Contacts of the helix formed by residues 60 - 79 (chain B) in PDB entry 4H3K
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 THR 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B LYS 3.7 2.5 + - - -
59B THR* 1.3 75.4 - - - +
61B TYR* 1.3 63.5 + - - +
62B ASP* 3.0 28.5 - - + +
63B GLN* 3.0 36.1 + - + +
64B MET* 3.0 22.6 + - - +
89B LYS* 5.9 0.2 - - + -
93B PRO* 3.3 23.1 + - - +
94B ARG* 4.0 6.6 - - - +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN 2.9 18.8 + - - -
16B GLN* 3.4 39.9 - - - -
20B MET* 3.4 11.5 - - + +
59B THR 3.9 0.6 + - - -
60B THR* 1.3 71.9 - - - +
62B ASP* 1.3 56.2 + - - +
64B MET* 3.2 5.9 + - - +
65B TYR* 2.8 28.6 + - - +
85B LEU* 3.9 26.6 - - + +
88B ASN* 3.5 31.4 - - + -
89B LYS* 4.2 7.0 - - + +
92B LYS* 3.2 39.0 - - + -
93B PRO 3.1 16.9 + - - +
94B ARG* 3.4 16.1 - - - +
95B PRO* 3.3 21.9 - - + +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.0 14.0 - - + +
61B TYR* 1.3 76.4 - - - +
63B GLN* 1.3 66.8 + - - +
65B TYR* 3.3 12.7 + - - +
66B ASN* 3.0 49.8 + - - +
89B LYS* 3.8 38.8 + - + +
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 5.7 0.4 - - - -
58B LYS 4.5 2.3 - - - +
59B THR* 3.7 17.5 - - + -
60B THR* 3.0 47.7 + - + +
62B ASP* 1.3 76.0 - - + +
64B MET* 1.3 56.7 + - - +
66B ASN* 3.3 7.3 + - - +
67B ASP* 2.9 31.1 + - - +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.2 31.6 - - - +
42B VAL* 4.2 3.4 - - + -
44B LEU* 3.8 13.7 - - + -
55B TYR* 3.9 40.3 + - + -
56B ASP 4.4 1.6 - - - +
59B THR* 3.2 38.6 - - + +
60B THR 3.0 11.5 + - - +
61B TYR* 3.2 8.9 + - - +
63B GLN* 1.3 71.9 - - - +
65B TYR* 1.3 60.9 + - - +
67B ASP* 3.7 6.2 - - - +
68B LEU* 2.9 35.3 + - - +
85B LEU* 3.8 17.5 - - + -
95B PRO* 4.0 12.3 - - + -
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR 2.8 13.7 + - - +
62B ASP* 3.3 17.5 - - - +
64B MET* 1.3 77.4 - - - +
66B ASN* 1.3 65.1 + - - +
68B LEU 3.2 1.0 + - - -
69B LEU* 2.8 59.3 + - + +
82B LEU* 3.3 56.3 - - + +
85B LEU* 3.6 17.9 - - + +
86B ASP* 4.3 17.7 - - + -
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.0 42.5 + - - +
63B GLN* 3.9 6.4 - - - +
65B TYR* 1.3 85.2 - - - +
67B ASP* 1.3 64.3 + - - +
69B LEU* 3.7 13.9 - - + +
70B ARG* 2.9 38.0 + - + +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 2.4 35.9 + - + +
63B GLN 2.9 17.9 + - - +
64B MET* 3.7 5.2 - - - +
66B ASN* 1.3 76.8 - - - +
68B LEU* 1.3 55.7 + - - +
70B ARG* 3.4 9.2 + - - +
71B LYS* 3.1 46.8 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.2 12.8 - - + -
53B ASN* 3.8 21.3 - - - +
55B TYR* 3.2 24.9 - - - +
64B MET 2.9 21.7 + - - +
65B TYR 3.8 3.4 - - - +
67B ASP* 1.3 76.6 - - - +
69B LEU* 1.3 64.5 + - - +
71B LYS* 3.9 13.5 - - + +
72B ASP 3.2 22.0 + - - -
73B LYS* 4.4 0.3 - - - -
76B TYR* 3.6 31.1 - - + +
81B ILE* 3.8 28.7 - - + -
