Contacts of the helix formed by residues 10 - 21 (chain B) in PDB entry 1B0P
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 GLY 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ASP* 1.3 74.7 - - - +
11B ASN* 1.3 54.0 + - - +
13B ALA* 3.4 1.8 + - - +
14B THR* 2.6 39.1 + - - +
146B VAL* 3.6 18.8 - - - +
149B ALA* 4.5 4.9 - - - -
171B PHE* 4.0 4.7 - - - -
176B THR* 3.1 26.7 + - - -
177B SER* 4.0 1.3 - - - -
179B GLU 3.4 1.4 + - - -
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Residues in contact with ASN 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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9B ASP* 3.3 5.1 - - - +
10B GLY* 1.3 72.7 - - - +
12B THR* 1.3 60.1 + - - +
14B THR 3.2 1.7 + - - -
15B ALA* 2.8 27.7 + - - +
32B PRO 3.0 19.8 + - - +
33B SER* 4.1 0.8 - - - +
35B THR* 4.0 22.6 - - + -
36B MET* 3.3 34.9 - - + +
39B GLU* 4.1 0.4 - - - -
112B THR* 3.4 28.9 - - - +
171B PHE* 3.8 1.4 - - - -
177B SER* 3.2 28.7 + - - +
178B HIS* 3.6 8.1 - - - -
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Residues in contact with THR 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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1206A PRO* 4.1 11.0 - - + -
6B MET* 4.1 6.6 - - - +
8B THR* 3.4 23.1 + - + +
9B ASP* 2.7 38.3 + - - +
11B ASN* 1.3 73.6 - - + +
13B ALA* 1.3 65.0 + - - +
15B ALA* 3.8 0.6 - - - +
16B HIS* 3.0 24.3 + - - +
39B GLU* 2.9 36.8 - - - +
43B TRP* 4.3 8.1 - - - -
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Residues in contact with ALA 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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6B MET* 4.9 3.6 - - - -
8B THR* 4.4 4.7 + - - +
9B ASP 3.0 16.4 + - - +
10B GLY 3.7 4.0 - - - +
12B THR* 1.3 76.4 + - - +
14B THR* 1.3 59.2 + - - +
16B HIS* 3.2 20.9 - - - +
17B VAL* 3.9 2.8 + - - +
146B VAL* 3.7 17.5 - - + +
150B HIS* 4.0 21.7 - - + +
183B ILE* 3.6 29.6 - - + -
185B VAL* 5.2 0.9 - - - -
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Residues in contact with THR 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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10B GLY 2.6 26.8 + - - +
11B ASN 4.1 0.9 - - - +
13B ALA* 1.3 75.2 - - - +
15B ALA* 1.3 57.9 + - - +
16B HIS 3.2 1.8 - - - -
17B VAL* 3.4 4.5 + - - +
18B ALA* 3.0 27.4 + - - +
36B MET* 3.5 17.7 - - - -
110B HIS* 3.9 12.8 + - - -
149B ALA* 3.4 33.2 - - + +
153B ALA* 4.0 12.7 - - - +
169B HIS* 4.1 2.2 - - - -
171B PHE* 3.4 23.2 - - + -
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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
----------------------------------------------------------
11B ASN 2.8 12.1 + - - +
12B THR 3.3 1.3 + - - +
14B THR* 1.3 74.3 + - - +
16B HIS* 1.3 65.3 + - - +
18B ALA* 3.9 8.5 - - - -
19B TYR* 3.0 20.6 + - - +
36B MET* 4.1 23.1 - - + +
39B GLU* 3.3 27.1 - - - +
40B ALA* 5.4 2.0 - - + +
43B TRP* 3.3 21.3 - - + -
84B PHE* 5.0 1.8 - - + -
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Residues in contact with HIS 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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4B LYS* 4.5 11.2 + - - -
6B MET* 4.2 19.3 - - + -
12B THR 3.0 13.7 + - - +
13B ALA* 3.2 17.5 - - - +
15B ALA* 1.3 76.2 - - - +
17B VAL* 1.3 60.3 + - - +
20B ALA 3.5 1.6 + - - -
43B TRP* 3.8 8.2 - + + -
48B ARG* 3.6 19.2 + - - -
150B HIS* 4.0 5.5 - - - -
185B VAL* 3.5 26.2 - - + +
186B LEU 2.8 29.5 + - - -
187B ASP* 5.6 0.2 - - - -
188B TYR* 2.5 44.3 + + - -
191B MET* 3.5 18.1 - - + +
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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
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13B ALA 4.3 2.9 - - - +
14B THR 3.4 7.0 + - - +
15B ALA 3.3 0.2 - - - -
16B HIS* 1.3 77.9 - - - +
18B ALA* 1.3 66.9 + - - +
19B TYR 3.2 1.8 - - - -
20B ALA* 3.0 3.1 + - - -
21B MET* 2.9 36.2 + - + +
150B HIS* 3.4 45.5 - - + +
153B ALA* 3.6 33.4 - - + +
154B LEU* 3.7 13.5 - - + +
157B HIS* 4.0 2.9 - - + -
191B MET* 4.1 17.0 - - + -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.0 17.7 + - - +
15B ALA* 3.9 4.7 - - - +
17B VAL* 1.3 74.6 - - - +
19B TYR* 1.3 62.8 + - - +
21B MET* 3.3 0.5 + - - -
22B SER* 2.9 30.1 + - - -
56B LEU* 6.0 0.2 - - - -
82B THR* 4.4 3.4 - - - +
84B PHE* 3.5 35.7 - - + -
110B HIS* 3.7 14.1 - - + +
157B HIS* 3.6 13.2 - - - +
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Residues in contact with TYR 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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15B ALA 3.0 19.3 + - - +
18B ALA* 1.3 77.4 - - - +
20B ALA* 1.3 62.9 + - - +
22B SER* 3.3 17.7 - - - +
40B ALA* 3.4 27.6 - - + +
43B TRP* 3.8 23.3 - + + -
44B ALA* 3.3 15.5 - - - -
48B ARG* 2.6 46.6 + - + -
49B LYS 3.8 10.8 - - - -
50B ASN* 3.4 7.2 - - - +
56B LEU* 3.2 50.6 + - + +
84B PHE* 5.5 0.6 - - - -
188B TYR* 3.6 21.1 - + - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS 3.5 1.8 + - - +
17B VAL 3.0 7.4 + - - +
19B TYR* 1.3 80.8 - - - +
21B MET* 1.3 59.6 + - - +
50B ASN* 3.3 8.4 - - - +
51B ILE* 3.0 37.4 + - + +
188B TYR* 3.4 50.0 - - + -
191B MET* 3.9 12.8 - - - -
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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
----------------------------------------------------------
17B VAL* 2.9 31.4 + - + +
20B ALA* 1.3 79.2 - - - +
22B SER* 1.3 59.7 + - - +
51B ILE* 4.0 19.9 - - + +
52B PHE* 4.7 1.2 - - - -
80B LEU* 3.4 28.1 - - - +
154B LEU* 4.4 2.9 - - + -
157B HIS* 3.4 42.7 + - + +
158B LEU* 3.9 26.0 - - + -
161B ILE* 4.1 13.6 - - + +
191B MET* 4.1 27.6 - - - +
195B VAL* 4.0 12.1 - - + -
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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