Contacts of the strand formed by residues 16 - 21 (chain G) in PDB entry 1H64
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 ASP 16 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G LYS* 1.3 75.7 - - - +
17G VAL* 1.3 67.1 + - - +
28G ARG* 4.6 8.5 + - - +
29G GLY* 3.2 29.2 + - - +
30G ARG* 4.4 3.8 - - + +
72G PRO* 3.8 2.1 - - - +
73G THR* 2.5 44.6 + - - +
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Residues in contact with VAL 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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9G ILE* 6.4 0.2 - - + -
12G SER* 4.0 25.6 - - - +
15G LYS 3.7 9.0 - - - +
16G ASP* 1.3 82.6 - - - +
18G LEU* 1.3 58.9 + - - +
19G VAL* 4.3 10.9 - - + +
27G PHE 4.1 0.2 - - - +
28G ARG* 3.4 7.1 - - - +
29G GLY 2.9 35.3 + - - +
31G LEU* 4.2 13.9 - - + -
42G LEU* 3.7 23.8 - - + -
70G ILE* 4.4 13.9 - - + -
71G SER 3.5 8.5 - - - +
72G PRO* 4.1 8.1 - - + -
73G THR* 4.1 6.5 - - - +
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Residues in contact with LEU 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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55A LYS* 3.7 17.7 - - - +
57A TYR* 4.2 11.7 - - + -
17G VAL* 1.3 74.3 - - - +
19G VAL* 1.3 60.7 + - - +
20G ILE* 3.8 25.4 + - + +
26G GLU* 3.3 34.5 - - + +
27G PHE 3.6 8.3 - - - +
28G ARG* 3.2 36.3 - - + +
48G ILE* 5.0 1.6 - - + -
70G ILE* 3.3 6.1 - - - +
71G SER* 2.9 39.1 + - - +
73G THR* 4.0 12.1 - - + -
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Residues in contact with VAL 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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17G VAL* 4.3 13.2 - - + -
18G LEU* 1.3 74.4 - - - +
20G ILE* 1.3 60.1 + - - +
21G LEU* 3.7 9.1 + - + +
26G GLU* 3.4 5.3 - - - -
27G PHE* 2.8 40.6 + - + +
40G VAL* 4.2 17.0 - - + -
42G LEU* 4.0 22.2 - - + -
62G ILE* 4.2 13.5 - - + -
67G VAL* 3.7 33.2 - - + -
69G ALA 3.7 3.1 - - - +
70G ILE* 4.4 11.0 - - + -
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Residues in contact with ILE 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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27A PHE* 4.9 1.1 - - + -
47A MET* 4.2 11.7 - - + -
55A LYS* 5.3 1.1 - - - -
57A TYR* 3.6 30.7 - - + +
60A ILE* 4.3 13.9 - - + -
18G LEU* 3.8 27.8 - - + +
19G VAL* 1.3 71.2 - - - +
21G LEU* 1.3 65.4 + - - +
24G GLY 6.4 0.2 - - - -
25G PHE 4.5 0.7 - - - +
26G GLU* 3.9 17.5 - - + +
67G VAL* 3.7 3.3 - - - +
68G LEU* 2.7 48.2 + - + -
69G ALA* 2.8 25.7 + - + +
71G SER* 5.9 1.6 - - - +
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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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68F LEU* 3.8 21.8 - - + -
19G VAL* 4.3 7.9 - - + +
20G ILE* 1.3 85.7 - - - +
22G LYS* 1.3 66.1 + - - +
23G LYS* 3.4 2.1 + - + +
24G GLY* 3.7 9.2 + - - -
25G PHE* 3.1 58.9 + - + +
26G GLU* 4.8 0.2 - - - -
27G PHE* 3.3 33.7 - - + -
62G ILE* 4.2 11.0 - - + -
66G ASN* 3.6 14.8 - - + +
67G VAL* 4.2 17.3 - - + -
68G LEU* 4.1 4.8 - - - +
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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