Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 1TUB
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 ALA 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 2.6 4.8 + - - +
11A GLN* 1.3 77.6 - - - +
13A GLY* 1.3 54.4 + - - +
15A GLN* 4.3 1.0 - - - +
16A ILE* 2.9 30.5 + - - +
138A PHE* 5.0 0.4 - - - -
139A HIS 4.6 4.7 - - - +
140A SER* 4.0 23.3 - - - +
171A ILE* 3.9 22.7 - - + +
500A GTP 3.3 38.1 + - + +
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Residues in contact with GLY 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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8A HIS* 2.9 16.0 + - - -
9A VAL 4.2 0.7 - - - -
10A GLY 1.8 28.9 + - - +
12A ALA* 1.3 68.1 - - - +
14A VAL* 1.3 61.2 + - - -
15A GLN 3.0 2.0 - - - -
16A ILE* 2.6 29.1 - - - +
17A GLY 3.1 0.5 + - - -
67A PHE* 3.9 0.2 - - - -
138A PHE* 3.3 19.6 + - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A HIS* 4.6 0.7 - - + -
10A GLY 2.8 14.4 + - - +
11A GLN 3.6 0.2 + - - -
13A GLY* 1.3 71.2 - - - +
15A GLN* 1.4 59.2 + - - +
18A ASN* 2.9 16.6 + - - +
67A PHE* 3.3 31.9 - - + -
68A VAL 3.7 10.8 - - - +
69A ASP* 2.5 32.8 - - + +
74A VAL* 2.9 50.9 - - + -
75A ILE* 3.8 1.6 - - - +
78A VAL* 3.7 16.6 - - + +
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Residues in contact with GLN 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 GLN* 3.4 16.1 + - + +
13A GLY 3.0 0.4 - - - -
14A VAL* 1.4 74.7 - - - +
16A ILE* 1.3 60.9 - - - +
17A GLY 2.8 2.0 - - - -
18A ASN* 2.1 73.2 + - + +
19A ALA* 2.9 3.3 + - - +
74A VAL* 3.6 4.6 - - + +
77A GLU* 2.8 24.9 + - - +
225A THR* 5.1 4.0 - - - +
228A ASN* 4.0 13.7 + - - +
500A GTP 3.7 19.7 - - - +
247B GLN* 4.6 21.1 - - + +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 2.9 19.1 + - - +
13A GLY* 2.6 31.2 - - - +
15A GLN* 1.3 81.8 - - - +
17A GLY* 1.3 47.3 + - - +
19A ALA* 2.8 15.2 + - + +
20A CYS* 2.7 37.3 + - - -
138A PHE* 2.6 59.7 - - + -
139A HIS 5.7 0.7 - - - +
169A PHE* 4.2 14.6 - - + -
170A SER 5.9 0.2 - - - +
171A ILE* 4.6 15.3 - - + -
228A ASN* 4.8 10.1 - - + +
231A ILE* 4.4 23.3 - - + -
232A GLY* 5.5 2.0 - - - +
235A VAL* 5.8 0.7 - - + -
500A GTP 4.7 0.2 + - - -
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Residues in contact with GLY 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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8A HIS* 3.3 27.4 - - - -
13A GLY 3.1 2.6 + - - -
15A GLN 2.8 1.2 - - - -
16A ILE* 1.3 78.2 - - - +
18A ASN* 1.5 58.9 - - - +
19A ALA 2.9 1.1 - - - -
20A CYS* 2.7 9.0 + - - -
21A TRP* 2.1 53.0 + - - -
67A PHE* 3.8 2.2 - - - -
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Residues in contact with ASN 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 VAL 2.9 8.3 + - - -
15A GLN* 2.1 78.7 + - - +
17A GLY* 1.5 46.3 - - - +
19A ALA* 1.4 50.0 - - - +
21A TRP* 4.5 3.4 - - - -
22A GLU* 2.5 61.7 + - + +
67A PHE* 5.5 0.7 - - - -
74A VAL* 4.5 0.4 - - - +
77A GLU* 4.5 2.2 + - - +
78A VAL* 2.8 32.1 - - - +
83A TYR* 5.9 4.5 - - - -
85A GLN* 5.3 3.4 - - - +
87A PHE* 5.6 0.3 - - - -
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Residues in contact with ALA 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 GLN 2.9 3.6 + - - -
16A ILE* 2.8 15.3 + - - +
18A ASN* 1.4 74.4 - - - +
20A CYS* 1.2 63.3 + - - +
22A GLU* 4.2 6.0 - - - +
23A LEU* 3.0 24.8 + - - +
228A ASN* 3.3 42.6 - - + +
229A ARG* 4.6 5.4 - - + +
232A GLY* 3.7 9.5 - - - -
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Residues in contact with CYS 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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16A ILE* 2.7 24.6 + - - -
17A GLY* 2.7 9.8 + - - +
19A ALA* 1.2 74.4 - - - +
21A TRP* 1.5 57.1 - - + +
23A LEU* 3.4 5.9 + - - +
24A TYR* 1.9 55.5 + - + +
138A PHE* 3.1 42.2 - - + -
232A GLY* 4.5 8.7 - - - -
235A VAL* 3.8 22.0 - - + -
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Residues in contact with TRP 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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6A SER* 3.5 21.8 + - - -
8A HIS* 3.9 20.0 + + - -
17A GLY* 2.1 62.7 + - - +
18A ASN* 4.1 4.3 - - - +
20A CYS* 1.5 68.4 - - + +
22A GLU* 1.3 64.9 + - - +
24A TYR* 3.3 34.7 - + + +
25A CYS* 3.9 4.7 + - - +
28A HIS 5.9 0.2 - - - -
29A GLY* 5.3 3.6 - - - -
30A ILE* 3.9 25.8 - - + -
63A PRO* 3.3 39.5 - - + -
64A ARG 3.7 4.5 - - - -
65A ALA* 3.7 11.0 - - - -
67A PHE* 4.5 4.9 - + - -
85A GLN* 4.5 10.6 - - - +
87A PHE* 5.4 20.9 - + + -
138A PHE* 5.0 2.6 - - - -
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Residues in contact with GLU 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 ASN* 2.5 45.5 + - - +
19A ALA* 4.2 4.1 - - - +
21A TRP* 1.3 70.5 - - - +
23A LEU* 1.4 58.8 - - - +
24A TYR 2.9 4.9 - - - -
25A CYS* 2.4 37.6 - - - +
83A TYR* 5.0 10.9 - - - -
85A GLN* 2.7 39.2 + - - +
229A ARG* 4.8 14.6 + - - -
363A VAL* 5.5 3.8 - - - +
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Residues in contact with LEU 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 ALA 3.0 21.8 + - - +
20A CYS* 3.5 6.3 - - - +
21A TRP 3.3 0.2 - - - -
22A GLU* 1.4 76.4 - - - +
24A TYR* 1.2 64.4 + - - +
25A CYS* 4.2 0.2 - - - +
26A LEU* 4.0 16.3 - - - +
232A GLY 3.4 19.1 - - - +
233A GLN* 3.4 21.3 - - + +
236A SER* 2.8 43.3 - - - +
320A ARG* 5.9 0.4 - - - +
361A THR* 4.4 29.7 - - + +
362A VAL* 5.2 2.9 - - - +
363A VAL* 6.2 2.5 - - + -
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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