Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 2K6N
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 PRO 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA 4.7 0.2 - - - +
61A LEU* 1.3 110.5 - - + +
63A ALA* 1.3 53.1 + - - +
64A TRP* 3.4 7.9 - - + +
65A LYS* 3.5 37.7 - - + +
66A GLN* 2.7 33.7 - - - +
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Residues in contact with ALA 63 (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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61A LEU 4.6 0.2 - - - -
62A PRO* 1.3 72.6 - - - +
64A TRP* 1.3 52.9 + - - +
66A GLN* 3.1 17.9 - - - +
67A VAL* 2.7 36.2 - - - +
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Residues in contact with TRP 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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62A PRO* 4.6 7.2 - - + -
63A ALA* 1.3 78.6 - - - +
65A LYS* 1.3 91.7 + - + +
66A GLN 3.2 0.2 - - - -
67A VAL* 3.0 8.5 + - + +
68A ASN* 2.4 81.9 + - + -
71A LYS* 6.3 1.1 - - + -
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Residues in contact with LYS 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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61A LEU* 5.4 4.5 - - + -
62A PRO* 3.5 31.5 - - + +
63A ALA 3.6 0.2 - - - -
64A TRP* 1.3 109.5 - - + +
66A GLN* 1.3 68.0 + - - +
68A ASN* 2.9 24.1 - - + +
69A LEU* 3.4 12.0 + - + +
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Residues in contact with GLN 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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39A GLU* 2.5 25.4 + - - +
58A TYR* 2.7 65.5 + - + -
59A ASN* 5.0 0.4 - - - +
61A LEU* 3.6 5.7 + - + +
62A PRO* 2.7 24.1 + - - +
63A ALA* 3.1 22.6 - - - +
65A LYS* 1.3 80.0 - - - +
67A VAL* 1.3 74.8 + - - +
69A LEU 3.3 7.3 + - - -
70A LYS* 3.1 24.3 + - - +
76A PHE* 5.6 1.6 - - - -
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Residues in contact with VAL 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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63A ALA 2.7 24.9 - - - +
64A TRP* 3.0 9.6 + - + +
66A GLN* 1.3 79.4 - - + +
68A ASN* 1.3 67.2 + - - +
69A LEU 3.0 2.5 - - - -
70A LYS* 2.7 29.7 + - - +
71A LYS* 3.1 40.2 + - + +
76A PHE* 3.9 37.2 - - + -
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Residues in contact with ASN 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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64A TRP* 2.4 63.7 + - + +
65A LYS* 2.9 20.9 - - - +
67A VAL* 1.3 69.3 - - - +
69A LEU* 1.3 64.1 + - + +
71A LYS* 3.8 11.1 + - - +
72A ALA* 3.4 17.3 + - - +
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Residues in contact with LEU 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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51A LEU* 3.4 19.1 - - + +
52A ASP* 4.5 9.9 - - + +
53A MET* 5.5 5.8 - - - -
58A TYR* 2.7 31.4 - - + +
65A LYS* 3.4 11.8 + - + +
66A GLN 3.3 1.9 + - - +
67A VAL 2.8 1.4 + - - -
68A ASN* 1.3 86.9 - - + +
70A LYS* 1.3 57.0 + - - +
72A ALA* 2.7 35.1 + - + +
73A LYS* 2.9 16.4 + - + +
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Residues in contact with LYS 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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39A GLU* 2.6 33.1 + - + +
51A LEU* 2.9 45.1 - - + +
58A TYR* 3.3 3.8 - - - -
66A GLN* 3.1 45.1 + - - +
67A VAL* 2.7 19.3 + - - +
69A LEU* 1.3 70.7 - - - +
71A LYS* 1.3 48.8 + - - +
73A LYS* 3.2 1.8 + - - +
74A GLY 2.6 32.1 + - - -
75A LEU* 2.7 23.2 + - + -
76A PHE* 2.8 47.9 - - + +
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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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64A TRP* 6.3 1.2 - - + -
67A VAL* 3.1 33.8 + - + +
68A ASN* 4.0 10.5 - - - +
70A LYS* 1.3 75.7 - - - +
72A ALA* 1.3 63.7 + - - +
74A GLY* 3.2 14.2 + - - +
75A LEU 4.9 0.2 - - - +
76A PHE* 4.8 16.8 - - + +
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Residues in contact with ALA 72 (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 ASN 3.4 12.2 + - - +
69A LEU* 2.7 34.1 + - + +
71A LYS* 1.3 74.9 - - - +
73A LYS* 1.3 62.0 + - + +
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Residues in contact with LYS 73 (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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25A LEU* 4.3 17.7 - - + +
49A PHE 3.9 10.0 + - - +
50A ALA* 2.7 37.2 - - - +
51A LEU* 4.5 0.2 - - - -
52A ASP* 3.1 35.1 + - - +
69A LEU* 2.9 11.8 + - + +
70A LYS 3.9 5.2 - - - +
72A ALA* 1.3 83.1 - - - +
74A GLY* 1.3 60.1 + - - +
75A LEU* 4.6 5.2 - - + +
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Residues in contact with GLY 74 (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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25A LEU* 4.0 16.2 - - - +
38A LEU* 4.9 0.5 - - - +
70A LYS 2.6 12.5 + - - -
71A LYS* 3.2 13.1 + - - -
73A LYS* 1.3 77.1 - - - +
75A LEU* 1.3 63.0 + - - +
76A PHE* 4.5 3.5 - - - +
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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