Contacts of the strand formed by residues 61 - 67 (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 VAL 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F SER 5.6 0.9 - - - +
57F VAL* 3.9 17.6 - - + +
58F GLU* 3.4 39.0 + - + +
59F PRO 3.3 3.1 - - - +
60F GLY* 1.3 85.1 - - - +
62F GLN* 1.3 74.9 + - - +
63F LEU* 5.1 6.3 - - + -
74F ILE 3.6 1.7 - - - +
75F ARG* 3.3 4.1 - - - -
76F ARG 3.0 25.0 + - - -
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Residues in contact with GLN 62 (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 4.3 0.4 + - - -
61F VAL* 1.3 85.2 - - - +
63F LEU* 1.3 67.5 + - - +
64F THR* 3.5 17.2 + - - +
73F PHE* 3.3 42.7 - - + -
74F ILE 3.4 11.7 - - - +
75F ARG* 4.1 17.6 + - + +
138F GLY* 4.0 13.9 - - - +
139F GLY 5.8 1.6 - - - +
147F TRP* 2.9 31.8 + - - +
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Residues in contact with LEU 63 (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* 3.8 28.3 - - + -
53F ASP 4.2 9.0 - - - +
54F VAL* 4.8 3.4 - - + -
56F SER* 5.7 2.7 - - - +
57F VAL* 4.1 29.6 - - + -
61F VAL* 5.1 5.8 - - + -
62F GLN* 1.3 79.8 - - - +
64F THR* 1.3 65.1 + - - +
65F VAL* 3.8 9.0 + - + +
72F ILE 3.2 5.2 - - - +
73F PHE* 3.7 0.5 - - - -
74F ILE* 2.6 50.4 + - + +
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Residues in contact with THR 64 (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* 3.9 31.4 - - + +
62F GLN* 3.5 24.4 + - - +
63F LEU* 1.3 74.1 - - - +
65F VAL* 1.3 66.8 + - - +
71F PRO* 3.9 17.9 - - + -
72F ILE 3.5 1.1 - - - +
73F PHE* 3.8 25.6 - - + -
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Residues in contact with VAL 65 (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* 4.0 5.6 - - - -
50F ILE* 3.9 16.8 - - + -
52F VAL* 4.3 28.5 - - + -
63F LEU* 4.7 13.5 - - + +
64F THR* 1.3 80.8 - - - +
66F LYS* 1.3 79.0 + - - +
71F PRO* 3.4 1.7 - - - +
72F ILE* 2.8 43.0 + - + +
74F ILE* 5.3 2.7 - - + -
186F LEU* 4.7 5.2 - - + -
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Residues in contact with LYS 66 (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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285A PRO* 4.0 35.0 - - - +
286A LEU* 3.7 21.2 - - + +
50F ILE* 3.4 7.6 - - - +
65F VAL* 1.3 84.5 - - - +
67F PHE* 1.3 72.5 + - - +
68F LEU 4.9 0.2 - - - +
69F GLY* 4.0 25.0 - - - +
70F LYS 3.7 4.0 - - - +
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Residues in contact with PHE 67 (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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47F LEU* 4.7 2.2 - - + -
48F ALA* 4.0 29.2 - - + -
50F ILE* 3.6 33.2 - - + -
65F VAL 4.8 0.2 - - - +
66F LYS* 1.3 81.7 - - - +
68F LEU* 1.3 105.5 + - + +
69F GLY 2.8 5.1 + - - +
70F LYS 2.9 20.1 + - - +
72F ILE* 3.5 23.8 - - + -
126F TRP* 3.3 31.4 - + - -
174F PRO* 5.3 3.1 - - + -
186F LEU* 4.2 15.0 - - + -
187F GLY* 4.1 19.7 - - - -
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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