Contacts of the strand formed by residues 16 - 21 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R LYS* 1.3 76.9 - - - +
17R VAL* 1.3 64.6 + - - +
28R ARG* 4.5 14.9 + - - +
29R GLY* 3.1 31.5 + - - +
30R ARG* 3.9 5.0 + - + +
72R PRO* 3.7 0.7 - - - +
73R THR* 2.7 59.1 + - + +
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Residues in contact with VAL 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R SER* 3.9 21.5 - - - -
15R LYS 3.8 9.0 - - - +
16R ASP* 1.3 82.4 - - - +
18R LEU* 1.3 60.0 + - - +
19R VAL* 4.3 10.8 - - + -
27R PHE 4.0 0.3 - - - +
28R ARG* 3.5 5.5 - - - +
29R GLY 2.9 29.2 + - - +
31R LEU* 4.1 13.7 - - + -
42R LEU* 3.7 30.7 - - + -
70R ILE* 4.2 16.2 - - + -
71R SER 3.6 7.4 - - - +
72R PRO* 3.9 13.2 - - + -
73R THR* 4.0 5.8 - - - -
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Residues in contact with LEU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R VAL* 1.3 74.8 - - - +
19R VAL* 1.3 60.0 + - - +
20R ILE* 3.9 16.4 + - + +
26R GLU* 3.3 35.7 - - + +
27R PHE 3.6 1.8 - - - +
28R ARG* 3.1 43.1 - - + +
69R ALA 3.9 0.3 - - - +
70R ILE* 3.2 6.9 - - - +
71R SER* 2.9 40.8 + - - +
73R THR* 5.4 1.1 - - - +
55S LYS* 6.3 0.2 - - + -
57S TYR* 3.7 31.9 - - + +
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Residues in contact with VAL 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R VAL* 4.3 11.0 - - + -
18R LEU* 1.3 76.3 - - - +
20R ILE* 1.3 61.1 + - - +
21R LEU* 3.7 12.1 + - + +
26R GLU* 3.0 6.6 - - - +
27R PHE* 2.8 40.9 + - + +
40R VAL* 4.3 16.4 - - + -
42R LEU* 3.9 25.6 - - + -
62R ILE* 4.5 9.6 - - + -
67R VAL* 3.8 34.1 - - + -
69R ALA 3.6 3.1 - - - +
70R ILE* 4.5 10.1 - - + -
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Residues in contact with ILE 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R LEU* 4.0 18.4 - - + +
19R VAL* 1.3 72.3 - - - +
21R LEU* 1.3 63.7 + - - +
24R GLY 6.5 0.4 - - - -
25R PHE 4.7 2.7 - - - +
26R GLU* 3.8 16.2 - - - +
67R VAL* 3.7 2.8 - - - -
68R LEU* 2.7 49.2 + - + +
69R ALA* 2.9 25.2 + - + +
71R SER* 5.7 1.3 - - - -
27S PHE* 5.0 0.2 - - + -
47S MET* 4.0 14.1 - - + -
55S LYS* 5.8 2.0 - - + +
57S TYR* 3.1 40.6 - - + +
60S ILE* 4.6 11.2 - - + -
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Residues in contact with LEU 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q LEU* 3.9 13.7 - - + -
19R VAL* 4.2 24.0 - - + +
20R ILE* 1.3 86.9 - - - +
22R LYS* 1.3 55.1 + - - +
23R LYS* 2.7 22.9 + - + +
24R GLY* 3.4 9.5 + - - -
25R PHE* 3.0 56.6 + - + +
27R PHE* 3.4 19.1 - - + -
62R ILE* 4.3 11.4 - - + -
66R ASN 3.6 16.2 - - - +
67R VAL* 4.2 8.5 - - + -
68R LEU* 4.3 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