Contacts of the strand formed by residues 63 - 71 (chain A) in PDB entry 3K5M
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 PHE 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLN* 5.8 6.5 - - + -
57A LEU* 4.0 27.6 - - + -
60A GLU* 3.5 44.2 - - + -
61A GLN 3.5 0.6 - - - -
62A GLY* 1.3 77.5 - - - +
64A ARG* 1.3 81.4 + - - +
65A LEU* 4.2 19.7 - - + -
81A LEU* 3.5 23.6 - - + -
82A TYR 2.9 15.3 - - - +
83A CYS* 4.1 3.4 - - - -
88A GLN* 4.4 0.2 - - - +
92A TYR* 4.0 21.5 - + + -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU* 2.6 43.8 + - - -
63A PHE* 1.3 84.9 - - - +
65A LEU* 1.3 60.7 + - - +
66A THR* 3.8 24.3 - - + +
80A GLY 3.5 1.2 - - - +
81A LEU* 3.5 3.3 - - - +
82A TYR* 2.8 59.2 + - + +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 4.0 14.8 - - + -
50A VAL* 4.1 22.9 - - + -
53A ALA* 4.5 14.6 - - + -
54A GLN* 4.1 26.0 + - + +
57A LEU* 5.5 1.8 - - + -
63A PHE* 4.2 13.7 - - + -
64A ARG* 1.3 74.1 - - - +
66A THR* 1.3 62.1 + - - +
67A PRO* 4.3 1.9 - - - +
79A TYR* 4.1 23.0 - - + -
80A GLY 3.3 7.0 - - - +
81A LEU* 3.7 37.2 - - + +
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.8 33.9 - - + +
65A LEU* 1.3 77.9 - - - +
67A PRO* 1.3 77.3 + - - +
68A LEU* 3.5 9.0 - - - +
79A TYR* 3.6 4.9 - - - -
80A GLY* 2.7 33.2 + - - +
82A TYR* 3.9 13.5 - - + -
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU 4.3 1.1 - - - +
66A THR* 1.3 100.0 + - - +
68A LEU* 1.3 62.4 + - - +
78A VAL 4.7 0.2 - - - +
79A TYR* 3.3 48.2 - - + +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.7 22.9 - - + -
66A THR* 3.5 15.0 - - - +
67A PRO* 1.3 84.4 - - - +
69A ALA* 1.3 59.7 + - - +
70A LEU* 2.8 32.9 + - + +
77A PRO* 5.1 4.0 - - - +
78A VAL* 2.9 19.1 + - + +
79A TYR 4.2 0.9 - - - -
80A GLY* 3.6 26.5 - - - +
82A TYR* 3.5 22.0 - - + +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 1.3 69.1 - - - +
70A LEU* 1.3 71.5 + - - +
71A LYS* 5.9 1.6 - - - +
385A GLY* 4.6 4.7 - - - -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.4 7.2 - - + -
68A LEU* 2.8 31.9 + - + +
69A ALA* 1.3 85.0 - - - +
71A LYS* 1.3 65.3 + - - +
77A PRO* 3.3 6.2 - - - +
78A VAL* 2.9 37.6 + - + +
382A HIS* 3.5 32.1 - - + +
385A GLY* 3.4 19.5 - - - -
386A TYR 3.9 5.8 - - - +
387A VAL* 4.2 17.3 - - + -
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 5.9 1.2 - - - +
70A LEU* 1.3 81.4 + - - +
72A ASP* 1.3 67.7 + - - +
75A ARG* 3.9 25.8 - - + +
76A GLN 3.2 13.2 - - - +
77A PRO* 3.8 23.7 - - + +
78A VAL* 4.2 1.1 - - - -
385A GLY 2.9 11.6 + - - +
386A TYR* 3.1 18.7 - - + +
387A VAL* 3.0 27.2 + - - -
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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