Contacts of the helix formed by residues 4 - 17 (chain G) in PDB entry 3F5O
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 MET 4 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G THR* 1.3 63.8 + - + +
6G GLN* 3.4 8.1 - - - +
7G SER* 3.4 26.7 + - - +
8G LEU* 3.0 41.3 + - + +
33G ALA* 4.5 9.0 - - + +
34G ALA* 6.1 1.6 - - - -
73G LEU* 4.0 29.2 - - + +
74G CYS* 3.5 33.4 - - + -
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Residues in contact with THR 5 (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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4G MET* 1.3 75.9 - - + +
6G GLN* 1.3 70.9 + - - +
9G ARG* 2.9 51.9 + - - +
30G LEU* 3.7 18.6 - - + +
32G SER* 4.8 3.1 - - - -
33G ALA* 3.8 34.3 - - + +
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Residues in contact with GLN 6 (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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4G MET 3.4 5.2 - - - +
5G THR* 1.3 86.8 + - - +
7G SER* 1.3 62.3 + - - +
9G ARG* 3.5 20.7 + - - +
10G GLU* 3.3 25.8 + - - +
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Residues in contact with SER 7 (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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4G MET* 3.4 32.2 + - - +
5G THR 3.2 0.4 - - - -
6G GLN* 1.3 78.5 - - - +
8G LEU* 1.3 62.5 + - - +
10G GLU* 3.1 25.4 + - - +
11G VAL* 3.2 16.6 + - - +
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Residues in contact with LEU 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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4G MET* 3.0 24.1 + - + +
7G SER* 1.3 73.9 - - - +
9G ARG* 1.3 66.9 + - - +
11G VAL* 3.2 19.2 + - + +
12G ILE* 3.0 28.0 + - + +
30G LEU* 3.8 22.2 - - + -
33G ALA* 3.9 12.1 - - + -
38G VAL* 3.7 30.5 - - + -
70G MET* 3.9 33.7 - - + +
73G LEU* 4.4 11.7 - - + -
74G CYS* 3.8 15.5 - - - -
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Residues in contact with ARG 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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5G THR* 2.9 52.3 + - - +
6G GLN* 3.7 20.3 - - - +
7G SER 3.3 0.2 - - - -
8G LEU* 1.3 77.2 - - - +
10G GLU* 1.3 56.3 + - + +
12G ILE* 3.3 8.5 + - + +
13G LYS* 2.9 28.4 + - - +
30G LEU* 4.1 25.3 + - + +
31G VAL 5.8 2.2 + - - -
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Residues in contact with GLU 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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6G GLN 3.3 14.3 + - - +
7G SER* 3.1 17.5 + - - +
9G ARG* 1.3 74.0 - - + +
11G VAL* 1.3 61.6 + - + +
13G LYS* 3.3 11.9 + - + +
14G ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 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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7G SER 3.2 14.5 + - - +
8G LEU* 3.2 25.3 + - + +
10G GLU* 1.3 76.7 - - + +
12G ILE* 1.3 62.9 + - - +
14G ALA* 3.1 9.8 + - - +
15G MET* 3.0 25.8 + - - +
70G MET* 4.8 4.7 - - + -
73G LEU* 4.8 1.3 - - + -
149G UOC 4.0 24.0 - - + -
1001G P6G 3.3 46.4 - - - +
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Residues in contact with ILE 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 LEU 3.0 18.1 + - - +
9G ARG* 3.7 9.9 - - + +
10G GLU 3.3 0.2 - - - -
11G VAL* 1.3 76.4 - - - +
13G LYS* 1.3 63.6 + - - +
15G MET* 3.0 18.8 + - + +
16G THR* 3.1 22.7 + - + +
25G LEU 5.2 1.6 - - - +
26G GLY 4.9 0.9 - - - +
28G ILE* 3.7 47.1 - - + +
29G THR 4.3 0.2 - - - -
30G LEU* 3.8 41.1 - - + +
40G CYS* 4.5 5.6 - - - -
70G MET* 4.4 12.6 - - + -
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Residues in contact with LYS 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 ARG 2.9 13.6 + - - +
10G GLU* 3.6 12.8 - - + +
12G ILE* 1.3 75.9 - - - +
14G ALA* 1.3 61.5 + - - +
16G THR* 2.8 31.9 + - - +
17G LYS* 3.4 22.2 + - + +
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Residues in contact with ALA 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 GLU 2.9 13.9 + - - +
11G VAL* 3.1 11.6 + - - +
13G LYS* 1.3 76.0 - - - +
15G MET* 1.3 61.1 + - - +
17G LYS* 3.6 10.8 + - - +
18G ALA* 3.2 17.7 + - - +
1001G P6G 3.4 29.7 - - - +
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Residues in contact with MET 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 VAL* 3.0 19.4 + - - +
12G ILE* 3.0 12.8 + - - +
14G ALA* 1.3 74.6 - - - +
16G THR* 1.3 65.0 + - - +
18G ALA* 3.2 10.3 + - - +
22G GLU* 3.3 30.3 - - + +
23G ARG* 3.3 21.8 - - - -
25G LEU* 3.3 33.9 - - + +
26G GLY* 4.5 1.3 - - - -
28G ILE* 4.9 3.1 - - - -
66G ASN* 3.1 25.4 - - + +
70G MET* 4.1 20.2 - - + -
1001G P6G 3.5 36.1 - - - +
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Residues in contact with THR 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 ILE* 3.1 19.2 + - + +
13G LYS* 2.8 25.8 + - - +
15G MET* 1.3 75.9 - - - +
17G LYS* 1.3 61.9 + - - +
18G ALA 3.6 2.9 + - - +
23G ARG* 5.0 4.9 - - - +
26G GLY* 3.0 37.5 - - - +
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Residues in contact with LYS 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 LYS* 3.6 32.3 - - + +
14G ALA* 3.8 9.9 - - - +
15G MET 3.2 0.4 - - - -
16G THR* 1.3 81.1 + - - +
18G ALA* 1.3 66.4 + - - +
19G ARG* 3.7 5.0 + - - +
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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