Contacts of the helix formed by residues 19 - 28 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F ALA* 5.9 6.5 - - + -
12F HIS 5.7 0.7 - - - +
13F ILE 3.4 29.4 - - - +
18F SER* 1.3 77.0 - - - +
20F LEU* 1.3 66.4 + - - +
21F SER* 4.2 15.9 - - - -
22F ASP* 3.1 23.8 + - - +
23F ARG* 3.4 12.2 + - - +
131F ASN* 5.5 0.9 - - - -
132F LYS* 5.5 2.7 - - - +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 5.1 2.7 - - + -
19F THR* 1.3 73.3 - - - +
21F SER* 1.3 65.2 + - - +
23F ARG* 3.1 18.8 + - - +
24F ILE* 3.0 36.9 + - + +
99F LEU* 4.0 22.2 - - + -
101F VAL* 3.5 40.9 - - + +
129F VAL* 4.2 8.7 - - + -
131F ASN* 4.5 3.4 + - - +
161F CYS* 4.1 23.1 - - - -
169F VAL* 3.9 27.6 - - + -
172F VAL* 4.2 13.9 - - + -
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Residues in contact with SER 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.1 23.7 - - - +
19F THR* 4.2 12.7 - - - -
20F LEU* 1.3 79.1 - - - +
22F ASP* 1.3 65.8 + - - +
24F ILE* 3.7 4.9 + - - +
25F ILE* 3.4 26.3 + - - +
59F VAL* 5.6 0.2 - - - +
75F PHE* 3.2 28.2 - - - -
77F ASP* 4.8 10.4 + - - -
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Residues in contact with ASP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F SER* 4.6 14.2 + - - +
19F THR* 3.1 27.9 + - - +
21F SER* 1.3 81.8 + - - +
23F ARG* 1.3 65.2 + - - +
25F ILE* 3.1 25.4 + - - +
26F GLN* 3.2 21.1 + - - +
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Residues in contact with ARG 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D GLN* 3.1 28.7 - - + +
18F SER* 2.7 42.4 + - - -
19F THR* 3.4 24.8 + - - +
20F LEU* 3.1 13.2 + - - +
22F ASP* 1.3 78.8 - - - +
24F ILE* 1.3 61.0 - - - +
26F GLN* 3.3 14.4 + - - +
27F ILE* 3.2 28.1 + - + +
131F ASN* 2.6 44.3 + - - +
132F LYS* 4.8 0.2 - - - +
161F CYS* 4.2 5.5 - - - -
162F SER 3.1 31.7 + - - +
163F ALA* 3.3 16.2 - - - +
169F VAL* 4.1 19.1 - - + +
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Residues in contact with ILE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 4.8 9.0 - - + -
9F ILE* 4.0 21.8 - - + -
20F LEU* 3.0 38.6 + - + +
21F SER* 3.8 5.6 - - - +
22F ASP 3.2 0.2 - - - -
23F ARG* 1.3 76.9 - - - +
25F ILE* 1.3 61.9 + - - +
27F ILE* 3.3 11.7 + - - +
28F CYS* 3.2 20.1 + - - -
61F LEU* 3.9 17.5 - - + -
73F LEU* 5.1 4.3 - - + -
75F PHE* 5.0 8.5 - - + -
99F LEU* 4.3 9.0 - - + -
169F VAL* 4.1 9.4 - - + -
172F VAL* 5.3 1.1 - - + -
173F LEU* 3.7 37.0 - - + -
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Residues in contact with ILE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F SER* 3.4 21.3 + - - +
22F ASP* 3.1 17.8 + - - +
24F ILE* 1.3 75.6 - - - +
26F GLN* 1.3 62.4 + - + +
28F CYS 3.2 11.3 + - - -
29F GLY 3.5 0.3 + - - -
30F GLY 3.3 42.9 + - - +
59F VAL* 4.1 28.3 - - + -
61F LEU* 4.0 22.7 - - + -
75F PHE* 4.8 2.9 - - + -
242F PRO* 4.3 22.0 - - + -
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Residues in contact with GLN 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D GLN* 3.1 42.2 - - - +
506D ASN* 5.4 0.3 - - - -
509D ARG* 3.4 48.3 + - + +
537D ILE 4.0 8.0 - - - +
538D ALA* 3.6 3.0 - - - +
539D ARG 2.9 31.7 + - - +
18F SER* 5.2 5.9 + - - -
22F ASP* 3.2 14.1 + - - +
23F ARG* 3.3 21.4 + - - +
25F ILE* 1.3 79.5 - - + +
27F ILE* 1.3 57.4 + - - +
30F GLY* 4.9 8.7 - - - -
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Residues in contact with ILE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D GLN* 5.5 2.0 - - - +
536D ILE* 3.7 17.5 - - + +
537D ILE* 3.2 28.9 - - - +
539D ARG* 3.3 36.5 + - - +
23F ARG* 3.2 12.5 + - + +
24F ILE 3.3 13.9 - - - +
26F GLN* 1.3 76.5 - - - +
28F CYS* 1.3 59.7 + - - +
63F TYR* 5.1 3.4 - - + -
166F GLY 5.1 0.9 - - - +
169F VAL* 3.9 15.0 - - + +
170F GLN* 3.6 35.2 - - + +
173F LEU* 3.5 31.2 - - + -
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Residues in contact with CYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D ARG* 2.7 36.0 - - - +
540D SER* 4.2 1.9 + - - -
541D THR* 5.3 2.2 + - - +
24F ILE 3.2 13.7 + - - +
25F ILE 3.2 3.7 + - - -
27F ILE* 1.3 80.4 - - - +
29F GLY* 1.3 62.3 + - - +
61F LEU* 3.8 28.7 - - + -
62F ASP 4.0 11.4 - - - +
63F TYR* 4.0 20.6 - - - -
73F LEU* 4.6 1.3 - - - -
173F LEU* 3.5 33.0 - - - -
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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