Contacts of the helix formed by residues 12 - 23 (chain B) 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 CYS 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ALA 4.5 0.2 + - - -
11B GLN* 1.3 72.4 - - - +
13B GLY* 1.3 50.1 + - - +
16B ILE* 1.8 49.9 + - + +
138B THR* 4.5 0.7 - - - -
139B HIS 4.4 2.5 - - - +
140B SER* 3.8 14.5 - - - -
171B VAL* 3.8 24.7 - - + -
500B GDP 2.5 89.1 + - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.6 4.9 - - - +
9B ALA 2.8 16.3 + - - -
12B CYS* 1.3 81.0 - - - +
14B ASN* 1.4 61.0 + - - +
17B GLY* 2.9 21.3 + - - -
138B THR* 2.2 43.8 + - - +
139B HIS* 4.5 1.8 - - - +
140B SER* 5.6 0.2 - - - -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 2.9 18.8 - - - +
9B ALA 3.4 1.2 + - - -
10B GLY 2.1 26.1 + - - +
11B GLN 3.4 1.2 + - - +
13B GLY* 1.4 72.2 - - - +
15B GLN* 1.3 66.3 + - - +
17B GLY* 3.1 7.6 + - - -
18B ALA* 3.3 10.2 + - - +
67B LEU* 3.0 7.3 - - - +
68B VAL 2.7 22.0 + - - +
69B ASP* 2.2 36.4 + - - +
74B THR* 2.3 42.5 + - + +
77B SER* 6.0 0.2 - - - -
78B VAL* 4.8 3.8 - - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN* 2.8 30.0 + - + +
14B ASN* 1.3 73.5 - - - +
16B ILE* 1.3 56.4 - - - +
17B GLY 2.7 4.5 - - - -
18B ALA* 2.7 37.7 + - + +
19B LYS 3.3 2.3 + - - -
74B THR* 4.4 1.0 + - - +
77B SER* 5.8 6.1 - - - +
78B VAL* 5.5 3.6 - - + -
224B TYR* 4.5 14.1 + - - +
225B GLY* 5.4 1.2 - - - +
228B ASN* 4.3 20.1 + - - +
500B GDP 1.8 42.9 + - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B CYS* 1.8 42.9 + - + +
13B GLY* 3.7 5.6 - - - +
15B GLN* 1.3 76.3 - - - +
17B GLY* 1.4 61.7 + - - +
19B LYS* 3.2 3.4 + - + +
20B PHE* 3.1 21.7 + - - +
138B THR* 4.1 15.7 - - + -
169B PHE* 5.8 1.6 - - + -
171B VAL* 5.0 7.0 - - + -
204B ILE* 5.3 6.1 - - + -
228B ASN* 3.3 23.8 - - - +
231B VAL* 4.3 32.5 - - + -
235B MET* 4.7 4.9 - - + -
500B GDP 3.4 30.1 - - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.6 20.6 - - - -
13B GLY 2.9 16.1 + - - -
14B ASN 3.1 7.4 + - - -
15B GLN 2.7 1.4 - - - -
16B ILE* 1.4 79.7 - - - +
18B ALA* 1.3 63.4 - - - +
20B PHE* 4.7 0.9 - - - -
21B TRP* 2.9 34.9 + - - +
138B THR* 5.2 1.8 - - - -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 3.3 4.6 + - - +
15B GLN* 2.7 22.0 + - + +
17B GLY* 1.3 79.2 - - - +
19B LYS* 1.3 62.7 + - + +
22B GLU* 2.9 41.8 + - - +
78B VAL* 3.8 31.0 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN 3.3 1.7 + - - +
16B ILE* 3.2 5.5 + - + +
17B GLY 3.1 0.6 - - - -
18B ALA* 1.3 86.8 - - + +
20B PHE* 1.3 62.9 + - - +
22B GLU* 3.7 6.3 - - - +
23B VAL* 3.1 22.9 - - - +
225B GLY* 3.1 28.3 + - - +
228B ASN* 2.0 67.2 - - + +
229B HIS* 3.7 6.3 - - + +
231B VAL* 6.1 0.9 - - + -
232B SER* 3.5 5.2 - - - -
501B TXL 5.2 7.4 - - + -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.1 14.8 + - + +
17B GLY* 4.7 0.4 - - - -
19B LYS* 1.3 72.1 - - - +
21B TRP* 1.2 96.5 - + + +
22B GLU 2.9 2.5 + - - -
23B VAL* 3.0 20.8 + - - +
24B ILE* 3.5 14.1 - - + +
28B HIS* 6.1 0.2 - - - -
30B ILE* 3.9 24.2 - - + -
136B GLN* 4.4 4.3 - - - -
169B PHE* 3.3 5.6 - + - -
232B SER* 4.3 6.5 - - - -
235B MET* 1.3 118.6 - - + +
236B SER* 4.4 1.1 - - - -
239B THR* 3.4 28.3 - - + -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 2.6 69.1 + + + -
8B GLN* 2.3 36.1 - - - +
17B GLY* 2.9 21.3 - - - +
18B ALA 4.8 0.7 - - - +
20B PHE* 1.2 96.3 - + + +
22B GLU* 1.3 67.3 - - + -
23B VAL 2.7 0.4 + - - -
24B ILE* 3.2 44.1 + - + +
25B SER 4.2 0.9 + - - -
30B ILE* 3.9 2.2 - - + -
58B GLY* 4.2 16.4 - - - -
63B PRO* 5.3 7.0 - - + -
64B ARG 3.0 13.2 - - - -
65B ALA* 4.0 5.6 - - + -
83B PHE* 3.5 4.2 - - + -
136B GLN* 5.0 0.2 - - - -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 2.9 36.4 + - - +
19B LYS* 3.7 7.6 - - - +
20B PHE 2.9 5.5 + - - -
21B TRP* 1.3 80.5 - - + +
23B VAL* 1.1 61.7 + - + +
24B ILE 2.7 5.7 + - - -
25B SER* 3.9 3.5 + - - -
26B ASP 4.6 1.0 + - - -
78B VAL* 4.9 5.0 - - - +
82B PRO* 5.3 1.0 - - - +
83B PHE* 2.3 97.0 + - + +
501B TXL 4.3 10.5 - - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS 3.1 20.2 - - - +
20B PHE 3.1 8.3 - - - +
21B TRP 2.9 0.4 - - - -
22B GLU* 1.1 81.0 - - + +
24B ILE* 1.3 56.9 - - + +
26B ASP* 2.5 31.5 - - - +
28B HIS* 5.0 3.8 - - - -
232B SER* 3.2 18.6 - - - +
236B SER* 5.4 2.7 - - - -
501B TXL 3.0 82.2 - - + +
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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