Contacts of the helix formed by residues 13 - 23 (chain B) in PDB entry 1C72
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 ALA 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.7 7.2 - - + -
6B TYR* 3.6 37.1 - - + -
10B ARG 3.4 1.5 + - - -
11B GLY 3.3 1.2 - - - -
12B LEU* 1.3 77.3 - - - +
14B HIS* 1.3 57.7 + - - +
15B ALA 3.4 1.3 - - - -
16B ILE* 3.3 13.8 + - + +
17B ARG* 2.9 47.5 + - - +
60B PRO* 4.5 8.1 - - + -
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Residues in contact with HIS 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 ARG* 3.3 50.1 + - + +
11B GLY 3.8 5.6 - - - +
12B LEU 3.2 1.2 - - - -
13B ALA* 1.3 77.9 - - - +
15B ALA* 1.3 62.5 + - - +
17B ARG* 3.3 14.6 + - - +
18B LEU* 3.1 49.0 + - + +
160B TYR* 4.4 7.9 - + - -
161B ASP* 3.4 29.8 - - + +
196B TYR* 5.8 1.3 - + - -
202B PHE* 3.7 28.8 - + - -
203B MET* 3.4 22.0 + - - +
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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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12B LEU 4.4 5.0 + - - +
13B ALA 3.4 0.2 - - - -
14B HIS* 1.3 79.0 - - - +
16B ILE* 1.3 58.0 + - - +
18B LEU* 3.6 11.8 + - - +
19B LEU* 3.1 28.4 + - - +
76B LEU* 3.9 7.8 - - + +
107B ARG* 5.2 0.4 - - - +
157B PHE* 3.5 35.3 - - + +
158B LEU* 4.0 20.0 - - + -
161B ASP* 4.2 11.2 + - + +
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Residues in contact with ILE 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 LEU* 4.0 14.1 - - + -
12B LEU 4.0 15.0 - - - +
13B ALA* 3.6 9.4 - - - +
14B HIS 3.2 0.6 - - - -
15B ALA* 1.3 75.2 - - + +
17B ARG* 1.3 59.8 + - - +
19B LEU* 3.3 1.4 + - - +
20B LEU* 3.0 45.5 + - + +
60B PRO* 3.7 32.8 - - + -
72B SER* 4.3 9.6 - - - -
75B ILE* 4.0 30.3 - - + -
76B LEU* 3.6 25.8 - - + -
79B ILE* 4.4 7.2 - - + -
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Residues in contact with ARG 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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4B LEU* 3.7 15.6 - - + +
6B TYR* 3.9 11.7 - - - +
7B TRP 3.5 15.2 + - - -
9B ILE 3.1 28.3 + - - -
10B ARG* 3.4 20.0 + - - +
13B ALA* 2.9 27.8 + - - +
14B HIS* 3.5 11.5 + - - +
16B ILE* 1.3 77.9 - - - +
18B LEU* 1.3 60.9 + - - +
20B LEU* 3.4 8.5 + - - +
21B GLU* 3.1 29.2 + - - +
27B TYR* 4.7 5.6 + - + +
29B GLU* 3.2 35.5 + - - +
31B ARG* 4.0 16.2 - - - +
196B TYR* 3.7 23.1 - - + +
203B MET* 4.6 12.1 - - - +
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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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14B HIS* 3.1 45.1 + - + +
15B ALA* 3.8 9.2 - - - +
17B ARG* 1.3 78.6 - - - +
19B LEU* 1.3 58.0 + - - +
21B GLU* 3.5 3.9 + - - +
22B TYR* 2.9 23.6 + - - +
157B PHE* 3.9 13.2 - - + +
160B TYR* 4.0 20.9 - - + -
187B PHE* 4.3 6.3 - - + -
193B ILE* 3.3 36.6 - - + +
196B TYR* 3.7 28.2 - - + -
197B MET* 4.4 4.5 - - + -
202B PHE* 4.3 9.9 - - + -
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Residues in contact with LEU 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 3.1 17.2 + - - +
16B ILE 3.6 4.7 - - - +
17B ARG 3.2 0.4 - - - -
18B LEU* 1.3 73.1 - - - +
20B LEU* 1.3 62.0 + - - +
22B TYR 3.3 0.2 + - - -
23B THR* 2.9 47.5 + - + -
76B LEU* 3.9 26.2 - - + +
79B ILE* 3.4 41.5 - - + -
80B ALA 4.4 3.1 - - - +
85B MET* 4.0 13.0 - - + -
154B PHE* 4.8 9.6 - - + -
157B PHE* 3.6 34.5 - - + -
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Residues in contact with LEU 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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2B VAL* 4.3 12.6 - - + -
4B LEU* 4.4 11.4 - - + -
16B ILE* 3.0 34.4 + - + +
17B ARG* 3.7 4.9 - - - +
19B LEU* 1.3 75.9 - - - +
21B GLU* 1.3 61.3 + - - +
23B THR* 3.4 3.8 + - - -
24B GLU* 3.2 2.6 + - - -
25B THR* 3.1 59.7 + - + +
27B TYR* 4.0 34.1 - - + -
62B LEU* 4.5 13.5 - - + -
79B ILE* 3.5 24.5 - - + -
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Residues in contact with GLU 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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17B ARG 3.1 17.7 + - - +
18B LEU 3.6 5.6 - - - +
19B LEU 3.2 0.2 - - - -
20B LEU* 1.3 76.0 - - - +
22B TYR* 1.3 64.5 + - - +
24B GLU* 3.1 15.2 + - - +
27B TYR* 2.6 36.8 + - - +
192B LYS* 3.9 17.3 - - - +
193B ILE* 4.6 2.5 - - + -
196B TYR* 3.5 39.8 - - + +
201B ARG* 3.2 29.6 + - - -
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Residues in contact with TYR 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 2.9 19.2 + - - +
19B LEU 3.7 3.4 - - - +
21B GLU* 1.3 77.3 - - - +
23B THR* 1.3 64.7 + - + +
24B GLU* 3.2 0.9 + - - +
85B MET* 3.5 30.9 - - + +
151B LYS* 5.1 4.7 + - - -
152B LEU* 3.6 21.7 - - + +
157B PHE* 3.7 20.2 - + + -
190B LEU* 4.0 31.3 - - + +
191B GLU 6.1 0.2 - - - -
192B LYS* 3.8 28.8 + - + +
193B ILE* 3.6 15.9 - - + +
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Residues in contact with THR 23 (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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19B LEU* 2.9 38.9 + - + +
20B LEU* 3.4 4.7 + - - -
22B TYR* 1.3 79.3 - - + +
24B GLU* 1.3 68.3 + - - +
25B THR* 2.6 27.1 + - - -
79B ILE* 3.9 6.3 - - + +
83B HIS* 3.7 47.5 - - + -
85B MET* 4.2 9.0 - - - -
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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