Contacts of the strand formed by residues 58 - 65 (chain C) in PDB entry 2QJ9
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 HIS 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.0 1.8 - - - -
38C CYS* 4.0 4.7 - - - -
55C THR* 3.9 2.4 - - - +
57C GLY* 1.3 80.4 - - - -
59C CYS* 1.3 67.4 + - - +
77C CYS* 3.6 2.8 - - - -
78C MET* 2.9 38.4 + - + +
80C TYR* 3.8 15.2 - + - -
83C SER* 2.9 40.3 + - - -
87C CYS* 4.4 10.5 - - - -
101C CYS* 4.1 15.7 - - + +
102C CYS* 3.6 10.4 + - - +
103C ARG* 3.3 31.7 - - + +
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Residues in contact with CYS 59 (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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36C LEU* 3.8 11.4 - - - +
37C LYS 3.6 8.1 - - - -
38C CYS* 2.0 53.2 - - - -
58C HIS* 1.3 73.9 - - - +
60C PHE* 1.3 61.5 + - - +
76C GLY 3.5 1.1 - - - -
101C CYS* 3.2 6.8 - - - +
102C CYS 2.9 27.6 + - - -
104C THR 3.9 2.9 - - - -
106C LEU 4.5 0.7 - - - -
107C CYS* 3.5 28.5 - - - -
108C ASN* 3.5 17.3 - - + -
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Residues in contact with PHE 60 (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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50A PRO* 3.4 36.6 - - + -
52A ALA* 4.7 5.8 - - + -
43C HIS* 4.0 24.9 - + + -
59C CYS* 1.3 78.1 - - - +
61C ALA* 1.3 71.6 + - - +
62C ILE* 4.3 5.6 - - + -
75C SER* 3.2 8.2 - - - -
76C GLY* 2.8 58.0 + - - -
77C CYS 3.6 21.3 - - - -
78C MET* 3.9 18.4 - - + -
99C ILE* 4.4 7.0 - - + -
100C GLU 3.3 13.0 - - - +
101C CYS* 4.0 12.1 - - - -
108C ASN* 2.7 28.9 + - - -
111C LEU* 4.6 0.7 - - - -
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Residues in contact with ALA 61 (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* 1.3 78.7 - - - +
62C ILE* 1.3 60.0 + - - +
73C LEU* 4.8 4.9 - - + -
74C ALA 3.4 11.4 - - - +
75C SER* 4.3 5.6 - - - -
99C ILE* 3.4 1.9 - - - +
100C GLU 3.0 30.4 + - - +
108C ASN 4.4 8.1 - - - +
111C LEU* 4.2 26.8 - - + +
113C PRO* 3.5 16.0 - - + +
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Residues in contact with ILE 62 (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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49A PHE* 3.9 21.8 - - + +
50A PRO* 4.3 8.5 - - + -
43C HIS* 4.8 0.4 - - - +
60C PHE* 4.3 13.0 - - + -
61C ALA* 1.3 76.2 - - - +
63C ILE* 1.3 72.6 + - - +
64C GLU* 3.9 21.0 - - - +
72C THR 3.9 0.5 - - - +
73C LEU* 3.1 19.3 - - - +
74C ALA* 2.9 35.9 + - + +
97C ARG* 3.9 26.5 - - - -
98C SER 3.3 13.0 - - - +
99C ILE* 4.2 11.9 - - + -
113C PRO* 4.1 1.3 - - - -
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Residues in contact with ILE 63 (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* 1.3 75.8 - - - +
64C GLU* 1.3 65.4 + - - +
71C THR* 3.8 29.2 - - + +
72C THR 3.5 5.2 - - - +
73C LEU* 4.3 16.4 - - + -
97C ARG* 3.1 5.4 - - - +
98C SER* 3.0 39.6 + - - +
113C PRO* 3.6 36.1 - - + +
114C THR* 4.9 0.4 - - - -
115C LEU* 3.5 32.7 - - + +
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Residues in contact with GLU 64 (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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49A PHE 4.3 11.2 - - - +
43C HIS* 5.0 3.5 + - - -
62C ILE* 3.9 33.1 - - + +
63C ILE* 1.3 78.8 - - - +
65C GLU* 1.3 62.1 + - - +
66C ASP 3.9 1.2 + - - -
71C THR* 3.6 4.7 - - - -
72C THR* 3.2 45.2 + - - +
74C ALA* 4.8 6.5 - - + +
95C GLN* 5.3 7.8 + - + +
96C ARG 3.5 5.2 - - - +
97C ARG* 3.8 19.0 + - + +
115C LEU* 4.5 1.1 - - - -
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Residues in contact with GLU 65 (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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64C GLU* 1.3 73.5 - - - +
66C ASP* 1.3 77.0 + - - +
67C ASP* 5.5 0.3 - - - -
69C GLY* 3.7 29.6 + - - +
70C GLU 3.3 13.5 - - - +
71C THR* 3.7 9.0 - - - +
95C GLN* 3.0 27.4 + - - +
96C ARG* 2.9 47.7 + - - +
115C LEU* 3.7 13.6 - - + +
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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