Contacts of the strand formed by residues 61 - 67 (chain R) in PDB entry 2QJK
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 VAL 61 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56R SER 5.6 0.4 - - - +
57R VAL* 3.9 17.9 - - + +
58R GLU* 3.4 39.4 + - + +
59R PRO 3.3 3.1 - - - +
60R GLY* 1.3 86.1 - - - +
62R GLN* 1.3 73.9 + - - +
63R LEU* 5.1 5.8 - - + -
74R ILE 3.6 2.3 - - - +
75R ARG* 3.3 4.4 - - - -
76R ARG 3.1 24.7 + - - -
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Residues in contact with GLN 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60R GLY 4.3 0.2 + - - -
61R VAL* 1.3 84.6 - - - +
63R LEU* 1.3 67.5 + - - +
64R THR* 3.4 14.0 + - - +
73R PHE* 2.8 50.6 - - + -
74R ILE 3.4 16.8 - - - +
75R ARG* 4.1 17.5 + - + +
138R GLY* 3.8 10.7 - - - +
139R GLY 4.5 2.7 + - - +
147R TRP* 2.7 30.7 + - - -
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Residues in contact with LEU 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R VAL* 3.8 29.4 - - + -
53R ASP 4.1 8.5 - - - +
54R VAL* 4.7 4.0 - - + -
56R SER* 5.6 3.4 - - - +
57R VAL* 4.0 31.2 - - + -
61R VAL* 5.1 5.4 - - + -
62R GLN* 1.3 80.0 - - - +
64R THR* 1.3 63.5 + - - +
65R VAL* 3.7 9.1 + - + +
72R ILE 3.2 6.2 - - - +
73R PHE* 3.8 0.3 - - - -
74R ILE* 2.6 47.5 + - + +
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Residues in contact with THR 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286M LEU* 3.9 30.3 - - + +
62R GLN* 3.4 22.0 + - - +
63R LEU* 1.3 75.6 - - - +
65R VAL* 1.3 66.1 - - - +
71R PRO* 3.9 18.2 - - + -
72R ILE 3.5 1.8 - - - +
73R PHE* 3.8 25.0 - - + -
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Residues in contact with VAL 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286M LEU* 3.8 6.7 - - - -
50R ILE* 3.8 16.6 - - + -
52R VAL* 4.3 30.1 - - + -
63R LEU* 4.8 12.8 - - + +
64R THR* 1.3 81.5 - - - +
66R LYS* 1.3 78.3 + - - +
71R PRO* 3.4 1.9 - - - +
72R ILE* 2.7 44.7 + - + +
74R ILE* 5.3 2.0 - - + -
186R LEU* 4.7 4.5 - - + -
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Residues in contact with LYS 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285M PRO* 3.9 36.4 - - - +
286M LEU* 3.7 21.3 - - + +
50R ILE* 3.2 7.6 - - - +
65R VAL* 1.3 86.0 - - - +
67R PHE* 1.3 72.3 + - - +
68R LEU 5.0 0.2 - - - +
69R GLY* 4.1 24.5 - - - +
70R LYS 3.7 4.0 - - - +
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Residues in contact with PHE 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R LEU* 5.4 2.2 - - + -
48R ALA* 3.9 29.4 - - + -
50R ILE* 3.6 33.9 - - + -
65R VAL 4.8 0.2 - - - +
66R LYS* 1.3 82.7 - - - +
68R LEU* 1.3 103.6 + - + +
69R GLY 2.9 3.6 - - - +
70R LYS 2.9 20.2 + - - +
72R ILE* 3.5 23.3 - - + -
126R TRP* 3.4 31.4 - + - -
174R PRO* 5.3 3.8 - - + -
186R LEU* 4.2 24.0 - - + -
187R GLY* 4.2 10.8 - - - -
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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