Contacts of the helix formed by residues 11 - 20 (chain B) in PDB entry 3UBT
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 GLY 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B SER 3.5 10.4 + - - -
9B GLY 3.4 2.2 - - - -
10B ALA* 1.3 80.5 - - - +
12B GLY* 1.3 66.8 + - - +
13B LEU 3.4 2.7 - - - -
14B ASP* 3.2 18.4 + - - +
15B LEU* 3.1 30.3 + - - +
38B TYR* 4.4 4.0 - - - -
42B HIS* 3.9 9.4 - - - -
286B PHE* 4.8 2.5 - - - -
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Residues in contact with GLY 12 (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 SER 4.7 2.2 + - - -
10B ALA 3.9 0.6 - - - -
11B GLY* 1.3 78.0 - - - +
13B LEU* 1.3 63.0 + - - +
15B LEU* 3.4 4.5 + - - +
16B GLY 3.3 13.9 + - - -
286B PHE* 4.3 20.0 - - - -
307B ALA* 4.4 9.8 - - - +
308B VAL 3.5 23.9 - - - +
310B VAL* 4.1 8.4 - - - -
313B ALA* 4.1 4.0 - - - +
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Residues in contact with LEU 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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5B SER* 5.6 1.1 - - - +
8B SER 5.8 0.6 + - - +
11B GLY 3.4 0.2 - - - -
12B GLY* 1.3 72.7 - - - +
14B ASP* 1.3 70.4 + - - +
16B GLY* 3.0 2.6 + - - -
17B PHE* 3.0 33.5 + - + -
66B ILE* 4.4 10.3 - - + -
67B GLY* 3.7 34.8 - - - +
107B LEU* 3.9 26.5 - - + -
108B ALA* 6.4 0.2 - - - -
109B GLU* 6.2 3.6 - - + +
157B PHE* 5.5 3.8 - - + -
308B VAL* 4.2 31.0 + - + +
313B ALA* 4.0 20.9 - - + -
316B ILE* 5.9 0.4 - - + -
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Residues in contact with ASP 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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5B SER* 2.9 26.7 + - - -
8B SER* 4.9 2.3 - - - +
11B GLY* 3.2 20.4 + - - +
13B LEU* 1.3 78.0 - - - +
15B LEU* 1.3 58.3 + - - +
17B PHE* 3.3 0.9 + - - -
18B GLN* 2.8 33.2 + - - +
24B ILE* 3.7 27.9 - - + +
38B TYR* 2.8 30.0 + - - -
42B HIS* 3.9 14.8 + - + +
66B ILE* 4.1 6.1 - - - +
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Residues in contact with LEU 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 GLY 3.1 10.0 + - - +
12B GLY 3.8 5.4 - - - +
14B ASP* 1.3 76.6 - - - +
16B GLY* 1.3 62.5 + - - +
18B GLN* 3.9 8.3 - - + +
19B LYS* 3.2 24.4 + - - +
41B ASN 5.4 3.4 - - - +
42B HIS* 3.9 19.3 - - + +
286B PHE* 3.9 32.3 - - + -
287B PRO* 4.2 16.8 - - + -
290B PHE* 4.2 12.3 - - + -
310B VAL* 3.9 25.4 - - + +
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Residues in contact with GLY 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 GLY 3.3 4.8 + - - -
13B LEU 3.0 6.9 + - - -
15B LEU* 1.3 79.5 - - - +
17B PHE* 1.3 62.0 + - - +
19B LYS* 3.3 14.0 + - - +
20B ALA* 3.3 8.8 + - - +
310B VAL* 3.5 25.0 - - - +
313B ALA* 3.7 3.1 - - - -
314B TYR* 3.6 25.0 - - - -
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Residues in contact with PHE 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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3B LEU* 3.6 23.1 - - + -
13B LEU* 3.0 28.5 + - + +
14B ASP 4.0 2.0 - - - +
16B GLY* 1.3 71.8 - - - +
18B GLN* 1.3 66.5 + - - +
20B ALA* 2.9 12.1 + - - +
21B GLY 3.3 0.5 + - - -
22B PHE* 3.1 36.6 + + + +
24B ILE* 4.5 1.8 - - + -
66B ILE* 3.5 33.0 - - + -
105B PHE* 4.0 16.2 - + - -
107B LEU* 3.6 30.1 - - + -
313B ALA 4.1 9.4 - - - -
317B ALA* 3.6 31.2 - - + -
320B ILE* 3.9 14.4 - - + -
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Residues in contact with GLN 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 ASP 2.8 19.0 + - - +
15B LEU* 3.9 9.0 - - + +
17B PHE* 1.3 77.2 - - - +
19B LYS* 1.3 68.3 + - - +
21B GLY* 3.1 14.4 + - - -
22B PHE 3.4 19.3 + - - +
23B ARG* 5.8 1.1 - - - -
24B ILE* 4.3 8.8 - - + +
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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 LEU 3.2 11.2 + - - +
16B GLY 3.4 10.5 - - - +
17B PHE 3.1 0.2 - - - -
18B GLN* 1.3 87.0 + - - +
20B ALA* 1.3 59.9 + - - +
21B GLY 3.3 0.7 + - - -
310B VAL* 4.7 15.8 - - + +
311B ASN* 4.9 11.0 + - - +
314B TYR* 3.5 38.7 + - + -
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Residues in contact with ALA 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 GLY 3.3 3.9 + - - +
17B PHE 2.9 11.4 + - - +
19B LYS* 1.3 78.3 - - - +
21B GLY* 1.3 58.0 + - - +
22B PHE* 3.6 6.7 - - + -
314B TYR* 3.9 15.3 - - + -
317B ALA* 3.6 28.3 - - + -
318B LYS* 4.2 14.9 - - + +
321B LYS* 3.3 23.1 - - + +
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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