Contacts of the strand formed by residues 70 - 76 (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 LYS 70 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M PRO* 3.2 30.7 + - - +
185M ALA* 3.7 12.8 - - + -
286M LEU* 4.2 3.8 - - - -
66R LYS* 3.7 0.2 - - - -
67R PHE* 2.9 30.8 + - - +
68R LEU* 3.9 10.7 + - - +
69R GLY* 1.3 83.4 - - - +
71R PRO* 1.4 73.9 - - + +
126R TRP* 4.0 25.6 - - + -
128R VAL* 4.0 27.5 - - + +
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Residues in contact with PRO 71 (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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157M TRP* 4.9 5.2 - - + -
285M PRO 3.3 17.5 - - - +
286M LEU* 3.4 22.0 - - + -
64R THR* 3.9 14.8 - - + -
65R VAL 3.4 7.0 - - - +
70R LYS* 1.4 91.3 - - + +
72R ILE* 1.3 60.0 + - - +
73R PHE* 4.3 2.0 - - + -
126R TRP* 3.4 12.8 - - - -
127R GLY 3.2 38.2 + - - +
128R VAL* 4.0 5.8 - - + +
135R SER* 3.8 16.8 - - - +
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Residues in contact with ILE 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R LEU 3.2 6.2 - - - +
64R THR* 3.5 1.4 - - - -
65R VAL* 2.7 36.9 + - + +
67R PHE* 3.5 34.5 - - + -
71R PRO* 1.3 71.6 - - - +
73R PHE* 1.3 72.3 - - - +
74R ILE* 4.1 10.9 - - + +
124R VAL* 4.8 2.2 - - + -
125R MET 3.6 4.0 - - - +
126R TRP* 3.2 40.6 - - + +
174R PRO* 4.0 16.4 - - + -
186R LEU* 3.6 32.1 - - + -
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Residues in contact with PHE 73 (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 5.5 0.2 - - - -
62R GLN* 2.8 31.9 - - + +
63R LEU 3.8 2.2 - - - -
64R THR* 3.8 18.2 - - + -
71R PRO* 4.3 2.9 - - + -
72R ILE* 1.3 79.9 - - - +
74R ILE* 1.3 61.7 + - - +
75R ARG 4.0 1.6 - - - +
123R LEU 3.7 1.3 - - - +
124R VAL* 3.4 4.5 - - - -
125R MET* 2.7 60.1 + - + +
127R GLY* 3.3 26.5 - - - -
135R SER* 2.8 28.9 - - - -
136R PRO* 3.4 28.0 - - + -
147R TRP* 3.5 21.5 - + + -
171R LEU* 5.2 0.9 - - + -
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Residues in contact with ILE 74 (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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52R VAL* 4.0 35.0 - - + -
54R VAL* 4.4 5.8 - - + -
57R VAL* 5.0 2.0 - - + +
61R VAL 3.6 2.3 - - - +
62R GLN* 3.4 1.7 - - - +
63R LEU* 2.6 53.5 + - + +
65R VAL* 5.3 3.4 - - + -
72R ILE* 4.1 14.4 - - + -
73R PHE* 1.3 79.2 - - - +
75R ARG* 1.3 58.4 + - - +
122R TRP* 4.4 18.4 - - + -
123R LEU 3.5 4.0 - - - -
124R VAL* 3.5 24.2 - - + -
184R ILE* 4.1 20.4 - - + -
186R LEU* 4.7 4.9 - - + -
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Residues in contact with ARG 75 (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* 3.6 29.6 + - - -
61R VAL 3.3 9.0 - - - +
62R GLN* 4.1 25.5 + - + +
73R PHE 4.0 0.6 - - - -
74R ILE* 1.3 74.9 - - - +
76R ARG* 1.3 66.2 + - - +
77R ARG* 3.4 17.7 + - - +
78R THR* 5.1 1.6 - - - +
81R ASP* 2.9 25.8 + - - -
121R GLU 3.1 2.4 - - - +
122R TRP* 3.8 5.1 - - - -
123R LEU* 2.9 41.6 + - + +
125R MET* 6.1 0.2 - - + -
139R GLY* 3.8 25.3 - - - +
140R VAL* 3.6 25.5 - - - +
147R TRP* 4.1 27.1 - - + -
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Residues in contact with ARG 76 (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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57R VAL* 3.4 26.2 + - + -
58R GLU* 3.6 12.0 - - - +
59R PRO* 3.2 36.7 - - - +
60R GLY* 2.6 34.8 + - - -
61R VAL 3.1 7.5 + - - -
74R ILE 4.2 0.4 + - - -
75R ARG* 1.3 73.2 - - - +
77R ARG* 1.3 56.4 + - - +
121R GLU* 3.1 32.5 + - + +
122R TRP* 3.3 44.6 - - + +
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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