Contacts of the strand formed by residues 97 - 102 (chain C) in PDB entry 2H62
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 ARG 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.4 40.8 + - - +
66B LEU* 4.0 4.6 - - - +
69B SER* 3.1 36.2 + - - -
62C ILE* 4.2 9.2 - - + -
63C ILE 3.1 14.8 - - - +
64C GLU* 3.9 17.1 + - + -
89C ASP* 2.9 40.0 + - - +
93C ALA* 3.8 16.9 - - + +
95C LEU* 3.6 14.3 + - + +
96C ARG* 1.3 78.4 - - - +
98C THR* 1.3 69.4 + - - +
115C LEU* 3.7 3.6 - - - -
116C PRO* 3.6 12.6 - - - +
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Residues in contact with THR 98 (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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62C ILE* 3.2 6.0 - - - -
63C ILE* 2.9 36.2 + - - +
89C ASP* 5.2 0.9 - - - -
97C ARG* 1.3 72.5 + - - +
99C ILE* 1.3 67.5 + - - +
100C GLU* 4.4 10.3 - - + +
113C PRO* 3.5 15.6 - - + +
114C THR 2.7 30.6 + - - +
115C LEU* 3.5 0.2 - - - -
116C PRO* 3.1 22.3 - - - +
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Residues in contact with ILE 99 (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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49B PHE* 3.9 5.8 - - + -
50B PRO* 3.8 25.1 - - + -
60C PHE* 3.9 9.0 - - + -
61C ALA 3.3 11.4 - - - +
62C ILE* 4.0 13.0 - - + -
78C MET* 3.7 29.6 - - + -
86C GLN 3.5 22.4 - - - +
87C CYS 4.0 12.2 - - - +
89C ASP* 3.8 26.3 + - + +
97C ARG 4.3 0.2 - - - -
98C THR* 1.3 77.8 - - - +
100C GLU* 1.3 78.0 + - - +
101C CYS* 4.6 2.7 - - - -
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Residues in contact with GLU 100 (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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60C PHE* 3.0 6.6 - - - +
61C ALA 2.8 33.0 + - - +
87C CYS 5.4 0.9 - - - -
98C THR* 4.4 9.4 - - + +
99C ILE* 1.3 79.9 - - - +
101C CYS* 1.3 66.0 + - - +
111C LEU* 3.4 25.2 - - + +
112C GLN 3.8 9.7 + - - +
113C PRO* 3.3 40.1 - - + +
114C THR 5.0 0.5 + - - -
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Residues in contact with CYS 101 (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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58C HIS* 4.4 4.3 - - + -
59C CYS 3.2 7.4 - - - +
60C PHE* 4.1 4.5 - - - -
78C MET* 3.8 15.7 - - - -
87C CYS* 2.0 57.6 - - + +
99C ILE* 4.6 2.0 - - - -
100C GLU* 1.3 81.0 - - - +
102C CYS* 1.3 64.3 + - - +
103C ARG* 3.5 20.5 + - - +
111C LEU* 4.0 8.5 - - - +
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Residues in contact with CYS 102 (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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58C HIS* 3.4 5.0 - - - +
59C CYS* 2.8 35.2 + - - +
101C CYS* 1.3 75.8 - - - +
103C ARG* 1.3 72.8 + - - +
107C CYS* 2.0 51.9 - - + -
108C ASN* 3.3 14.4 - - - -
111C LEU* 3.6 22.9 - - + -
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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