Contacts of the helix formed by residues 10 - 24 (chain A) in PDB entry 1CF5
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR 4.1 9.0 - - - +
9A ALA* 1.3 79.4 - - - +
11A ALA* 1.3 64.6 + - - +
12A LYS* 3.0 30.4 + - + +
13A THR* 2.8 22.4 + - - -
14A TYR* 3.1 23.2 + - - +
127A LEU* 4.3 2.3 - - - +
173A VAL* 4.4 14.1 - - - -
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Residues in contact with ALA 11 (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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10A THR* 1.3 73.9 - - - +
12A LYS* 1.3 59.6 + - - +
14A TYR* 3.5 5.8 + - - +
15A THR* 3.2 30.9 + - - +
170A ALA* 3.2 33.8 - - + +
173A VAL* 3.9 12.9 - - + +
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Residues in contact with LYS 12 (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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8A THR 5.5 1.2 + - - -
10A THR* 3.0 26.1 + - + +
11A ALA* 1.3 76.2 - - - +
13A THR* 1.3 83.0 + - - +
14A TYR 3.1 1.1 - - - -
15A THR* 2.7 23.0 + - - -
16A LYS* 3.1 12.0 + - + +
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Residues in contact with THR 13 (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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4A PHE* 3.8 9.8 - - - -
8A THR* 4.2 14.1 - - - +
9A ALA* 3.1 10.3 - - - +
10A THR* 2.8 29.0 + - - +
12A LYS* 1.3 103.6 - - - +
14A TYR* 1.3 55.1 + - - +
16A LYS* 3.6 12.8 + - + +
17A PHE* 3.0 27.2 + - - +
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Residues in contact with TYR 14 (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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4A PHE* 3.8 32.3 - + + -
10A THR 3.1 17.5 + - - +
11A ALA* 3.8 2.9 - - - +
12A LYS 3.1 0.2 - - - -
13A THR* 1.3 77.0 + - - +
15A THR* 1.3 62.0 + - - +
17A PHE* 3.5 7.3 + + - +
18A ILE* 3.1 44.8 + - + +
127A LEU* 3.9 16.2 - - + -
130A LEU* 5.9 2.0 - - + -
155A THR* 3.0 27.7 + - - -
159A ALA* 3.1 14.9 - - - +
166A GLU* 3.4 22.4 - - + -
169A VAL* 3.0 36.2 - - + +
170A ALA* 3.9 20.2 - - + -
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Residues in contact with THR 15 (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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11A ALA 3.2 14.8 + - - +
12A LYS* 2.7 23.6 + - - -
14A TYR* 1.3 77.3 - - - +
16A LYS* 1.3 53.0 + - - +
18A ILE* 3.4 1.0 + - - -
19A GLU* 2.7 40.3 + - - +
166A GLU* 3.3 29.4 - - + +
167A ARG* 5.2 9.4 - - - +
170A ALA* 4.0 20.4 - - + -
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Residues in contact with LYS 16 (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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12A LYS* 3.1 12.5 + - + +
13A THR* 3.8 11.9 - - + +
15A THR* 1.3 81.0 + - - +
17A PHE* 1.3 57.2 + - - +
19A GLU* 3.9 7.0 - - + -
20A ASP* 2.8 50.4 + - - +
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Residues in contact with PHE 17 (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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2A VAL* 3.5 30.5 - - + -
3A ASN 3.5 17.3 - - - +
4A PHE* 3.6 32.5 - + + -
13A THR 3.0 15.1 + - - +
14A TYR* 3.5 22.2 - + - +
16A LYS* 1.3 74.6 - - - +
18A ILE* 1.3 90.6 + - + +
20A ASP* 3.5 5.7 - - - +
21A PHE* 2.8 35.8 + + + +
50A LEU* 4.3 15.7 - - + -
52A LEU* 4.5 7.2 - - + -
130A LEU* 6.2 0.2 - - + -
