Contacts of the helix formed by residues 7 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE 3.7 1.0 + - - -
6B GLN* 1.4 71.9 - - - +
8B GLU* 1.3 82.7 + - - +
10B LEU 3.2 0.7 + - - -
11B LEU* 2.8 64.9 + - + +
79B CYS* 3.1 26.9 + - - +
80B LYS* 2.8 25.7 + - - +
82B LEU* 2.9 18.6 + - + -
83B PRO 3.3 27.1 - - - +
84B ASN* 4.0 13.7 + - - -
86B VAL* 3.0 19.5 + - + +
88B ILE* 3.6 16.8 - - + -
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Residues in contact with GLU 8 (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 GLN* 3.3 6.5 + - + +
7B ARG* 1.3 104.0 + - - +
9B ALA* 1.4 64.2 + - - +
11B LEU* 3.9 7.4 - - + +
12B LYS* 3.3 25.8 + - - +
84B ASN* 3.5 6.9 - - - +
85B ASP* 3.1 47.0 + - - +
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Residues in contact with ALA 9 (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 ILE* 3.8 17.0 - - + -
6B GLN* 3.1 20.9 + - + +
8B GLU* 1.4 75.1 - - - +
10B LEU* 1.3 58.5 + - - +
12B LYS* 4.6 1.6 - - - +
13B PRO* 3.2 23.9 - - - +
57B VAL* 3.8 20.6 - - + +
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Residues in contact with LEU 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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3B PHE* 5.2 1.1 - - + -
5B ILE* 3.8 20.8 - - + +
6B GLN 3.1 9.0 + - - +
7B ARG 3.7 6.3 - - - +
9B ALA* 1.3 77.7 - - - +
11B LEU* 1.3 64.2 + - - +
13B PRO* 3.3 5.0 - - - +
14B LEU* 3.2 38.3 + - + +
35B LEU* 6.1 1.6 - - + -
42B LEU* 4.2 17.5 - - + -
44B LEU* 3.9 24.7 - - + -
75B LEU* 5.3 8.7 - - + -
79B CYS* 3.9 19.3 - - + -
88B ILE* 4.1 9.9 - - + -
90B ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 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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7B ARG* 2.8 58.8 + - - +
8B GLU* 3.4 7.4 + - + +
10B LEU* 1.3 73.6 - - - +
12B LYS* 1.4 55.8 - - - +
14B LEU* 4.3 2.2 - - + -
15B GLN* 2.9 70.5 + - + +
76B MET* 4.1 9.2 - - + +
79B CYS* 3.7 11.6 - - + -
80B LYS* 3.7 31.4 - - + +
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Residues in contact with LYS 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 GLU 3.3 12.7 + - - +
9B ALA* 4.6 1.6 - - - +
11B LEU* 1.4 77.8 - - - +
13B PRO* 1.4 68.3 - - + +
15B GLN* 3.9 9.0 + - - +
16B LEU* 3.5 26.0 + - + +
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Residues in contact with PRO 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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9B ALA 3.2 19.3 - - - +
10B LEU 3.3 7.9 - - - +
12B LYS* 1.4 87.5 - - + +
14B LEU* 1.4 55.3 + - - +
16B LEU* 3.3 10.1 + - + +
17B VAL* 2.8 40.5 + - - +
44B LEU* 3.9 11.9 - - + -
55B GLY* 4.0 27.1 - - - -
56B ARG 4.6 2.5 - - - +
57B VAL* 3.6 27.6 - - + -
230B GLU 5.7 0.4 - - - +
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Residues in contact with LEU 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 LEU* 3.2 28.4 + - + +
11B LEU* 3.7 4.0 - - + +
13B PRO* 1.4 77.0 - - - +
15B GLN* 1.3 52.7 + - - +
17B VAL* 3.7 1.9 - - + -
18B ALA* 2.8 39.8 + - + +
33B VAL* 4.3 18.6 - - + -
44B LEU* 3.8 22.8 - - + +
72B ALA 4.7 4.5 - - - +
75B LEU* 3.6 50.3 - - + +
76B MET* 3.6 20.0 - - + +
79B CYS* 4.0 13.9 - - + -
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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 LEU* 2.9 52.7 + - + +
12B LYS* 3.9 7.7 + - - +
14B LEU* 1.3 72.1 - - - +
16B LEU* 1.3 65.7 + - + +
18B ALA* 4.1 1.4 - - - +
19B GLY* 3.2 19.6 + - - -
76B MET* 3.9 23.1 - - + +
80B LYS* 3.3 28.6 + - - +
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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 LYS* 3.5 15.0 + - + +
13B PRO* 3.3 13.7 + - + +
15B GLN* 1.3 78.7 - - + +
17B VAL* 1.3 64.0 + - + +
19B GLY* 3.4 13.5 + - - -
20B VAL* 3.9 4.3 + - - +
53B LEU* 3.4 23.2 - - + +
203B GLU* 4.4 3.6 - - - +
206B ARG 5.9 1.6 - - - +
207B LEU* 3.9 27.1 - - + +
230B GLU* 5.6 6.7 - - + +
231B PHE* 5.1 12.8 - - + -
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Residues in contact with VAL 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 PRO 2.8 24.0 + - - +
14B LEU* 4.0 3.4 - - + +
16B LEU* 1.3 70.2 - - + +
18B ALA* 1.4 63.3 + - - +
20B VAL* 3.1 25.8 + - - +
21B VAL* 3.7 5.2 - - + +
33B VAL* 3.6 21.8 - - + -
44B LEU* 3.3 26.9 - - + +
45B THR* 3.6 7.2 - - - -
46B GLY* 3.4 26.5 - - - +
53B LEU* 3.7 21.3 - - + +
55B GLY* 3.9 11.4 - - - +
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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 LEU* 2.8 23.6 + - + +
17B VAL* 1.4 72.2 - - - +
19B GLY* 1.3 57.2 + - - +
21B VAL* 3.1 35.7 + - - +
72B ALA* 4.2 19.7 - - + +
73B ARG* 4.8 10.6 + - - +
76B MET* 3.7 32.1 - - + -
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Residues in contact with GLY 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 3.2 13.6 + - - -
16B LEU 3.7 7.0 - - - -
17B VAL 3.1 2.0 - - - -
18B ALA* 1.3 76.8 - - - +
20B VAL* 1.4 59.1 + - - +
21B VAL 3.4 2.5 - - - +
76B MET* 5.5 0.4 - - - -
203B GLU* 4.6 8.4 - - - +
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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