Contacts of the strand formed by residues 67 - 73 (chain C) in PDB entry 2UUG
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 PRO 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.7 29.4 - - + -
57C LEU* 5.1 1.6 - - + -
58C LEU 4.0 0.7 - - - +
59C THR* 4.0 13.2 - - + -
65C TYR 3.2 9.8 - - - +
66C LYS* 1.4 95.6 - - + +
68C TRP* 1.3 62.2 + - - +
84C LEU* 3.9 34.2 - - + +
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Residues in contact with TRP 68 (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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29C VAL* 5.1 2.5 - - + -
33C ILE* 3.8 27.8 - - + -
35C ASN* 3.4 49.8 - - + -
36C LYS 4.4 1.6 - - - -
37C PRO* 3.9 32.6 - - + +
38C GLU 5.4 1.6 - - - +
41C ILE* 4.3 19.5 - - + -
58C LEU* 2.8 32.4 + - + +
60C SER* 6.6 0.7 - - - -
66C LYS 3.2 6.2 + - - +
67C PRO* 1.3 76.4 - - - +
69C ALA* 1.3 71.8 + - + +
83C MET* 4.2 12.8 - - + +
84C LEU* 3.2 23.7 + - - +
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Residues in contact with ALA 69 (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* 4.9 8.7 - - + -
57C LEU* 3.3 8.3 - - - +
58C LEU* 3.0 36.1 + - + -
68C TRP* 1.3 96.3 - - + +
70C LEU* 1.3 62.7 + - - +
71C VAL* 4.2 0.7 - - + -
81C ILE* 5.0 3.1 - - + -
82C LYS 3.5 14.8 - - - +
83C MET* 4.3 12.6 - - - -
84C LEU* 3.7 10.9 - - - +
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Residues in contact with LEU 70 (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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7C ILE 5.1 0.7 - - - +
8C ILE* 4.7 10.3 - - + +
11C GLU* 3.4 34.3 - - + -
12C THR* 3.9 18.8 - - + -
55C VAL* 4.1 19.3 - - + -
56C MET 3.6 11.9 - - - +
57C LEU* 4.0 22.2 - - + -
69C ALA* 1.3 74.5 - - - +
71C VAL* 1.3 61.3 + - - +
72C ILE* 4.3 10.8 - - + -
80C LYS 3.6 3.5 - - - +
81C ILE* 3.7 0.5 - - - -
82C LYS* 2.9 50.4 + - + +
84C LEU* 4.4 11.2 - - + -
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Residues in contact with VAL 71 (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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191A LEU* 4.2 9.0 - - + -
33C ILE* 3.7 31.0 - - + -
54C ASN 3.5 1.7 - - - +
55C VAL* 3.6 1.9 - - - +
56C MET* 2.7 60.8 + - + +
58C LEU* 3.9 14.4 - - + -
69C ALA* 5.0 0.7 - - + -
70C LEU* 1.3 79.7 - - - +
72C ILE* 1.3 64.1 + - - +
79C ASN* 3.6 35.7 - - + +
80C LYS 3.8 2.7 - - - +
81C ILE* 4.3 11.7 - - + -
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Residues in contact with ILE 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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12C THR* 3.9 25.6 - - + -
14C LYS* 5.7 3.6 - - - +
53C GLU* 3.9 38.4 - - + +
54C ASN 3.4 4.0 - - - +
55C VAL* 4.5 19.3 - - + -
70C LEU* 4.5 10.3 - - + +
71C VAL* 1.3 78.5 - - - +
73C GLN* 1.3 62.3 + - - +
78C GLU 3.4 1.7 - - - +
79C ASN* 3.1 4.4 - - - -
80C LYS* 2.8 62.8 + - + +
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Residues in contact with GLN 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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91A ASN* 5.7 0.3 + - - -
190A PRO* 3.1 34.5 + - - +
194A HIS* 3.7 13.7 - - - -
52C ASP 4.2 0.2 - - - +
53C GLU* 3.1 7.5 - - - +
54C ASN* 2.8 55.6 + - + +
56C MET* 3.8 11.2 - - + +
71C VAL 4.2 0.2 - - - -
72C ILE* 1.3 74.5 - - - +
74C ASP* 1.3 64.7 + - - +
77C GLY* 3.5 27.6 + - - -
78C GLU 3.4 3.8 - - - -
79C ASN* 3.1 28.5 - - - +
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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