156A THR* 3.9 30.7 - - + -
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Residues in contact with ILE 18 (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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14A TYR* 3.1 45.1 + - + +
15A THR 3.7 6.3 - - - +
17A PHE* 1.3 103.7 - - + +
19A GLU* 1.3 54.7 + - - +
21A PHE* 3.2 5.5 + - + +
22A ARG* 2.8 56.1 + - - +
155A THR 4.1 2.5 - - - +
156A THR 4.2 7.6 - - - +
159A ALA* 3.7 27.8 - - + +
160A ALA* 3.8 8.5 - - + -
166A GLU* 4.0 9.0 - - - +
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Residues in contact with GLU 19 (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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15A THR* 2.7 24.4 + - - +
16A LYS* 3.7 9.9 - - + +
17A PHE 3.3 0.2 - - - -
18A ILE* 1.3 75.5 - - - +
20A ASP* 1.3 61.1 + - - +
22A ARG* 2.7 46.1 + - - +
23A ALA* 3.4 10.3 + - - +
163A LYS* 3.7 21.0 + - - -
166A GLU* 3.8 7.3 - - - +
167A ARG* 5.3 0.2 + - - -
236A LYS* 5.2 3.4 + - - +
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Residues in contact with ASP 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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2A VAL* 4.4 11.2 - - + -
16A LYS* 2.8 43.7 + - - +
17A PHE* 3.5 5.0 - - - +
19A GLU* 1.3 73.8 - - - +
21A PHE* 1.3 61.0 + - - +
23A ALA* 3.1 16.2 + - - +
24A THR* 3.2 19.7 + - + +
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Residues in contact with PHE 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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2A VAL* 3.6 19.9 - - + +
17A PHE* 2.8 35.0 + + + +
18A ILE* 3.6 6.7 - - + +
20A ASP* 1.3 66.6 - - - +
22A ARG* 1.3 62.6 + - - +
23A ALA 3.0 5.5 + - - -
24A THR* 3.4 10.4 + - - -
25A LEU* 3.8 17.3 + - + +
48A ILE* 3.6 26.7 - - + -
50A LEU* 3.8 23.8 - - + -
64A ILE* 4.3 15.0 - - + -
69A VAL* 3.6 24.7 - - + -
156A THR* 3.3 30.3 - - - -
157A ALA* 4.3 1.8 - - - -
160A ALA* 3.7 18.8 - - + -
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Residues in contact with ARG 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 ILE* 2.8 21.9 + - - +
19A GLU* 2.7 46.0 + - - +
20A ASP 3.3 0.2 - - - -
21A PHE* 1.3 72.2 - - - +
23A ALA* 1.3 57.1 + - + +
24A THR 3.7 0.2 - - - -
25A LEU* 4.0 24.0 - - - +
35A PRO* 6.1 0.7 - - - +
159A ALA 2.8 27.0 + - - -
160A ALA* 3.1 29.4 + - + +
163A LYS* 3.8 21.2 - - - +
166A GLU* 2.8 28.9 + - - -
236A LYS* 3.2 32.5 - - - +
237A LEU* 4.3 15.2 - - + +
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Residues in contact with ALA 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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19A GLU 3.4 11.6 + - - +
20A ASP* 3.1 10.4 + - - +
21A PHE 3.0 1.4 + - - -
22A ARG* 1.3 78.7 - - + +
24A THR* 1.3 61.0 + - - +
25A LEU 3.4 4.3 - - - +
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Residues in contact with THR 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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1A ASP 6.0 0.9 - - - -
2A VAL* 3.8 22.2 - - + +
20A ASP* 3.2 15.6 + - + +
21A PHE 3.4 2.6 + - - -
23A ALA* 1.3 78.2 - - - +
25A LEU* 1.3 60.4 + - - +
26A PRO* 2.8 18.5 - - - +
45A ARG* 4.9 4.5 + - - -
48A ILE* 3.5 32.4 - - - +
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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