Contacts of the helix formed by residues 19 - 28 (chain B) in PDB entry 3CB4
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 THR 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ILE 4.3 24.0 - - - +
18B SER* 1.3 75.4 - - - +
20B LEU* 1.3 64.8 + - - +
21B SER* 3.8 11.7 - - - -
22B ASP* 3.0 33.9 + - - +
23B ARG* 3.2 16.0 + - - +
132B LYS* 5.6 1.1 - - - +
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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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9B ILE* 5.3 3.6 - - + -
19B THR* 1.3 72.5 - - - +
21B SER* 1.3 62.6 + - - +
23B ARG* 3.1 22.1 + - - +
24B ILE* 3.0 36.4 + - + +
99B LEU* 3.8 24.5 - - + -
101B VAL* 3.6 34.0 - - + +
129B VAL* 4.2 12.1 - - + -
131B ASN* 4.0 10.2 + - - +
161B CYS* 4.1 12.1 - - - -
169B VAL* 3.9 34.8 - - + -
172B VAL* 4.4 6.3 - - + -
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Residues in contact with SER 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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9B ILE* 4.0 19.7 - - - +
19B THR* 3.8 12.8 - - - -
20B LEU* 1.3 79.4 - - - +
22B ASP* 1.3 65.3 + - - +
24B ILE* 3.7 6.1 + - - +
25B ILE* 3.4 28.4 + - - +
75B PHE* 3.1 38.7 - - - -
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Residues in contact with ASP 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 SER* 4.5 14.9 + - - +
19B THR* 3.0 29.0 + - - +
21B SER* 1.3 83.5 + - - +
23B ARG* 1.3 62.7 + - - +
24B ILE 3.4 0.2 - - - -
25B ILE* 3.7 13.7 + - - +
26B GLN* 3.2 28.6 + - - +
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Residues in contact with ARG 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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18B SER* 3.1 35.3 + - - -
19B THR* 3.2 11.7 + - - +
20B LEU* 3.1 38.3 + - - +
22B ASP* 1.3 74.6 - - - +
24B ILE* 1.3 65.5 + - - +
26B GLN* 3.2 23.9 + - - +
27B ILE* 3.3 19.1 + - + +
131B ASN* 2.7 42.4 + - - +
132B LYS* 4.4 2.2 - - - +
161B CYS* 4.2 3.6 - - - -
162B SER 3.4 17.4 + - - -
163B ALA* 3.6 20.8 - - - +
169B VAL* 4.1 18.9 - - + +
505F GLN* 3.2 29.8 + - + +
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Residues in contact with ILE 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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7B PHE* 4.6 11.9 - - + -
9B ILE* 4.4 12.6 - - + -
20B LEU* 3.0 41.2 + - + +
21B SER* 3.9 5.6 - - - +
22B ASP 3.4 0.2 - - - -
23B ARG* 1.3 76.5 - - - +
25B ILE* 1.3 62.0 + - - +
27B ILE* 3.4 12.3 - - - +
28B CYS* 3.2 21.2 + - - -
61B LEU* 3.9 18.8 - - + -
73B LEU* 4.8 4.0 - - + -
75B PHE* 6.3 4.0 - - + -
99B LEU* 4.2 13.2 - - + -
169B VAL* 4.0 11.2 - - + -
172B VAL* 5.3 1.1 - - + -
173B LEU* 3.7 38.1 - - + -
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Residues in contact with ILE 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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21B SER* 3.4 24.1 + - - +
22B ASP* 3.9 14.8 - - - +
23B ARG 3.3 0.4 - - - -
24B ILE* 1.3 77.2 - - - +
26B GLN* 1.3 61.2 + - + +
28B CYS 3.1 22.5 + - - +
30B GLY 3.4 29.0 + - - +
59B VAL* 3.8 30.3 - - + -
61B LEU* 4.0 24.9 - - + -
75B PHE* 5.2 1.8 - - + -
242B PRO* 4.4 22.0 - - + -
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Residues in contact with GLN 26 (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 SER* 5.0 6.1 + - - -
22B ASP* 3.2 22.9 + - - +
23B ARG* 3.2 27.3 + - - +
25B ILE* 1.3 79.5 - - + +
27B ILE* 1.3 57.8 + - - +
28B CYS 3.8 0.5 - - - +
30B GLY* 4.3 12.5 - - - -
505F GLN* 3.8 21.6 - - - +
506F ASN* 4.9 3.1 - - - +
509F ARG* 3.3 48.3 + - + +
537F ILE 4.4 9.0 - - - +
538F ALA* 3.4 7.4 - - + +
539F ARG 3.2 22.0 + - - +
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Residues in contact with ILE 27 (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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23B ARG* 3.3 8.7 + - + +
24B ILE* 3.4 13.5 - - - +
26B GLN* 1.3 74.8 - - - +
28B CYS* 1.3 62.6 + - - +
63B TYR* 5.0 4.1 - - + -
166B GLY 5.6 0.4 - - - +
169B VAL* 3.7 28.9 - - + -
170B GLN* 3.9 23.8 - - + +
173B LEU* 3.7 24.7 - - + -
505F GLN* 5.6 1.6 - - - +
536F ILE* 3.6 17.4 - - + +
537F ILE* 3.1 34.5 - - - +
538F ALA 3.7 0.2 - - - +
539F ARG* 3.2 36.4 + - - +
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Residues in contact with CYS 28 (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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24B ILE 3.2 16.5 + - - +
25B ILE 3.1 8.4 + - - +
26B GLN 3.8 1.2 - - - +
27B ILE* 1.3 81.6 - - - +
29B GLY* 1.3 71.0 + - - +
30B GLY 3.2 0.2 + - - -
61B LEU* 3.7 25.4 - - + -
62B ASP 3.4 23.8 - - - +
63B TYR* 4.0 11.7 - - - -
73B LEU* 4.4 2.5 - - - -
173B LEU* 3.7 26.0 - - - -
539F ARG* 2.7 22.5 - - - +
540F SER* 5.5 0.4 - - - -
541F THR* 6.4 2.0 - - - -
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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