Contacts of the helix formed by residues 7 - 20 (chain A) in PDB entry 4TR8
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 ARG 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE 3.7 0.8 + - - -
6A GLN* 1.3 71.8 - - - +
8A GLU* 1.4 91.1 + - - +
10A LEU* 3.3 0.7 + - - +
11A LEU* 2.9 49.2 + - + +
79A CYS* 3.2 27.3 + - - +
80A LYS* 2.7 30.9 + - - +
82A LEU* 3.0 27.3 + - + -
83A PRO 3.4 12.6 - - - -
84A ASN* 3.5 17.4 + - - -
86A VAL* 2.8 24.6 + - + +
88A ILE* 3.7 17.9 - - + -
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Residues in contact with GLU 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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6A GLN* 3.3 6.5 + - + +
7A ARG* 1.4 104.2 + - - +
9A ALA* 1.4 64.9 + - - +
11A LEU* 4.0 7.8 - - + +
12A LYS* 3.3 25.1 + - - +
84A ASN* 3.5 5.9 - - - +
85A ASP* 2.9 48.0 + - - +
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Residues in contact with ALA 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 ILE* 3.8 17.9 - - + -
6A GLN* 3.1 21.6 + - + +
8A GLU* 1.4 76.1 - - - +
10A LEU* 1.3 57.0 + - - +
12A LYS* 4.4 2.0 - - - +
13A PRO* 3.2 23.7 - - - +
57A VAL* 3.8 19.2 - - + +
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Residues in contact with LEU 10 (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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3A PHE* 4.8 3.6 - - + -
5A ILE* 3.7 24.1 - - + +
6A GLN 3.1 6.7 + - - +
7A ARG* 3.7 7.2 - - - +
9A ALA* 1.3 78.5 - - - +
11A LEU* 1.3 64.8 + - - +
13A PRO* 3.3 7.3 - - - +
14A LEU* 3.2 37.4 + - + +
35A LEU* 5.6 0.9 - - + -
42A LEU* 4.1 20.0 - - + -
44A LEU* 3.9 24.5 - - + -
75A LEU* 5.3 6.7 - - + -
79A CYS* 3.9 19.5 - - + -
88A ILE* 4.2 8.3 - - + -
90A ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 11 (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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7A ARG* 2.9 52.1 + - - +
8A GLU* 3.5 6.9 + - - +
10A LEU* 1.3 75.5 - - - +
12A LYS* 1.3 56.5 + - - +
14A LEU* 4.3 3.1 - - + -
15A GLN* 2.9 67.8 + - + +
76A MET* 4.2 9.4 - - + +
79A CYS* 3.9 11.6 - - + -
80A LYS* 3.9 32.3 - - + +
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Residues in contact with LYS 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 GLU 3.3 14.3 + - - +
9A ALA* 4.4 1.8 - - - +
10A LEU 3.3 0.6 - - - -
11A LEU* 1.3 79.1 - - - +
13A PRO* 1.4 69.4 - - + +
15A GLN* 3.7 8.8 + - - +
16A LEU* 3.7 24.0 + - + +
210A GLU* 6.4 0.6 - - - +
230A GLU* 5.4 11.7 - - - +
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Residues in contact with PRO 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 ALA 3.2 22.4 - - - +
10A LEU 3.3 7.6 - - - +
12A LYS* 1.4 92.2 - - + +
14A LEU* 1.4 57.3 + - - +
16A LEU* 3.3 8.4 + - + +
17A VAL* 2.9 34.3 + - - +
44A LEU* 3.8 26.9 - - + -
55A GLY* 4.1 21.5 - - - -
56A ARG 4.4 4.9 - - - +
57A VAL* 4.3 13.9 - - + -
230A GLU 5.5 0.4 - - - +
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Residues in contact with LEU 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 LEU* 3.2 29.6 + - + +
11A LEU* 3.9 3.8 - - - +
13A PRO* 1.4 75.6 - - - +
15A GLN* 1.3 56.9 + - - +
17A VAL* 4.6 1.6 - - + +
18A ALA* 2.8 39.5 + - + +
33A VAL* 4.4 17.5 - - + -
44A LEU* 4.0 22.4 - - + +
72A ALA 4.5 10.8 - - - +
75A LEU* 3.9 29.8 - - + +
76A MET* 3.6 33.2 - - + +
79A CYS* 4.2 14.4 - - + -
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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 LEU* 2.9 53.4 + - + +
12A LYS* 4.2 4.4 - - - +
14A LEU* 1.3 71.2 - - - +
16A LEU* 1.3 65.0 + - + +
18A ALA* 4.0 1.0 - - - +
19A GLY* 3.1 20.3 + - - -
76A MET* 3.8 24.0 - - - +
80A LYS* 3.9 30.3 - - - +
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Residues in contact with LEU 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 LYS* 3.7 23.2 + - + +
13A PRO* 3.3 9.3 + - + +
15A GLN* 1.3 79.6 - - + +
17A VAL* 1.3 63.0 + - + +
19A GLY* 3.2 14.1 + - - -
20A VAL* 3.8 4.9 + - - +
53A LEU* 3.4 22.8 - - + +
203A GLU* 4.3 6.1 - - - +
206A ARG* 5.2 10.5 - - + +
207A LEU* 3.7 27.4 - - + +
209A THR* 6.1 0.4 - - - +
231A PHE* 5.9 4.7 - - + -
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Residues in contact with VAL 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 PRO 2.9 21.5 + - - +
14A LEU* 4.0 3.1 - - + +
16A LEU* 1.3 76.7 - - + +
18A ALA* 1.3 61.7 + - - +
19A GLY 3.2 0.7 + - - -
20A VAL* 3.3 22.0 + - - +
21A VAL* 3.7 4.7 - - - +
33A VAL* 3.7 19.1 - - + -
44A LEU* 3.4 25.1 - - + +
45A THR 3.5 7.6 - - - -
46A GLY* 3.2 30.5 - - - +
53A LEU* 3.8 18.4 - - + +
55A GLY* 3.6 19.1 - - - +
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Residues in contact with ALA 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 LEU* 2.8 24.6 + - + +
17A VAL* 1.3 72.6 - - - +
19A GLY* 1.3 56.3 + - - +
21A VAL* 3.1 35.5 + - - +
72A ALA* 4.1 27.6 - - + +
73A ARG* 4.8 2.9 - - - +
76A MET* 3.9 24.5 - - + -
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Residues in contact with GLY 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 3.1 14.9 + - - -
16A LEU 3.6 6.5 - - - -
17A VAL 3.2 1.2 - - - -
18A ALA* 1.3 76.7 - - - +
20A VAL* 1.4 59.7 + - - +
21A VAL 3.7 3.1 + - - +
76A MET* 5.5 0.8 - - - -
199A LYS* 6.1 0.3 - - - -
203A GLU* 5.2 5.3 - - - +
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Residues in contact with VAL 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 LEU 4.1 5.8 - - - +
17A VAL 3.3 14.1 + - - +
19A GLY* 1.4 75.3 - - - +
21A VAL* 1.3 62.5 + - - +
22A GLU* 3.5 0.7 + - - +
46A GLY 3.6 29.4 - - - +
47A THR* 4.0 3.4 - - - +
48A ASP* 3.5 26.2 + - - +
51A VAL* 4.0 19.1 - - + -
53A LEU* 4.1 18.8 - - + +
199A LYS* 5.7 5.7 + - - +
203A GLU* 3.7 39.0 - - + +
233A PHE* 6.1 0.2 - - + -
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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