Contacts of the strand formed by residues 9 - 16 (chain G) in PDB entry 4HOK
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 TYR 9 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 3.2 9.9 - - - +
5G VAL* 2.8 50.6 + - + -
6G GLY* 4.8 2.7 - - - -
8G LYS* 1.3 109.9 + - + +
10G ARG* 1.3 60.4 + - - +
27G ALA 2.7 20.6 - - - +
28G ASN* 3.5 23.9 + - + -
29G ILE* 5.6 1.6 - - - -
35G VAL* 4.0 25.1 - - + -
37G ILE* 4.0 8.3 - - + -
69G LYS* 4.1 23.0 + - + +
70G TRP* 4.1 23.3 - + + -
81G VAL* 4.1 20.0 - - + -
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Residues in contact with ARG 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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2G GLU* 4.4 25.8 - - + +
3G LEU 3.9 9.4 - - - +
4G ARG* 4.5 6.7 - - + +
9G TYR* 1.3 73.3 - - - +
11G LEU* 1.3 83.4 + - - +
12G GLY* 3.2 13.3 + - - -
13G ARG 5.3 0.4 - - - +
26G GLY* 3.1 23.4 - - - -
27G ALA* 2.8 14.0 + - + +
29G ILE* 4.2 23.5 - - + +
37G ILE* 4.5 1.6 - - - -
242M LYS* 5.9 4.6 - - - +
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Residues in contact with LEU 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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2G GLU* 5.9 0.5 - - - -
3G LEU* 3.0 51.2 + - + +
4G ARG* 4.7 0.4 - - - +
5G VAL* 5.1 2.6 - - + +
9G TYR 4.0 1.2 + - - -
10G ARG* 1.3 87.7 + - - +
12G GLY* 1.3 65.6 + - - +
24G TYR* 3.3 36.8 - - + -
25G LEU 4.3 0.9 - - - -
37G ILE* 3.8 28.6 - - + +
39G LEU* 4.0 11.4 - - + -
238M GLU* 5.9 0.2 - - + -
239M VAL* 3.3 34.8 - - + -
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Residues in contact with GLY 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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10G ARG* 3.2 20.4 + - - -
11G LEU* 1.3 80.2 - - - +
13G ARG* 1.3 65.0 + - - +
24G TYR* 3.7 12.5 - - - -
25G LEU* 2.8 24.2 + - - +
26G GLY* 4.7 1.3 - - - -
239M VAL* 5.7 0.5 - - - +
242M LYS* 5.2 2.7 - - - -
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Residues in contact with ARG 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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99E LYS* 6.0 6.7 - - - +
101E SER* 3.3 37.6 + - - +
103E LYS* 5.7 4.0 - - - +
289E ASP* 3.7 16.2 + - - -
292E MET* 4.7 10.9 - - - +
10G ARG* 5.3 0.6 - - - +
12G GLY* 1.3 72.8 - - - -
14G LYS* 1.3 69.5 + - - +
15G ILE* 2.9 30.4 - - + +
24G TYR* 3.8 0.2 - - - -
25G LEU* 2.9 43.4 + - + +
34G GLU* 5.4 1.6 + - - -
242M LYS* 3.7 33.4 - - - +
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Residues in contact with LYS 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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13G ARG* 1.3 86.1 + - - +
15G ILE* 1.3 61.9 + - - +
16G GLY 4.1 7.6 - - - +
17G SER* 4.0 12.2 + - - -
22G ASP* 3.3 35.8 + - - +
23G ILE 3.6 5.8 - - - +
24G TYR* 3.2 35.3 - - + +
231M LYS* 4.3 13.7 - - - +
239M VAL* 5.8 1.3 - - + -
242M LYS* 5.6 0.2 - - - +
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Residues in contact with ILE 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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292E MET* 4.8 9.6 - - + -
293E LEU* 3.3 53.6 - - + +
294E LYS* 3.4 6.8 - - - +
13G ARG* 2.9 32.3 - - + +
14G LYS* 1.3 74.2 - - - +
16G GLY* 1.3 58.0 + - - +
23G ILE* 2.7 22.9 + - + +
24G TYR 4.1 2.7 - - - +
25G LEU* 3.0 34.8 - - + +
36G ALA* 5.0 0.4 - - + -
84G LEU* 3.7 21.1 - - + -
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Residues in contact with GLY 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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293E LEU* 5.2 1.6 - - - -
294E LYS* 3.1 18.4 - - - -
14G LYS* 3.9 7.0 - - - +
15G ILE* 1.3 81.4 - - - +
17G SER* 1.3 67.2 + - - -
22G ASP* 3.4 5.5 - - - +
23G ILE* 2.9 32.6 + - - +
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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