Contacts of the helix formed by residues 7 - 21 (chain G) in PDB entry 4U7B
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 ASN 7 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G VAL 4.1 0.6 + - - -
6G PRO* 1.3 77.4 - - - +
8G LYS* 1.3 75.0 + - - +
9G GLU* 3.0 22.1 + - - +
10G GLN* 2.8 40.9 + - + +
11G THR* 2.8 33.4 + - - -
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Residues in contact with LYS 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASN* 1.3 77.7 + - - +
9G GLU* 1.3 66.6 + - - +
11G THR* 4.0 5.5 - - - -
12G ARG* 2.9 55.8 + - - +
21H T 5.8 1.1 - - - +
39I T 5.5 0.7 - - - -
40I C 4.2 25.4 + - - +
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Residues in contact with GLU 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASN* 2.8 21.8 + - - +
8G LYS* 1.3 82.3 - - - +
10G GLN* 1.3 65.2 + - + +
12G ARG* 3.2 7.8 + - - +
13G THR* 3.1 23.3 + - - -
60G VAL* 3.6 26.6 - - + +
61G ASP* 2.8 33.9 - - - +
62G ASP* 5.0 1.7 - - - +
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Residues in contact with GLN 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 3.3 38.9 - - - +
6G PRO 4.0 0.9 - - - +
7G ASN* 2.8 42.7 + - + +
9G GLU* 1.3 76.4 - - + +
11G THR* 1.3 59.7 + - - +
13G THR* 3.4 11.9 - - - +
14G VAL* 3.3 25.5 + - - +
36G PHE* 6.6 0.2 - - - -
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Residues in contact with THR 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G PRO* 5.1 3.3 - - - +
7G ASN 2.8 30.1 + - - -
8G LYS* 4.0 7.4 - - - +
10G GLN* 1.3 70.7 - - - +
12G ARG* 1.3 66.1 + - + +
14G VAL* 3.0 24.4 + - - +
15G LEU* 3.1 17.4 + - + +
32G LEU* 4.5 14.8 - - + -
36G PHE* 5.4 8.3 - - - -
40G VAL* 5.4 4.3 - - - +
41G PRO* 4.0 33.1 - - + +
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Residues in contact with ARG 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LYS* 2.9 42.5 + - - +
9G GLU* 3.2 10.0 + - - +
11G THR* 1.3 80.4 - - + +
13G THR* 1.3 61.5 + - - +
15G LEU* 3.3 13.1 + - + +
16G ILE* 3.2 25.8 + - - +
49G TRP* 3.6 43.9 - - + +
53G PHE* 4.3 1.8 - - + -
60G VAL* 3.2 34.3 + - + -
61G ASP* 4.6 0.2 - - - +
62G ASP* 2.7 34.1 + - - -
20H A 3.9 4.8 + - - -
21H T 2.7 29.3 + - - +
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Residues in contact with THR 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLU 3.1 12.6 + - - -
10G GLN* 3.4 15.9 - - - +
12G ARG* 1.3 76.9 - - - +
14G VAL* 1.3 66.2 + - + +
16G ILE* 3.1 20.7 + - - +
17G PHE* 3.2 12.3 + - + +
60G VAL* 4.2 14.1 - - - +
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Residues in contact with VAL 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLN 3.3 13.9 + - - +
11G THR* 3.0 10.8 + - - +
13G THR* 1.3 79.9 - - + +
15G LEU* 1.3 57.8 + - + +
17G PHE* 3.1 15.4 + - + +
18G CYS* 2.9 39.8 + - - -
32G LEU* 3.6 28.0 - - + -
36G PHE* 4.8 18.4 - - + -
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G THR* 3.1 23.9 + - + +
12G ARG* 3.6 15.0 - - + +
13G THR 3.2 0.2 - - - -
14G VAL* 1.3 76.6 - - + +
16G ILE* 1.3 63.2 + - - +
18G CYS* 4.1 3.4 - - - +
19G PHE* 3.2 22.9 + - - +
28G SER* 5.2 6.7 - - - -
32G LEU* 3.6 32.8 - - + -
41G PRO* 6.1 1.1 - - + -
45G THR 5.0 0.2 - - - -
46G CYS* 3.8 36.1 - - - +
49G TRP* 4.0 22.2 - - + -
50G PHE* 3.6 15.3 - - + -
53G PHE* 3.3 15.4 - - + -
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG 3.2 14.5 + - - +
13G THR* 3.1 12.0 + - - +
15G LEU* 1.3 75.5 - - - +
17G PHE* 1.3 59.9 + - - +
19G PHE* 3.4 4.8 + - - +
20G HIS* 3.0 40.2 + - + +
53G PHE* 3.2 37.5 - - + -
58G PHE* 3.5 49.6 - - + +
59G ASP 5.9 0.2 - - - +
60G VAL* 5.7 6.1 - - + -
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Residues in contact with PHE 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G THR* 3.2 9.9 + - + +
14G VAL* 3.2 20.9 - - + +
16G ILE* 1.3 78.0 - - - +
18G CYS* 1.3 71.8 + - - +
20G HIS* 3.1 8.8 + - + +
21G LEU* 3.0 52.0 + - + +
31G MET* 6.3 2.7 - - + -
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Residues in contact with CYS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 2.9 32.0 + - - +
15G LEU* 4.5 4.7 - - - +
17G PHE* 1.3 81.3 - - - +
19G PHE* 1.3 62.7 + - - +
21G LEU* 3.1 16.4 + - - +
23G LYS* 3.1 28.4 + - + +
28G SER* 3.2 41.5 - - - +
31G MET* 4.5 22.4 - - - -
32G LEU* 5.6 0.4 - - - -
50G PHE* 4.4 1.6 - - + -
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Residues in contact with PHE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU 3.2 19.8 + - - +
16G ILE 3.5 4.0 - - - +
17G PHE 3.3 0.4 - - - -
18G CYS* 1.3 78.0 - - - +
20G HIS* 1.3 74.5 + + - +
22G LYS* 3.1 20.4 + - - +
23G LYS 4.8 1.1 - - - -
50G PHE* 3.7 34.0 - + + -
53G PHE* 3.9 35.9 - + + -
54G LYS* 3.9 36.1 - - + -
58G PHE* 4.0 16.8 - + - -
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Residues in contact with HIS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.0 27.4 + - + +
17G PHE* 3.1 8.5 + - + +
19G PHE* 1.3 92.3 - + - +
21G LEU* 1.3 63.1 + - + +
22G LYS* 3.1 16.2 + - - +
58G PHE* 3.5 27.2 - + - -
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G PHE* 3.0 51.3 + - + +
18G CYS* 3.1 11.4 + - - +
20G HIS* 1.3 77.9 - - + +
22G LYS* 1.3 69.5 + - - +
23G LYS* 3.0 34.7 + - + +
31G MET* 5.8 2.9 - - + -
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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