82B LEU* 3.9 12.8 - - + -
85B LEU* 3.8 9.4 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 2.8 43.1 + - + +
66B ASN* 3.3 15.0 + - - +
68B LEU* 1.3 72.9 - - - +
70B ARG* 1.3 62.1 + - - +
73B LYS* 3.5 40.0 + - + +
82B LEU* 4.0 23.3 - - + +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 2.9 27.8 + - - +
67B ASP* 3.6 9.6 - - - +
69B LEU* 1.3 78.0 - - + +
71B LYS* 1.3 69.1 + - + +
72B ASP* 3.5 0.5 + - - -
73B LYS 4.9 0.3 + - - -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 6.5 0.2 - - - -
53B ASN* 3.4 23.9 + - - -
67B ASP* 3.1 41.5 + - - +
68B LEU* 3.4 12.7 + - + +
70B ARG* 1.3 83.5 - - + +
72B ASP* 1.3 63.0 + - + +
76B TYR* 4.5 11.0 - - + -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 3.2 6.9 + - - -
70B ARG 4.5 0.2 - - - -
71B LYS* 1.3 81.9 - - + +
73B LYS* 1.3 67.0 + - - +
74B GLU* 2.8 14.5 + - - +
75B LEU* 3.0 45.0 + - + +
76B TYR* 3.2 30.0 + - + -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 4.4 2.2 - - - -
69B LEU* 3.5 40.2 + - + +
70B ARG 4.9 0.4 + - - -
72B ASP* 1.3 73.8 + - - +
74B GLU* 1.3 66.1 + - + +
77B THR* 2.5 48.0 + - - +
82B LEU* 4.0 3.6 - - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 2.8 10.8 + - - +
73B LYS* 1.3 92.9 - - + +
75B LEU* 1.3 65.1 + - - +
77B THR* 3.4 5.1 + - - -
78B GLN* 3.0 42.2 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 4.2 3.4 - - - +
47B PRO* 3.6 41.1 - - + +
72B ASP* 3.0 32.0 + - + +
74B GLU* 1.3 75.7 - - - +
76B TYR* 1.3 77.0 + - + +
78B GLN* 3.2 9.8 + - + +
79B ASN* 2.9 47.2 + - + +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO 3.4 20.9 - - - -
46B GLY* 3.5 12.3 - - - -
47B PRO* 3.6 10.0 - - - +
53B ASN* 2.9 26.5 + - - -
68B LEU* 3.6 35.0 - - + +
71B LYS* 4.5 8.5 - - + -
72B ASP* 3.2 42.9 + - + +
75B LEU* 1.3 82.8 - - + +
77B THR* 1.3 61.7 + - - +
79B ASN* 3.2 24.7 - - - +
80B GLY 4.1 0.2 - - - -
81B ILE* 3.4 17.4 + - + -
82B LEU* 2.8 53.6 + - + +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 2.5 38.3 + - - +
74B GLU* 3.8 5.8 - - - -
76B TYR* 1.3 76.7 - - - +
78B GLN* 1.3 70.8 + - - +
80B GLY* 3.4 12.1 + - - -
82B LEU* 3.8 14.3 - - + +
83B HIS* 6.0 0.6 - - - +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU* 3.0 42.5 + - + +
75B LEU* 3.2 12.1 + - + +
77B THR* 1.3 84.4 - - - +
79B ASN* 1.3 57.5 + - + +
80B GLY 3.2 3.2 + - - -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 4.7 6.6 + - + +
46B GLY 4.9 4.2 + - - -
75B LEU* 2.9 36.5 + - + +
76B TYR* 3.2 21.8 - - - -
78B GLN* 1.3 74.8 - - + +
80B GLY* 1.3 54.8 + - - +
81B ILE* 3.1 44.6 + - - +
145B HIS* 3.1 18.7 + - - -
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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
------------------------------------------------------------
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