Contacts of the helix formed by residues 4 - 18 (chain A) in PDB entry 1CBM
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A HIS* 4.6 15.5 - - + +
3A LEU* 1.3 77.6 - - - +
5A PRO* 1.3 61.8 - - - +
6A GLU* 3.7 12.3 + - - +
7A GLU* 2.7 44.0 + - - +
8A LYS* 2.6 33.1 + - - +
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Residues in contact with PRO 5 (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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3A LEU 3.9 1.8 - - - +
4A THR* 1.3 88.7 - - - +
6A GLU* 1.3 68.9 + - - +
8A LYS* 3.5 10.1 - - + +
9A SER* 2.6 41.9 + - - +
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Residues in contact with GLU 6 (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 THR* 3.1 11.1 + - - +
5A PRO* 1.3 95.7 - - - +
7A GLU* 1.3 60.3 + - + +
9A SER* 3.4 6.9 + - - -
10A ALA* 3.1 29.5 + - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS 4.3 2.3 - - - +
3A LEU* 3.4 20.3 - - + +
4A THR* 2.7 54.1 + - - +
6A GLU* 1.3 80.4 - - + +
8A LYS* 1.3 66.7 + - - +
9A SER 3.2 0.2 + - - -
10A ALA* 3.2 5.4 + - - +
11A VAL* 3.0 29.6 + - - +
125A PRO* 4.4 12.0 - - + +
128A ALA* 4.8 5.2 - - - +
129A ALA* 4.2 27.3 + - + -
132A LYS* 4.7 10.2 + - - +
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Residues in contact with LYS 8 (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 VAL 4.9 5.1 + - - -
3A LEU* 3.2 43.8 - - + +
4A THR 2.6 25.2 + - - +
5A PRO* 3.1 8.0 + - + +
7A GLU* 1.3 74.1 - - - +
9A SER* 1.3 58.1 + - - +
11A VAL* 3.3 8.5 - - + +
12A THR* 2.9 37.2 + - + +
78A LEU* 4.3 24.9 - - + +
79A ASP* 5.7 0.8 - - - +
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Residues in contact with SER 9 (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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5A PRO* 2.6 24.3 + - - +
6A GLU* 3.6 7.3 - - - -
8A LYS* 1.3 72.9 - - - +
10A ALA* 1.3 57.1 + - - +
12A THR* 3.4 7.5 + - - -
13A ALA* 2.8 35.8 + - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 3.1 15.2 + - - +
7A GLU* 3.2 4.5 + - - +
9A SER* 1.3 77.5 - - - +
11A VAL* 1.3 66.4 + - + +
13A ALA* 4.0 5.6 - - - +
14A LEU* 3.2 23.4 + - - +
126A VAL* 3.7 30.7 - - + +
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Residues in contact with VAL 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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3A LEU* 4.2 12.3 - - + -
7A GLU 3.0 15.5 + - - +
8A LYS* 3.3 16.6 - - - +
10A ALA* 1.3 76.5 - - + +
12A THR* 1.3 77.8 + - + +
14A LEU 3.1 2.1 + - - -
15A TRP* 2.9 16.4 + - - +
75A LEU* 4.8 16.6 - - + -
78A LEU* 5.7 1.1 - - + -
126A VAL* 4.8 1.6 - - + +
129A ALA* 3.2 38.4 - - + -
130A TYR* 2.7 49.9 + - + -
133A VAL* 5.4 2.0 - - + -
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Residues in contact with THR 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 LYS* 2.9 22.4 + - + +
9A SER* 3.4 9.2 + - - -
11A VAL* 1.3 84.2 - - + +
13A ALA* 1.3 59.3 + - - +
15A TRP* 3.6 8.0 - - - +
16A GLY* 2.9 27.5 + - - -
75A LEU* 5.8 9.0 - - + +
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Residues in contact with ALA 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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9A SER 2.8 23.8 + - - +
10A ALA* 4.0 6.5 - - - +
11A VAL 3.2 0.2 - - - -
12A THR* 1.3 74.8 + - - +
14A LEU* 1.3 62.6 + - - +
16A GLY* 3.7 3.7 + - - -
17A LYS* 3.3 25.1 - - - +
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Residues in contact with LEU 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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10A ALA 3.2 15.3 + - - +
11A VAL 3.1 3.5 + - - +
13A ALA* 1.3 77.6 - - - +
15A TRP* 1.3 68.8 - - - +
17A LYS* 3.0 23.1 + - - +
18A VAL* 3.6 4.7 + - + +
114A LEU* 4.4 9.2 - - + -
118A PHE* 3.6 51.7 - - + -
121A GLU* 4.2 26.0 - - + +
122A PHE* 4.3 11.2 - - + -
126A VAL* 4.3 10.1 - - + -
130A TYR* 3.3 34.3 - - + +
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Residues in contact with TRP 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 VAL 2.9 15.0 + - - +
12A THR* 3.6 8.1 - - - +
14A LEU* 1.3 73.7 - - - +
16A GLY* 1.3 54.2 + - - +
17A LYS 2.7 5.4 + - - -
18A VAL* 2.7 50.7 + - + +
20A VAL* 5.2 6.3 - - + +
23A VAL* 5.8 0.2 - - + -
68A LEU* 3.4 44.0 - - + -
71A PHE* 4.3 9.0 - + + -
72A SER* 3.1 35.6 + - - -
75A LEU* 3.4 33.2 - - + +
110A LEU* 4.6 9.6 - - + -
114A LEU* 4.4 19.1 - - + -
130A TYR* 3.6 26.2 + + - +
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Residues in contact with GLY 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 THR 2.9 15.9 + - - -
13A ALA* 4.1 3.4 - - - -
14A LEU 3.3 0.8 - - - -
15A TRP* 1.3 75.4 - - - +
17A LYS* 1.3 61.9 + - - +
18A VAL 3.4 3.0 + - - +
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Residues in contact with LYS 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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13A ALA* 3.3 20.9 - - + +
14A LEU* 3.0 9.6 + - - +
15A TRP 2.7 6.5 + - - -
16A GLY* 1.3 76.6 - - - +
18A VAL* 1.3 60.9 + - - -
19A ASN* 3.6 2.8 + - - +
118A PHE* 3.8 18.4 - - + -
121A GLU* 2.8 37.1 + - - +
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Residues in contact with VAL 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 LEU 3.9 3.4 - - - +
15A TRP* 2.7 40.0 + - + +
16A GLY 4.7 2.3 - - - +
17A LYS* 1.3 72.9 - - - +
19A ASN* 1.3 60.6 + - - +
20A VAL* 3.0 25.1 + - + +
23A VAL* 4.2 15.5 - - + -
68A LEU* 3.8 28.3 - - + -
114A LEU* 3.8 17.7 - - + -
118A PHE* 3.4 31.0 - - + -
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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