Contacts of the strand formed by residues 70 - 73 (chain H) in PDB entry 5UQ9
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 70 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H ASP 3.3 20.4 + - - +
6H ILE* 3.5 22.5 - - + -
7H ALA 3.0 22.9 + - - -
65H LEU* 3.5 13.1 - - - +
66H LYS* 2.9 35.0 + - - +
68H PRO* 3.3 49.7 + - - +
69H ARG* 1.3 75.5 - - - +
71H ILE* 1.3 61.7 + - - +
97H ILE* 3.5 15.7 - - + -
99H ILE* 4.9 1.1 - - + -
152H HIS* 3.5 35.0 + - - +
153H ILE* 3.9 18.4 - - + -
156H ILE* 4.7 9.0 - - - +
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Residues in contact with ILE 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ALA* 3.4 6.3 - - + +
9H ILE* 3.7 36.6 - - + -
61H MET* 4.1 13.9 - - + -
62H VAL* 5.5 1.1 - - + -
65H LEU* 3.9 17.0 - - + -
69H ARG* 4.3 2.0 - - + -
70H ARG* 1.3 84.4 - - - +
72H ILE* 1.3 61.5 + - - +
73H LEU* 4.2 5.2 - - + -
88H LEU* 4.2 14.8 - - + -
92H LEU* 3.7 36.3 - - + -
97H ILE 3.1 17.0 + - - +
98H ILE* 3.6 4.5 - - + +
99H ILE* 2.7 35.5 + - - +
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ILE* 3.7 26.0 - - + -
7H ALA 2.6 18.1 + - - +
8H LEU* 3.2 21.3 - - + +
9H ILE* 2.7 35.3 + - - +
18H LEU* 5.9 2.9 - - + -
22H MET* 4.4 19.7 - - + -
71H ILE* 1.3 74.7 - - - +
73H LEU* 1.3 66.9 + - - +
74H LEU* 4.5 8.7 - - + -
99H ILE* 3.5 28.0 - - + +
101H GLY* 5.1 4.0 - - - +
157H PHE* 4.3 16.4 - - + -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 3.7 39.0 - - + -
71H ILE* 4.2 6.3 - - + -
72H ILE* 1.3 72.9 - - - +
74H LEU* 1.3 61.3 + - - +
75H VAL* 3.7 10.5 - - + -
81H VAL* 4.0 33.9 - - + +
84H PHE* 4.1 17.9 - - + -
85H ILE* 4.3 5.2 - - + +
88H LEU* 4.8 2.5 - - + -
98H ILE* 3.8 27.1 - - + -
99H ILE 2.5 17.8 + - - +
100H ASP* 3.8 9.8 - - - +
101H GLY* 2.8 31.4 + - - -
102H GLY 3.7 2.4 + - - -
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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