Contacts of the helix formed by residues 19 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE 4.1 25.4 - - - +
18A SER* 1.3 76.4 - - - +
20A LEU* 1.3 67.0 + - - +
21A SER* 4.3 7.5 + - - -
22A ASP* 2.9 35.3 + - - +
23A ARG* 3.3 11.2 + - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.7 7.2 - - + -
19A THR* 1.3 73.6 - - - +
21A SER* 1.3 57.8 + - - +
23A ARG* 3.1 34.2 + - - +
24A ILE* 2.9 43.2 + - + +
99A LEU* 3.8 23.6 - - + -
101A VAL* 3.4 39.3 - - + -
129A VAL* 4.7 4.7 - - + -
131A ASN* 4.5 3.7 + - - +
161A CYS* 4.0 19.5 - - - -
169A VAL* 4.3 15.0 - - + -
172A VAL* 4.5 10.8 - - + -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.8 14.4 - - - +
19A THR* 4.3 7.4 - - - -
20A LEU* 1.3 79.3 - - - +
22A ASP* 1.3 70.2 + - - +
24A ILE* 3.3 7.2 + - - +
25A ILE* 3.1 33.8 + - - +
75A PHE* 3.2 39.4 - - - -
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Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 4.9 8.1 - - - -
19A THR* 2.9 30.6 + - - +
21A SER* 1.3 82.7 + - - +
23A ARG* 1.3 58.0 + - - +
25A ILE* 3.6 12.9 + - - +
26A GLN* 3.2 40.0 + - - +
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 2.8 47.9 + - - -
19A THR* 3.3 10.8 + - - +
20A LEU* 3.1 34.8 + - - +
22A ASP* 1.3 75.3 - - - +
24A ILE* 1.3 65.5 + - - +
26A GLN* 3.4 13.9 + - - +
27A ILE* 3.3 28.9 + - + +
131A ASN* 2.6 47.9 + - - +
161A CYS* 4.3 1.4 - - - -
162A SER 3.4 15.2 + - - -
163A ALA* 3.6 23.7 - - - +
166A GLY* 5.2 7.4 - - - -
169A VAL* 3.9 20.8 - - + +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.4 15.9 - - + -
9A ILE* 4.7 5.4 - - + -
20A LEU* 2.9 31.1 + - + +
21A SER* 3.3 6.0 + - - +
23A ARG* 1.3 73.2 - - - +
25A ILE* 1.3 63.8 + - - +
26A GLN 3.3 0.3 + - - -
27A ILE* 3.3 4.6 + - - +
28A CYS* 3.1 27.0 + - - -
61A LEU* 3.6 22.9 - - + -
73A LEU* 4.7 3.6 - - + -
75A PHE* 6.3 1.6 - - + -
99A LEU* 4.2 24.2 - - + -
169A VAL* 4.0 15.3 - - + -
172A VAL* 5.1 2.0 - - + -
173A LEU* 3.7 33.2 - - + -
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Residues in contact with ILE 25 (chain A).
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* 3.1 28.4 + - - +
22A ASP* 3.8 12.8 - - - +
24A ILE* 1.3 75.1 - - - +
26A GLN* 1.3 61.3 + - + +
28A CYS 3.3 7.4 + - - -
29A GLY 3.6 0.2 + - - -
30A GLY 2.8 44.1 + - - +
59A VAL* 3.7 37.5 - - + -
61A LEU* 4.0 15.9 - - + -
75A PHE* 5.8 0.7 - - + -
242A PRO* 4.1 26.2 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 5.7 4.0 - - - -
22A ASP* 3.2 34.0 + - - +
23A ARG* 3.7 16.8 - - - +
24A ILE 3.2 0.4 - - - -
25A ILE* 1.3 78.6 - - + +
27A ILE* 1.3 63.0 + - + +
28A CYS 3.3 4.7 + - - +
30A GLY* 4.0 16.9 - - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG* 3.3 12.1 + - + +
24A ILE 3.6 11.7 - - - +
26A GLN* 1.3 79.7 - - + +
28A CYS* 1.3 61.3 + - - +
62A ASP 5.1 0.2 - - - +
63A TYR* 5.1 7.6 - - + -
166A GLY 5.6 3.4 - - - +
169A VAL* 3.8 14.8 - - + -
170A GLN* 3.7 36.6 - - + +
173A LEU* 3.5 28.7 - - + -
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Residues in contact with CYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.1 21.8 + - - +
25A ILE 3.4 0.2 - - - -
26A GLN 3.9 1.7 - - - +
27A ILE* 1.3 83.7 - - - +
29A GLY* 1.3 71.3 + - - +
30A GLY* 2.9 6.5 + - - -
61A LEU* 3.7 25.1 - - + -
62A ASP 3.4 25.1 - - - +
63A TYR* 4.3 9.0 - - - -
73A LEU* 4.5 2.2 - - - -
173A LEU* 3.7 26.9 - - - -
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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