Contacts of the strand formed by residues 70 - 76 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PRO* 3.6 29.2 + - - +
185A ALA* 3.6 17.0 - - + -
286A LEU* 4.4 2.9 - - - -
66F LYS* 3.7 0.2 - - - -
67F PHE* 2.9 30.5 + - - +
68F LEU* 4.1 13.6 - - - +
69F GLY* 1.3 77.8 - - - +
71F PRO* 1.3 73.2 - - + +
126F TRP* 3.9 33.6 - - + -
128F VAL* 4.0 22.0 - - + -
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Residues in contact with PRO 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TRP* 5.0 5.4 - - + -
285A PRO 3.5 16.8 - - - +
286A LEU* 3.5 22.0 - - + -
64F THR* 3.9 14.1 - - + -
65F VAL 3.4 6.7 - - - +
70F LYS* 1.3 89.4 - - + +
72F ILE* 1.3 60.0 + - - +
73F PHE* 4.3 3.8 - - + -
126F TRP* 3.4 13.0 - - - -
127F GLY 3.1 39.4 + - - +
128F VAL* 3.9 6.4 - - + +
135F SER* 3.9 14.1 - - - +
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Residues in contact with ILE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU 3.2 5.9 - - - +
64F THR* 3.5 1.4 - - - -
65F VAL* 2.8 37.4 + - + +
67F PHE* 3.5 34.8 - - + -
71F PRO* 1.3 72.7 - - - +
73F PHE* 1.3 71.7 + - - +
74F ILE* 4.1 10.8 - - + -
124F VAL* 4.9 2.2 - - + -
125F MET 3.6 4.7 - - - +
126F TRP* 3.3 36.1 - - + +
174F PRO* 4.0 18.2 - - + -
186F LEU* 3.6 31.2 - - + -
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Residues in contact with PHE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU 5.6 0.2 - - - -
62F GLN* 3.3 31.9 - - + +
63F LEU 3.7 2.2 - - - -
64F THR* 3.8 19.5 - - + -
71F PRO* 4.3 2.7 - - + -
72F ILE* 1.3 77.8 - - - +
74F ILE* 1.3 63.0 + - - +
75F ARG* 4.0 1.3 - - + +
123F LEU 4.3 0.7 - - - -
124F VAL* 3.4 3.8 - - - -
125F MET* 2.7 56.2 + - + +
127F GLY* 3.4 28.3 - - - -
135F SER* 3.0 29.8 - - - -
136F PRO* 3.4 27.8 - - + -
147F TRP* 3.6 24.2 - + + -
171F LEU* 5.0 1.8 - - + -
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Residues in contact with ILE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F VAL* 4.0 35.2 - - + -
54F VAL* 4.5 6.1 - - + -
57F VAL* 5.0 2.4 - - + +
61F VAL 3.6 2.3 - - - +
62F GLN* 3.4 1.4 - - - -
63F LEU* 2.6 53.3 + - + +
65F VAL* 5.3 3.1 - - + -
72F ILE* 4.1 15.3 - - + -
73F PHE* 1.3 78.7 - - - +
75F ARG* 1.3 57.6 + - - +
122F TRP* 4.4 18.2 - - + -
123F LEU 3.5 4.0 - - - -
124F VAL* 3.5 24.7 - - + -
184F ILE* 4.1 19.5 - - + -
186F LEU* 4.7 5.6 - - + -
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F GLY* 3.6 29.2 + - - -
61F VAL 3.3 9.6 - - - +
62F GLN* 4.1 21.8 + - + +
73F PHE* 4.0 1.1 - - + -
74F ILE* 1.3 74.7 - - - +
76F ARG* 1.3 66.4 + - - +
77F ARG* 3.5 16.8 + - - +
78F THR* 5.0 1.6 - - - +
81F ASP* 3.0 27.1 + - - -
121F GLU 3.3 1.9 - - - +
122F TRP* 3.8 6.2 - - - -
123F LEU* 2.9 42.3 + - + +
139F GLY* 4.1 23.2 - - - +
140F VAL* 3.7 23.9 - - - +
147F TRP* 4.1 31.1 - - + -
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F VAL* 3.3 27.4 + - + +
58F GLU* 3.6 12.1 - - - +
59F PRO* 3.3 38.8 - - + +
60F GLY* 2.6 34.8 + - - -
61F VAL 3.0 7.1 + - - -
74F ILE 4.2 0.4 + - - -
75F ARG* 1.3 73.2 - - - +
77F ARG* 1.3 56.6 + - - +
121F GLU* 3.1 40.4 + - + +
122F TRP* 3.3 39.8 - - + -
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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