Contacts of the helix formed by residues 9 - 23 (chain B) in PDB entry 4TLG
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 SER 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASP 4.0 0.6 + - - -
8B LEU* 1.3 75.0 - - - +
10B PRO* 1.3 68.1 - - - +
11B GLN* 3.4 10.7 + - - +
12B GLN* 3.0 41.1 + - - +
13B GLN* 2.8 27.3 + - - +
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Residues in contact with PRO 10 (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 LEU 4.3 2.2 - - - +
9B SER* 1.3 86.9 - - - +
11B GLN* 1.3 56.7 + - - +
13B GLN* 3.3 9.7 + - + +
14B GLU* 2.9 29.8 + - - +
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Residues in contact with GLN 11 (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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9B SER* 3.1 9.6 + - - +
10B PRO* 1.3 79.9 - - - +
12B GLN* 1.3 59.6 + - + +
14B GLU* 3.4 6.7 + - - +
15B ALA* 2.9 28.3 + - + +
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Residues in contact with GLN 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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7B ASP 4.7 1.2 - - - +
8B LEU* 3.5 15.5 - - + +
9B SER* 3.0 40.5 + - - +
11B GLN* 1.3 76.6 - - + +
13B GLN* 1.3 60.1 + - - +
15B ALA* 3.6 8.4 - - - +
16B LEU* 2.9 28.9 + - - +
39B LEU* 5.4 0.5 - - - +
47B PHE* 3.8 46.9 - - + -
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Residues in contact with GLN 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 LEU* 4.1 10.2 - - + +
9B SER 2.8 12.4 + - - +
10B PRO* 3.4 14.6 - - + +
12B GLN* 1.3 77.4 - - - +
14B GLU* 1.3 57.1 + - - +
16B LEU* 3.3 10.4 + - - +
17B ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 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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10B PRO 2.9 16.1 + - - +
11B GLN* 3.6 8.1 - - - +
13B GLN* 1.3 72.4 - - - +
15B ALA* 1.3 60.6 + - - +
17B ALA* 3.1 8.6 + - - +
18B ARG* 2.8 39.1 + - + +
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Residues in contact with ALA 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* 2.9 19.7 + - + +
12B GLN* 3.6 6.3 - - - +
14B GLU* 1.3 74.5 - - - +
16B LEU* 1.3 57.8 + - - +
18B ARG* 4.6 3.1 - - - +
19B PHE* 2.8 32.3 + - - +
42B LEU* 4.7 2.9 - - + -
47B PHE* 4.0 33.2 - - + +
49B LEU* 3.6 15.8 - - + +
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Residues in contact with LEU 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 GLN 2.9 17.2 + - - +
13B GLN* 3.5 7.6 - - - +
14B GLU 3.2 0.2 - - - -
15B ALA* 1.3 72.3 - - - +
17B ALA* 1.3 66.1 + - - +
19B PHE* 3.5 1.0 + - + +
20B ARG* 3.0 24.5 + - - +
35B ASP* 3.8 38.4 - - + +
38B LEU* 3.8 37.0 - - + -
39B LEU* 4.5 16.6 - - + -
42B LEU* 4.0 19.2 - - + +
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Residues in contact with ALA 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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13B GLN 3.0 14.1 + - - +
14B GLU* 3.4 11.7 - - - +
16B LEU* 1.3 79.3 - - - +
18B ARG* 1.3 62.8 + - + +
20B ARG* 3.5 6.3 + - - +
21B GLU* 3.2 27.3 + - - +
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Residues in contact with ARG 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 GLU* 2.8 26.2 + - + +
15B ALA* 3.9 4.3 - - - +
17B ALA* 1.3 70.2 - - + +
19B PHE* 1.3 56.5 + - - +
21B GLU* 3.2 22.0 + - + +
22B ASN* 2.8 43.1 + - - +
49B LEU* 4.2 25.1 - - + -
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Residues in contact with PHE 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 ALA 2.8 22.2 + - - +
16B LEU 3.6 5.2 - - - +
18B ARG* 1.3 71.8 - - - +
20B ARG* 1.3 63.0 + - - +
22B ASN* 3.1 8.0 + - + +
23B LEU* 3.0 53.7 + - + +
38B LEU* 3.7 38.1 - - + -
41B TRP* 4.2 5.8 - - + -
42B LEU* 3.7 27.8 - - + -
49B LEU* 3.8 17.1 - - + +
52B SER* 3.7 22.9 - - - -
53B GLU* 3.6 33.0 - - + -
56B LEU* 4.1 10.3 - - + -
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Residues in contact with ARG 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 LEU* 3.0 20.5 + - - +
17B ALA* 3.7 6.3 - - - +
19B PHE* 1.3 76.2 - - - +
21B GLU* 1.3 61.7 + - - +
23B LEU* 3.3 15.0 + - - +
24B GLN* 3.6 9.2 + - - -
27B LEU* 5.9 5.1 - - + +
33B ALA 3.5 16.0 + - - -
34B ASP* 3.5 23.0 - - - +
35B ASP* 2.7 29.9 + - - +
38B LEU* 3.7 25.5 - - + +
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Residues in contact with GLU 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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17B ALA* 3.2 13.0 + - - +
18B ARG* 3.2 41.6 + - - +
20B ARG* 1.3 72.8 - - - +
22B ASN* 1.3 69.7 + - - +
23B LEU 3.1 2.5 + - - -
24B GLN* 3.4 21.3 + - - +
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Residues in contact with ASN 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 ARG* 2.8 25.8 + - - +
19B PHE* 3.1 8.0 + - + +
21B GLU* 1.3 82.3 - - - +
23B LEU* 1.3 58.5 + - + +
24B GLN 3.4 2.1 + - - -
25B ASP* 3.8 2.1 - - - +
49B LEU* 4.6 23.0 - - - +
53B GLU* 3.6 24.1 + - - +
57B ARG* 3.0 19.6 + - - -
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Residues in contact with LEU 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 PHE* 3.0 54.6 + - + +
20B ARG* 3.8 8.7 - - - +
21B GLU 3.1 0.8 - - - -
22B ASN* 1.3 75.8 - - + +
24B GLN* 1.3 65.9 + - - +
25B ASP* 3.2 4.0 - - - -
26B LEU* 2.9 40.3 + - + +
27B LEU* 4.0 3.7 + - - +
30B LEU* 6.0 2.7 - - + -
38B LEU* 3.7 13.9 - - + -
53B GLU* 4.0 26.7 - - + -
56B LEU* 3.7 19.7 - - + -
57B ARG* 3.9 8.3 - - + +
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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