Contacts of the strand formed by residues 71 - 78 (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 THR 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.4 37.2 - - + -
64C GLU 3.2 7.3 + - - +
65C GLU* 4.4 2.8 + - - +
69C GLY 3.4 10.6 + - - -
70C GLU* 1.3 70.8 - - - +
72C THR* 1.3 77.3 + - - +
73C LEU* 4.4 4.5 - - + -
115C LEU* 3.9 17.6 - - + +
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Residues in contact with THR 72 (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 3.8 0.5 - - - +
63C ILE* 3.4 3.1 - - - +
64C GLU* 3.0 48.3 + - - +
66C ASP* 5.9 2.2 - - - +
70C GLU* 4.9 6.1 - - + +
71C THR* 1.3 82.8 - - - +
73C LEU* 1.3 70.2 + - - +
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Residues in contact with LEU 73 (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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41C SER* 4.6 7.3 + - - -
62C ILE 3.4 5.6 - - - +
63C ILE* 3.6 38.1 - - + -
71C THR* 4.4 5.2 - - + -
72C THR* 1.3 79.7 - - - +
74C ALA* 1.3 64.2 + - - +
113C PRO* 5.5 3.4 - - + +
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Residues in contact with ALA 74 (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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41C SER* 3.3 17.3 - - - +
42C GLY* 4.7 3.6 - - - -
43C HIS* 3.5 22.2 - - + +
61C ALA* 3.5 2.3 - - - +
62C ILE* 3.0 41.7 + - + +
64C GLU* 4.6 6.5 - - - +
72C THR* 6.0 0.2 - - - +
73C LEU* 1.3 77.2 - - - +
75C SER* 1.3 65.2 + - - +
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C TYR* 3.8 6.2 + - - +
40C CYS* 3.3 6.5 - - - -
41C SER* 2.9 43.0 + - - +
43C HIS* 3.4 10.6 - - - +
60C PHE* 3.2 28.5 - - - -
61C ALA* 4.1 6.1 - - - -
74C ALA* 1.3 77.1 - - - +
76C GLY* 1.3 59.3 + - - +
108C ASN* 3.6 11.7 - - - -
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Residues in contact with GLY 76 (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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38C CYS* 3.8 1.2 - - - +
39C TYR 3.2 13.3 + - - -
40C CYS* 3.7 9.6 - - - -
43C HIS* 4.5 3.4 - - - -
53C CYS* 3.8 4.9 - - - -
59C CYS* 3.4 5.9 - - - -
60C PHE* 3.1 40.0 + - - -
75C SER* 1.3 79.9 - - - +
77C CYS* 1.3 59.5 + - - -
108C ASN* 3.6 3.3 + - - -
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Residues in contact with CYS 77 (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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52B ALA* 3.2 14.4 - - + +
53B ASP* 2.8 29.9 + - + +
54B HIS* 6.4 0.2 - - - +
38C CYS* 3.6 16.2 - - - -
43C HIS 5.1 1.4 + - - -
45C PRO* 6.2 0.4 - - + -
53C CYS* 2.1 64.6 - - + -
54C ILE 3.8 2.5 - - - +
55C THR* 3.6 20.6 - - - -
58C HIS 3.7 3.4 - - - -
60C PHE* 3.6 3.5 - - - -
76C GLY* 1.3 72.8 - - - -
78C MET* 1.3 60.3 + - - +
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Residues in contact with MET 78 (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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50B PRO* 4.4 6.7 - - + -
51B LEU 4.7 1.6 - - - +
52B ALA* 4.7 1.1 - - - +
53B ASP 4.0 2.7 - - - +
55C THR* 3.3 5.4 + - - -
57C GLY* 3.2 3.3 - - - -
58C HIS* 2.9 45.1 + - + +
60C PHE* 4.1 15.3 - - + -
76C GLY 4.2 0.2 + - - -
77C CYS* 1.3 74.8 - - - +
79C LYS* 1.3 74.8 + - - +
83C SER* 3.6 19.3 - - - -
86C GLN* 3.7 37.2 - - + +
87C CYS* 3.4 22.0 - - - -
99C ILE* 3.7 26.2 - - + -
101C CYS* 3.8 13.5 - - - -
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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