Contacts of the strand formed by residues 60 - 63 (chain H) in PDB entry 2QC8
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 TRP 60 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30H TYR* 3.6 43.5 - + + -
43H LYS* 3.2 63.3 - - + +
44H THR 3.5 25.1 - - - -
45H ARG* 3.5 42.4 - - + +
59H GLU* 1.3 77.4 - - - +
61H ASN* 1.3 87.4 + - - +
78H TYR* 3.6 10.0 - - - +
79H LEU* 3.0 28.3 + - + +
205I GLN* 5.2 5.2 - - - -
501I ADP 4.5 16.5 + - - -
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Residues in contact with ASN 61 (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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43H LYS* 2.9 29.1 + - - +
60H TRP* 1.3 92.0 - - - +
62H PHE* 1.3 67.1 + - - +
76H ASP* 4.5 11.8 + - + +
77H MET 2.9 25.6 - - - +
78H TYR* 4.4 2.9 - - + -
79H LEU* 3.9 6.9 - - - +
319I ARG* 5.2 0.2 - - - +
324I ARG* 4.4 9.5 - - - +
326I PRO* 6.1 1.5 - - - +
328I THR* 4.0 17.7 + - - -
501I ADP 4.2 17.0 + - - -
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Residues in contact with PHE 62 (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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32H TRP* 3.3 51.1 - + + -
43H LYS* 4.2 6.3 - - - +
61H ASN* 1.3 79.5 - - - +
63H ASP* 1.3 70.1 + - - +
64H GLY* 3.2 11.8 + - - -
67H THR* 3.4 23.3 - - + -
69H GLN* 3.8 8.5 - - - -
76H ASP* 3.4 6.9 - - - -
77H MET* 3.0 58.0 + - + -
78H TYR 4.0 1.1 - - - -
79H LEU* 3.7 26.5 - - + -
101H VAL* 3.8 18.2 - - + -
162I TYR* 3.7 11.0 - + - +
319I ARG* 4.4 6.7 - - - +
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Residues in contact with ASP 63 (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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62H PHE* 1.3 78.7 - - - +
64H GLY* 1.3 61.4 + - - +
65H SER* 2.8 22.7 + - - -
66H SER* 2.6 21.5 + - - -
67H THR* 3.6 8.7 - - - +
75H SER* 3.3 13.6 - - - -
162I TYR* 3.0 26.5 + - + +
305I GLU* 2.3 29.9 - - - +
319I ARG* 3.4 28.0 - - - +
601I P3S 3.6 5.1 - - - +
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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