Contacts of the helix formed by residues 59 - 73 (chain A) in PDB entry 4KBQ
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 3.5 39.5 - - - +
57A PRO 3.4 1.6 - - - -
58A LEU* 1.3 74.2 - - - +
60A ALA* 1.3 66.2 + - - +
61A VAL* 3.4 4.1 + - + +
62A TYR* 3.5 49.3 + - + +
63A TYR* 3.7 11.8 - - - -
89A LEU* 4.3 1.8 - - - -
608C THR* 4.0 13.5 - - + +
611C TYR* 3.7 31.6 - - + -
612C GLN* 4.2 9.6 - - + +
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Residues in contact with ALA 60 (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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58A LEU 4.0 2.8 + - - -
59A VAL* 1.3 72.1 - - - +
61A VAL* 1.3 67.3 + - + +
63A TYR* 2.9 23.8 + - - +
64A THR* 3.1 12.6 + - + -
86A ALA* 3.6 30.6 - - + +
89A LEU* 4.1 10.1 - - + +
90A ASP* 3.9 20.9 - - + +
93A SER* 5.9 2.2 - - - +
611C TYR 5.6 5.3 + - - +
612C GLN* 5.8 1.0 - - - +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 4.6 6.3 - - + -
59A VAL* 3.3 2.4 - - + +
60A ALA* 1.3 78.2 - - + +
62A TYR* 1.3 70.3 + - + +
64A THR* 2.8 23.8 + - - +
65A ASN* 2.8 34.1 + - - +
611C TYR* 3.9 39.2 - - + +
616C GLY* 5.5 3.4 - - - +
617C MET 5.1 7.6 - - - +
646C ASP* 3.7 30.5 - - + +
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Residues in contact with TYR 62 (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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26A ALA* 3.3 35.2 - - + +
27A GLN* 3.8 5.5 + - - -
30A LYS* 4.0 30.3 - - + -
49A TYR* 4.0 15.2 - + + +
52A ALA* 3.4 40.6 - - + -
53A ILE* 3.6 20.8 - - + +
56A ASN 3.8 15.3 - - - -
59A VAL* 3.5 37.5 + - + +
60A ALA 3.2 1.0 + - - -
61A VAL* 1.3 78.3 - - + +
63A TYR* 1.3 60.8 + - - +
65A ASN* 4.0 4.6 - - - +
66A ARG* 3.3 23.6 + - - +
608C THR* 4.1 13.2 + - - +
611C TYR* 5.0 5.6 - + - -
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.3 45.1 - - + +
57A PRO* 3.1 35.0 + - - +
59A VAL 3.7 14.6 - - - -
60A ALA* 2.9 12.8 + - - +
62A TYR* 1.3 75.8 - - - +
64A THR* 1.3 59.9 + - - +
66A ARG* 3.3 4.0 + - - -
67A ALA* 3.0 23.6 + - - +
82A ASP* 3.3 47.7 - - - +
85A ARG* 3.4 36.3 - - + -
86A ALA* 4.0 6.5 - - + -
89A LEU* 4.0 11.7 - - + -
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Residues in contact with THR 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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60A ALA* 3.1 4.9 + - + +
61A VAL* 2.8 30.5 + - - +
63A TYR* 1.3 71.9 - - - +
65A ASN* 1.3 66.8 + - - +
67A ALA* 3.3 9.0 + - - +
68A LEU* 3.2 20.8 + - - +
82A ASP 5.4 0.4 - - - -
83A CYS* 5.6 2.5 - - - -
86A ALA* 3.9 11.7 - - + -
93A SER* 4.4 4.3 - - - +
95A LYS* 4.2 7.7 - - + +
96A ALA* 3.7 41.3 - - + +
99A PHE* 3.9 17.1 - - + -
646C ASP* 5.6 0.9 + - - -
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Residues in contact with ASN 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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30A LYS* 4.1 5.1 - - - +
34A ASN* 3.5 4.2 + - - -
49A TYR* 3.5 38.6 - - + -
61A VAL* 2.8 33.0 + - - +
62A TYR 4.0 0.4 - - - +
64A THR* 1.3 73.6 + - - +
66A ARG* 1.3 63.9 + - - +
68A LEU* 3.1 16.7 + - - +
69A CYS* 3.2 14.2 + - - -
95A LYS* 5.8 0.2 + - - -
99A PHE* 5.8 1.1 - - - -
644C GLU 4.7 0.3 - - - +
645C VAL* 3.3 18.4 - - + +
646C ASP* 3.0 42.2 + - - +
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Residues in contact with ARG 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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46A ALA* 3.7 34.3 - - + +
49A TYR* 3.8 15.5 - - + -
50A GLY* 3.6 22.6 - - - -
53A ILE* 3.6 21.2 - - - +
62A TYR 3.3 14.1 + - - +
