Contacts of the helix formed by residues 4 - 20 (chain A) in PDB entry 4TMU
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 1.3 67.4 + - + +
6A VAL* 3.3 6.3 - - - +
7A TYR* 3.5 28.4 + - - +
8A SER* 3.2 27.0 + - - -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 1.3 80.3 - - - +
6A VAL* 1.3 65.1 + - + +
8A SER* 3.8 6.5 + - - -
9A GLN* 3.4 38.1 + - + +
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Residues in contact with VAL 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 ALA 4.6 4.7 - - - +
5A GLU* 1.3 82.6 - - + +
7A TYR* 1.3 88.3 + - + +
9A GLN* 3.6 8.6 - - - +
10A GLU* 3.2 22.9 + - - +
35A ASP* 4.4 11.2 - - - +
39A GLU* 3.0 37.9 - - + +
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Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 3.5 27.3 + - - +
6A VAL* 1.3 88.9 - - + +
8A SER* 1.3 54.0 + - - +
9A GLN 3.3 0.4 - - - -
10A GLU* 3.7 20.2 - - + +
11A THR* 2.7 42.2 + - - +
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Residues in contact with SER 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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4A ALA 3.2 16.8 + - - -
5A GLU* 3.8 11.3 - - - -
6A VAL 3.4 0.2 - - - -
7A TYR* 1.3 77.4 - - - +
9A GLN* 1.3 67.4 + - - +
11A THR* 3.3 8.8 + - - -
12A LEU* 3.1 27.6 + - - +
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Residues in contact with GLN 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 GLU* 3.4 29.0 + - + +
6A VAL* 3.6 12.8 - - - +
8A SER* 1.3 78.8 - - - +
10A GLU* 1.3 58.6 + - - +
12A LEU* 3.1 26.3 + - - +
13A ALA* 2.9 26.5 + - - +
35A ASP* 5.5 2.5 - - - +
38A LEU* 3.9 44.8 - - + +
39A GLU* 5.8 4.5 - - + -
63A VAL* 4.0 14.4 - - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL 3.2 11.7 + - - +
7A TYR* 3.3 22.2 + - + +
9A GLN* 1.3 76.0 - - - +
11A THR* 1.3 61.6 + - - +
13A ALA* 3.3 6.8 + - - +
14A LYS* 2.8 31.0 + - + +
26A PHE* 4.4 16.2 - - + -
31A ALA* 3.5 23.7 - - - +
35A ASP* 2.7 38.5 + - - +
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 2.7 25.5 + - - +
8A SER* 3.4 9.4 - - - -
10A GLU* 1.3 76.9 - - - +
12A LEU* 1.3 63.5 + - + +
14A LYS* 3.2 10.2 + - + +
15A GLN* 3.1 22.0 + - + +
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Residues in contact with LEU 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 SER 3.1 15.3 + - - +
9A GLN* 3.1 33.0 + - - +
11A THR* 1.3 78.6 - - + +
13A ALA* 1.3 61.9 + - - +
15A GLN* 3.3 8.6 + - + +
16A VAL* 3.2 24.9 + - - +
63A VAL* 4.0 23.6 - - + +
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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 GLN 2.9 12.7 + - - +
10A GLU* 3.5 11.7 - - - +
12A LEU* 1.3 73.1 - - - +
14A LYS* 1.3 56.2 + - - +
16A VAL* 3.1 4.7 + - - +
17A LEU* 2.8 33.6 + - - +
26A PHE* 3.8 17.0 - - + -
34A ILE* 3.9 15.3 - - + -
38A LEU* 4.3 5.6 - - + -
59A ILE* 3.7 18.0 - - + +
63A VAL* 3.8 10.5 - - + +
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Residues in contact with LYS 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 GLU* 2.8 19.3 + - + +
11A THR* 3.2 10.1 + - + +
13A ALA* 1.3 76.2 - - - +
15A GLN* 1.3 62.7 + - - +
17A LEU* 3.2 8.0 + - + +
18A GLN* 2.9 38.8 + - - +
24A GLN 2.8 22.7 + - - +
25A GLN* 2.7 42.2 + - - +
26A PHE* 3.8 22.1 - - + +
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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 THR* 3.1 9.8 + - + +
12A LEU* 3.6 12.3 - - + +
14A LYS* 1.3 78.6 - - - +
16A VAL* 1.3 54.1 + - + +
18A GLN* 3.7 14.7 - - - +
19A GLU* 2.6 76.4 + - + +
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Residues in contact with VAL 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 LEU 3.2 13.5 + - - +
13A ALA 3.1 8.6 + - - +
15A GLN* 1.3 75.2 - - + +
17A LEU* 1.3 66.8 + - - +
19A GLU* 4.8 1.1 - - - -
20A THR* 3.1 42.4 + - + -
21A PHE* 3.6 15.7 + - + -
59A ILE* 4.3 11.4 - - + -
62A LEU* 3.9 36.1 - - + +
63A VAL* 4.0 16.2 - - + -
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Residues in contact with LEU 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 2.8 16.3 + - - +
14A LYS* 3.2 15.2 + - + +
16A VAL* 1.3 72.3 - - - +
18A GLN* 1.3 57.6 + - - +
21A PHE* 3.4 9.4 - - + +
22A GLY 3.2 9.9 + - - -
23A TYR* 3.1 66.4 + - + +
24A GLN 3.8 4.5 - - - +
25A GLN 3.8 39.7 - - - +
26A PHE* 3.8 20.6 - - + +
30A GLN* 5.5 3.8 - - - +
55A LEU* 4.4 6.3 - - + -
59A ILE* 3.8 23.2 - - + +
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Residues in contact with GLN 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 LYS* 2.9 40.3 + - - +
15A GLN* 3.7 17.1 - - - +
17A LEU* 1.3 76.0 - - + +
19A GLU* 1.3 66.4 + - + +
22A GLY* 3.1 25.3 + - - -
23A TYR 3.2 20.0 - - - +
24A GLN* 3.2 38.1 + - - +
25A GLN* 4.7 0.4 + - - -
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Residues in contact with GLU 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* 2.6 57.3 + - + +
16A VAL* 4.8 0.2 - - - -
18A GLN* 1.3 79.2 - - + +
20A THR* 1.3 65.1 + - + +
22A GLY* 4.9 0.3 + - - -
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Residues in contact with THR 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 VAL* 3.1 31.0 + - + +
19A GLU* 1.3 81.0 - - + +
21A PHE* 1.3 85.9 + - - +
22A GLY 3.5 0.6 + - - -
62A LEU* 4.1 12.3 - - + +
88A ASN* 3.5 36.0 - - - +
90A VAL* 4.1 8.0 - - + +
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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