Contacts of the helix formed by residues 12 - 22 (chain B) in PDB entry 4R8U
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 CYS 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 1.3 70.9 - - - +
13B PHE* 1.3 65.3 + - - +
14B PHE 3.4 1.3 - - - -
15B ALA* 2.9 14.0 + - + -
16B ALA* 2.8 21.9 + - + +
19B MET* 5.3 4.5 - - + -
44B THR* 4.7 0.7 - - - +
45B ALA 4.1 9.2 - - - +
46B ASN* 4.6 5.6 - - + -
47B TYR* 3.3 41.7 - - - -
50B ARG* 3.7 20.6 - - - +
401B 1FZ 2.6 32.4 + - - -
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Residues in contact with PHE 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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10B MET* 3.8 29.2 - - + -
11B ASP 3.2 7.2 - - - -
12B CYS* 1.3 73.2 - - - +
14B PHE* 1.3 80.6 + + - +
16B ALA* 3.5 2.4 + - + +
17B VAL* 3.2 39.8 + - + +
80B TYR* 3.6 37.2 - - + -
83B ALA* 4.3 13.0 - - + -
84B SER 4.4 2.0 - - - -
87B ILE* 4.4 3.6 - - + -
103B LEU* 3.7 33.0 - - + -
104B ASP* 3.4 24.2 - - + -
137B LEU* 4.4 5.2 - - + -
401B 1FZ 2.9 26.9 + + + +
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 1.3 99.7 - + - +
15B ALA* 1.3 64.2 + - - +
17B VAL* 3.4 3.8 + - - +
18B GLU* 3.2 25.6 + - - +
32B ILE* 3.9 22.7 - - + -
43B SER* 4.1 9.0 - - - -
44B THR* 3.6 10.3 - - + -
77B PHE* 6.1 1.8 - + - -
80B TYR* 3.6 50.8 - + + +
103B LEU* 4.7 10.8 - - + -
401B 1FZ 3.1 45.6 + + - -
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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 CYS* 2.9 9.2 + - + +
14B PHE* 1.3 79.1 - - - +
16B ALA* 1.3 57.9 + - - +
18B GLU* 3.5 3.3 + - - +
19B MET* 2.9 35.3 + - - +
30B ILE* 4.0 5.5 - - + +
32B ILE* 3.5 19.7 - - + -
44B THR* 3.7 9.8 - - + +
45B ALA* 4.1 1.6 - - - -
46B ASN* 3.8 36.6 - - + +
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Residues in contact with ALA 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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11B ASP 3.5 15.5 - - - +
12B CYS* 2.8 16.0 + - + +
13B PHE* 3.8 3.8 - - - +
15B ALA* 1.3 76.5 - - - +
17B VAL* 1.3 58.9 - - - +
19B MET* 3.7 17.9 - - + +
20B ARG* 3.0 30.0 + - - +
26B ARG* 5.2 1.2 + - - -
137B LEU* 3.6 19.7 - - + +
138B THR* 5.8 3.8 - - - +
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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 PHE* 3.2 26.1 + - + +
14B PHE 3.4 6.7 + - - +
16B ALA* 1.3 76.9 - - - +
18B GLU* 1.3 62.5 + - - +
20B ARG* 3.6 16.0 + - - +
21B ASP* 3.2 28.6 + - - +
76B ARG* 4.4 2.5 - - - +
79B ALA* 3.8 20.9 - - + -
80B TYR* 3.7 33.4 - - + -
83B ALA* 4.8 3.8 - - + -
137B LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 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 PHE 3.2 14.0 + - - +
15B ALA 3.6 7.4 - - - +
17B VAL* 1.3 75.6 - - - +
19B MET* 1.3 60.4 + - - +
21B ASP* 4.1 0.5 - - - +
22B ASN* 2.8 35.0 + - - +
25B LEU* 4.1 2.6 - - - +
30B ILE* 4.4 6.5 - - + -
32B ILE* 4.0 8.1 - - + -
73B LEU* 3.3 38.8 - - + +
75B GLY* 4.5 1.4 - - - -
76B ARG* 3.1 47.2 + - - +
80B TYR* 3.2 23.1 + - + +
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Residues in contact with MET 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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12B CYS* 5.3 6.1 - - + -
15B ALA* 2.9 24.7 + - + +
16B ALA* 3.4 19.5 + - + +
18B GLU* 1.3 77.1 - - - +
20B ARG* 1.3 62.6 + - - +
22B ASN 3.1 20.9 - - - +
23B PRO* 3.4 2.3 - - - +
25B LEU* 3.7 15.3 - - - +
26B ARG* 3.2 54.3 + - - +
30B ILE* 3.9 9.4 - - + -
46B ASN* 3.4 36.8 - - + -
47B TYR 5.7 0.4 - - - +
48B PRO* 5.7 0.4 - - - -
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Residues in contact with ARG 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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16B ALA 3.0 16.4 + - - +
17B VAL* 3.7 17.9 + - - +
18B GLU 3.3 0.2 - - - -
19B MET* 1.3 78.9 - - - +
21B ASP* 1.3 87.5 + - - +
23B PRO* 3.8 12.8 - - - +
26B ARG* 3.9 18.2 + - - +
79B ALA* 5.0 8.3 + - - +
82B GLU* 5.5 4.4 + - - -
83B ALA* 5.1 6.5 - - - +
135B LEU* 2.9 35.9 + - - +
136B GLN* 3.9 30.9 - - + +
137B LEU* 3.8 24.8 - - + +
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Residues in contact with ASP 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 VAL* 3.2 16.1 + - - +
18B GLU* 4.1 1.3 - - - +
20B ARG* 1.3 110.4 + - - +
22B ASN* 1.3 60.6 + - + +
23B PRO* 3.4 7.0 - - - +
76B ARG* 2.8 41.7 + - - +
79B ALA* 4.6 0.3 - - - +
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Residues in contact with ASN 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 GLU* 2.8 15.7 + - - +
19B MET 3.1 10.0 - - - +
21B ASP* 1.3 78.2 - - + +
23B PRO* 1.3 58.7 - - - +
24B ALA* 3.2 22.0 + - - +
25B LEU* 3.2 52.1 + - + +
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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