63A TYR* 3.3 5.6 + - - +
64A THR 3.3 0.4 - - - -
65A ASN* 1.3 78.8 - - - +
67A ALA* 1.3 62.6 + - - +
69A CYS* 3.2 4.6 + - - +
70A TYR* 3.0 52.6 + - + -
82A ASP* 2.6 39.9 + - - +
85A ARG* 4.0 8.9 - - - +
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Residues in contact with ALA 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 TYR 3.0 13.7 + - - +
64A THR* 3.4 12.6 - - - +
66A ARG* 1.3 76.9 - - - +
68A LEU* 1.3 55.3 + - - +
70A TYR* 3.2 3.3 + - - -
71A LEU* 2.9 28.2 + - - +
79A ALA* 3.3 42.8 - - + +
82A ASP* 3.8 6.7 + - + -
83A CYS* 4.1 13.9 - - - +
99A PHE* 5.0 5.6 - - + -
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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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37A PHE* 3.5 30.3 - - + -
64A THR 3.2 8.8 + - - +
65A ASN* 3.1 14.4 + - - +
67A ALA* 1.3 77.1 - - - +
69A CYS* 1.3 60.9 + - - +
71A LEU* 3.4 21.0 + - + -
72A LYS* 3.1 29.6 + - + +
99A PHE* 4.3 22.8 - - + -
643C GLU* 4.0 21.1 - - - +
644C GLU 3.8 33.9 - - - +
645C VAL* 4.0 3.6 - - + +
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Residues in contact with CYS 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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37A PHE* 4.0 21.8 - - - -
42A TYR* 4.1 15.8 - - + +
45A ALA* 4.1 2.5 - - - -
46A ALA* 4.0 27.4 - - + -
49A TYR* 3.7 35.0 - - - -
65A ASN 3.2 10.6 + - - -
66A ARG* 3.2 9.1 + - - +
68A LEU* 1.3 75.0 - - - +
70A TYR* 1.3 59.3 + - - +
72A LYS* 3.3 2.6 + - - +
73A MET* 2.8 35.7 + - - +
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Residues in contact with TYR 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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46A ALA* 4.8 10.0 - - + +
66A ARG* 3.0 46.3 + - + -
67A ALA 3.3 7.2 - - - +
68A LEU 3.2 0.2 - - - -
69A CYS* 1.3 77.3 - - + +
71A LEU* 1.3 64.4 + - - +
73A MET* 3.1 15.6 + - + +
74A GLN 3.0 5.2 + - - -
75A GLN* 2.9 56.4 + - - +
78A GLN* 3.8 35.1 + - + -
79A ALA* 3.6 19.7 - - + +
82A ASP* 3.5 22.9 - - - -
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Residues in contact with LEU 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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67A ALA 2.9 17.9 + - - +
68A LEU* 3.5 22.2 - - + +
70A TYR* 1.3 76.8 - - - +
72A LYS* 1.3 61.4 + - + +
74A GLN* 3.1 19.2 + - - +
75A GLN 4.8 1.6 - - - +
76A HIS* 5.1 13.6 + - - +
79A ALA* 4.3 2.0 - - + +
99A PHE* 4.2 28.0 - - + +
102A GLN* 3.7 28.3 - - + +
103A CYS* 3.7 30.3 - - - +
106A GLU* 5.1 9.3 - - - +
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Residues in contact with LYS 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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37A PHE* 4.4 15.9 - - + -
42A TYR* 3.7 50.4 + - + +
68A LEU* 3.1 23.6 + - + +
69A CYS 3.8 3.8 - - - +
70A TYR 3.2 0.2 - - - -
71A LEU* 1.3 77.0 - - + +
73A MET* 1.3 59.8 + - - +
74A GLN* 3.1 8.5 + - - +
643C GLU* 3.9 27.6 + - - +
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Residues in contact with MET 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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42A TYR* 3.9 18.2 - - + +
43A PRO* 3.9 40.6 - - + -
46A ALA* 5.0 2.0 - - + -
69A CYS* 2.8 25.1 + - - +
70A TYR* 3.1 17.4 + - + +
72A LYS* 1.3 76.6 - - - +
74A GLN* 1.3 69.7 + - - +
75A GLN* 3.3 37.5 + - - +
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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
------------------------------------------------------------
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