Contacts of the strand formed by residues 61 - 67 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56L SER 5.6 0.7 - - - +
57L VAL* 3.9 16.9 - - + +
58L GLU* 3.4 40.3 + - + +
59L PRO 3.3 3.3 - - - +
60L GLY* 1.3 85.5 - - - +
62L GLN* 1.3 74.3 + - - +
63L LEU* 5.1 6.3 - - + -
74L ILE 3.6 2.3 - - - +
75L ARG* 3.3 4.8 - - - -
76L ARG 3.0 25.0 + - - -
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Residues in contact with GLN 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L GLY 4.3 0.4 + - - -
61L VAL* 1.3 85.4 - - - +
63L LEU* 1.3 67.3 + - - +
64L THR* 3.6 14.4 + - - +
73L PHE* 3.0 49.5 - - + -
74L ILE 3.4 12.6 - - - +
75L ARG* 4.0 19.5 + - + +
136L PRO 5.4 0.2 + - - -
138L GLY* 4.3 8.1 - - - +
139L GLY 4.5 1.2 + - - +
147L TRP* 2.8 30.9 + - - +
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Residues in contact with LEU 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L VAL* 3.8 28.3 - - + -
53L ASP 4.2 9.0 - - - +
54L VAL* 4.8 3.4 - - + -
56L SER* 5.7 3.1 - - - +
57L VAL* 4.1 30.7 - - + -
61L VAL* 5.1 4.9 - - + -
62L GLN* 1.3 79.5 - - - +
64L THR* 1.3 63.9 + - - +
65L VAL* 3.8 8.8 + - + +
72L ILE 3.2 5.5 - - - +
73L PHE* 3.8 0.2 - - - -
74L ILE* 2.7 49.9 + - + +
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Residues in contact with THR 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286G LEU* 3.8 33.9 + - + +
62L GLN* 3.6 20.0 + - - +
63L LEU* 1.3 75.7 - - - +
65L VAL* 1.3 66.7 + - - +
71L PRO* 3.9 16.8 - - + -
72L ILE 3.5 1.6 - - - +
73L PHE* 3.8 26.1 - - + -
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Residues in contact with VAL 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286G LEU* 4.2 6.1 - - - -
50L ILE* 3.9 17.7 - - + -
52L VAL* 4.3 29.6 - - + -
63L LEU* 4.8 12.3 - - + +
64L THR* 1.3 80.0 - - - +
66L LYS* 1.3 77.8 + - - +
67L PHE* 5.0 0.4 - - + -
71L PRO* 3.4 1.0 - - - +
72L ILE* 2.7 46.1 + - + +
74L ILE* 5.3 2.5 - - + -
186L LEU* 4.7 4.3 - - + -
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Residues in contact with LYS 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285G PRO* 4.5 24.2 - - + +
286G LEU* 3.8 23.3 - - + +
76K GLU* 5.6 6.4 + - - -
50L ILE* 3.5 7.3 - - - +
65L VAL* 1.3 83.5 - - - +
67L PHE* 1.3 67.7 + - - +
69L GLY* 3.9 26.7 - - - +
70L LYS 3.4 10.8 - - - +
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Residues in contact with PHE 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L LEU* 5.1 1.8 - - + -
48L ALA* 4.0 28.9 - - + -
50L ILE* 3.6 34.1 - - + -
65L VAL 4.8 0.4 - - - +
66L LYS* 1.3 79.6 - - - +
68L LEU* 1.3 105.4 + - + +
69L GLY 2.9 4.6 + - - -
70L LYS 2.9 16.7 + - - +
72L ILE* 3.4 23.6 - - + -
126L TRP* 3.4 32.7 - + - -
174L PRO* 5.3 3.6 - - + -
186L LEU* 4.1 24.2 - - + -
187L GLY* 4.1 11.7 - - - -
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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