +
18B LEU* 1.3 76.6 - - - +
20B ASP* 1.3 57.3 + - - +
21B LYS* 3.1 7.3 + - - +
27B ILE* 3.4 33.4 - - + +
31B GLU* 3.6 21.3 - - - +
32B LEU* 3.8 24.7 - - + -
35B VAL* 3.4 43.6 - - + +
36B MET* 5.6 0.2 - - + -
68B PHE* 4.4 7.9 - + - -
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Residues in contact with ASP 20 (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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54A ARG* 4.1 2.1 + - - -
16B PHE* 2.8 33.2 + - + +
17B SER* 3.1 14.7 - - - +
18B LEU 3.3 0.2 - - - -
19B PHE* 1.3 71.7 - - - +
21B LYS* 1.3 64.5 + - - +
22B ASP* 3.0 0.3 - - - +
23B GLY* 2.9 31.3 + - - -
24B ASP 3.4 0.9 + - - -
25B GLY* 3.0 30.8 + - - -
26B THR 3.3 6.5 + - - -
27B ILE* 4.5 5.2 - - + -
31B GLU* 4.3 2.5 - - - -
1148B CA 2.5 30.3 - - - -
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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