Contacts of the strand formed by residues 64 - 69 (chain A) in PDB entry 2HR6
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 LEU 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 4.2 30.5 - - + -
5A ILE* 4.4 5.4 - - + -
59A ILE* 3.8 20.7 - - + +
61A ASP* 3.0 22.1 + - + +
62A PRO 3.3 1.5 - - - +
63A SER* 1.3 81.0 - - - +
65A ALA* 1.3 67.5 + - - +
91A SER* 3.6 16.5 + - - -
122A PHE* 4.2 22.2 - - + +
123A VAL* 3.3 33.0 - - - +
124A PRO* 3.8 7.4 - - + -
125A VAL* 3.9 5.9 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 4.0 7.6 - - - -
64A LEU* 1.3 77.4 - - - +
66A ALA* 1.3 59.7 + - - +
88A LEU* 4.3 16.6 - - + -
89A ILE 3.6 15.7 - - - +
90A ASP* 5.4 2.2 - - - -
91A SER 5.5 0.2 - - - +
122A PHE* 3.3 5.2 - - - +
123A VAL* 3.0 32.3 + - + -
125A VAL* 3.6 28.3 - - + -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 5.1 0.4 - - + -
59A ILE* 3.7 3.2 - - + +
65A ALA* 1.3 74.4 - - - +
67A MET* 1.3 64.9 + - - +
88A LEU* 3.6 5.9 - - - +
89A ILE* 2.8 53.2 + - + -
120A MET* 3.9 16.2 - - + -
121A ILE 3.1 12.3 - - - +
122A PHE* 3.8 22.7 - - + -
123A VAL* 4.9 0.4 - - - +
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA* 1.3 79.0 - - - +
68A MET* 1.3 62.5 + - - +
69A LEU* 3.9 8.3 + - + +
86A VAL* 4.0 25.4 - - + -
87A GLY 3.2 3.4 - - - +
88A LEU* 4.1 18.2 - - + -
120A MET* 3.3 5.1 - - - -
121A ILE* 2.8 51.5 + - + +
123A VAL* 3.5 35.9 - - + +
125A VAL* 6.2 0.2 - - + -
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.2 16.6 - - + -
67A MET* 1.3 73.8 - - - +
69A LEU* 1.3 62.9 + - - +
82A LEU* 3.4 12.1 - - + +
86A VAL* 3.4 10.0 - - - +
87A GLY 2.7 41.3 + - - +
89A ILE* 4.2 9.2 - - + -
97A LEU* 5.5 4.3 - - - -
98A MET 3.5 21.8 - - - +
99A ILE* 3.7 38.1 - - + -
100A SER 5.1 0.2 - - - +
118A ALA* 4.6 3.4 - - + -
119A GLN 3.3 6.3 - - - +
120A MET* 4.0 23.1 - - + +
777A DUD 3.6 19.7 - - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 4.2 13.9 - - + +
68A MET* 1.3 85.0 - - - +
70A PRO* 1.3 84.0 - - + +
82A LEU* 3.7 6.5 - - - -
86A VAL* 4.1 26.5 - - + -
118A ALA* 3.6 4.2 - - - +
119A GLN* 2.9 41.8 + - + +
121A ILE* 4.6 28.3 - - + -
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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