Contacts of the strand formed by residues 85 - 89 (chain C) in PDB entry 2HHL
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 GLU 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 5.0 0.7 - - - +
21C VAL* 3.9 17.2 - - - +
22C THR 5.0 1.0 + - - -
25C ASP* 3.9 18.5 - - + +
28C LYS* 4.0 10.9 - - + +
29C LYS 3.0 11.9 + - - +
30C CYS* 3.4 17.2 - - - +
31C VAL 3.0 21.8 + - - +
84C PHE* 1.3 73.0 - - - +
86C CYS* 1.3 59.7 + - - +
87C VAL* 3.8 5.4 + - + +
111C ARG* 3.6 30.0 - - + +
135C ARG* 2.8 50.2 + - - -
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Residues in contact with CYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.2 11.7 - - - +
33C ILE* 4.1 16.6 - - + -
80C MET* 3.4 48.0 - - - -
81C GLY* 4.0 3.8 - - - -
84C PHE* 3.5 9.3 + - - -
85C GLU* 1.3 74.2 - - - +
87C VAL* 1.3 63.1 + - - +
109C VAL* 3.9 23.4 + - + +
110C PHE* 3.4 4.6 - - + -
111C ARG* 2.9 33.7 + - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.8 37.0 - - + -
30C CYS* 3.9 13.2 - - - -
31C VAL 2.8 10.8 + - - +
32C VAL* 3.3 12.0 - - + -
33C ILE* 2.8 28.8 + - - +
85C GLU* 4.2 7.6 - - + +
86C CYS* 1.3 81.5 - - - +
88C LEU* 1.3 74.2 + - - +
89C PHE* 4.6 4.3 - - + +
110C PHE* 3.9 4.0 - - - -
111C ARG* 5.3 1.3 - - + -
112C ALA* 3.7 13.2 - - + +
114C LEU* 4.0 22.9 - - + -
133C LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE 3.5 15.0 - - - +
34C ASP 4.3 4.3 - - - +
35C LEU* 4.1 33.9 - - + +
39C LEU* 4.4 0.9 - - + -
87C VAL* 1.3 76.2 - - - +
89C PHE* 1.3 58.1 + - - +
90C THR* 5.0 8.5 - - + -
97C ALA 4.8 2.0 - - - +
101C ALA* 3.7 30.1 - - + -
110C PHE* 3.5 39.1 - - + -
112C ALA 3.1 11.8 + - - +
113C ARG* 3.5 17.1 - - + -
114C LEU 2.7 31.4 + - - +
115C PHE* 4.7 10.3 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.9 16.2 - - + -
32C VAL* 3.2 31.8 - - + +
33C ILE 3.0 10.0 + - - -
34C ASP* 3.5 12.5 + - - -
87C VAL* 3.6 1.5 + - + -
88C LEU* 1.3 75.1 - - - +
90C THR* 1.3 63.1 + - - +
114C LEU* 3.3 36.3 - - + -
115C PHE 4.2 1.3 - - - -
118C SER* 3.6 25.1 - - - -
119C CYS* 3.8 14.4 - - - -
128C LYS* 2.9 66.5 + - + -
129C ASP 4.6 1.3 - - - -
130C LEU* 5.0 4.3 - - + -
133C LEU* 4.1 12.3 - - + -
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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