Contacts of the strand formed by residues 70 - 76 (chain C) 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 LYS 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C LYS* 4.5 0.2 - - - -
67C PHE* 2.9 30.4 + - - +
68C LEU* 3.2 16.3 - - - +
69C GLY* 1.3 78.0 - - - +
71C PRO* 1.3 74.0 - - + +
126C TRP* 4.1 25.2 - - + -
128C VAL* 3.9 28.3 - - + -
184D PRO* 3.1 33.2 + - - +
185D ALA* 3.8 12.3 - - + -
286D LEU* 4.5 3.8 - - - -
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Residues in contact with PRO 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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64C THR* 4.0 13.5 - - + -
65C VAL 3.4 6.1 - - - +
70C LYS* 1.3 93.8 - - + +
72C ILE* 1.3 65.6 + - - +
73C PHE* 4.2 4.9 - - + -
126C TRP* 3.4 7.1 - - - -
127C GLY 3.2 37.7 + - - +
128C VAL* 4.0 5.9 - - + +
134C CYS 6.0 0.2 - - - -
135C SER* 3.9 14.4 - - - -
157D TRP* 5.1 4.0 - - + -
285D PRO 3.5 16.8 - - - +
286D LEU* 3.5 21.7 - - + -
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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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63C LEU 3.2 5.7 - - - +
64C THR* 3.6 0.9 - - - -
65C VAL* 2.7 38.3 + - + +
67C PHE* 3.5 34.1 - - + -
71C PRO* 1.3 72.3 - - - +
73C PHE* 1.3 71.4 + - - +
74C ILE* 4.1 11.0 - - + -
124C VAL* 4.9 2.5 - - + -
125C MET 3.7 4.7 - - - +
126C TRP* 3.3 38.4 - - + -
174C PRO* 4.0 18.6 - - + -
186C LEU* 3.6 30.3 - - + -
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Residues in contact with PHE 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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62C GLN* 3.3 31.4 - - + +
63C LEU 3.7 2.5 - - - -
64C THR* 3.9 17.5 - - + -
71C PRO* 4.2 3.1 - - + -
72C ILE* 1.3 78.9 - - - +
74C ILE* 1.3 63.0 + - - +
75C ARG* 4.0 1.8 - - + +
123C LEU 3.8 1.1 - - - +
124C VAL* 3.4 4.2 - - - -
125C MET* 2.8 59.8 + - + +
127C GLY* 3.3 33.0 - - - -
135C SER* 3.2 26.7 - - - -
136C PRO* 3.4 26.9 - - + -
147C TRP* 3.5 23.3 - + + -
171C LEU* 5.2 0.4 - - + -
286D LEU 5.7 0.2 - - - -
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Residues in contact with ILE 74 (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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52C VAL* 4.0 34.3 - - + -
54C VAL* 4.4 6.3 - - + -
57C VAL* 5.0 2.2 - - + +
61C VAL 3.6 1.9 - - - +
62C GLN* 3.4 1.5 - - - +
63C LEU* 2.7 52.7 + - + +
65C VAL* 5.2 3.4 - - + -
72C ILE* 4.1 15.3 - - + -
73C PHE* 1.3 78.3 - - - +
75C ARG* 1.3 57.2 + - - +
76C ARG 4.2 0.3 + - - -
122C TRP* 4.4 18.6 - - + -
123C LEU 3.6 4.0 - - - +
124C VAL* 3.5 21.3 - - + -
184C ILE* 4.1 23.6 - - + -
186C LEU* 4.7 6.1 - - + -
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Residues in contact with ARG 75 (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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60C GLY* 3.6 29.0 + - - -
61C VAL 3.3 9.9 - - - +
62C GLN* 4.1 21.4 + - + +
73C PHE* 4.0 1.1 - - + -
74C ILE* 1.3 75.2 - - - +
76C ARG* 1.3 67.0 + - - +
77C ARG* 3.5 16.9 + - - +
78C THR* 5.1 1.8 - - - +
81C ASP* 2.9 26.2 + - - -
121C GLU 3.3 1.7 - - - +
122C TRP* 3.8 6.2 - - - -
123C LEU* 3.0 41.5 + - + +
139C GLY* 4.0 25.7 - - - +
140C VAL* 3.6 24.4 - - - +
147C TRP* 4.1 29.8 - - + -
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Residues in contact with ARG 76 (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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57C VAL* 3.4 26.4 + - + -
58C GLU* 3.6 11.5 - - - +
59C PRO* 3.2 37.9 - - - +
60C GLY* 2.6 34.1 + - - -
61C VAL 3.1 7.3 + - - -
74C ILE 4.2 0.2 + - - -
75C ARG* 1.3 73.3 - - - +
77C ARG* 1.3 56.1 + - - +
121C GLU* 3.3 36.2 + - + -
122C TRP* 3.3 41.7 - - + +
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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