Contacts of the helix formed by residues 62 - 76 (chain B) in PDB entry 4H3E
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 LYS 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASN* 3.8 39.9 - - + +
54B ARG* 5.3 9.0 - - - +
57B GLU* 5.4 4.3 - - - -
58B LEU* 3.1 31.1 + - + +
61B THR* 1.3 95.5 + - - +
63B HIS* 1.3 62.9 + - - +
65B LYS* 3.9 0.5 - - - +
66B ALA* 2.9 32.2 + - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU* 3.7 8.2 + - - -
201A TYR* 2.8 30.6 + + - -
206A ASN* 3.5 26.0 - - + +
58B LEU 3.0 29.6 + - - -
59B HIS* 3.4 19.5 - - + +
62B LYS* 1.3 76.5 - - - +
64B HIS* 1.3 64.1 + - - +
66B ALA* 3.2 6.7 + - - +
67B TYR* 3.1 36.0 + - + -
110B HIS* 4.9 0.2 - - - +
198B HIS* 3.4 44.2 + + + +
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 13.2 - - + +
37B PRO* 3.9 14.4 - - + -
59B HIS 2.9 13.5 + - - +
60B TYR* 3.3 19.3 + + - +
63B HIS* 1.3 75.2 - - - +
65B LYS* 1.3 66.0 + - - +
67B TYR* 3.0 18.8 + - + +
68B VAL* 3.0 12.4 + - + +
107B HIS* 3.1 39.2 + - - -
110B HIS* 3.6 19.4 - + + +
111B THR* 3.3 34.5 - - - -
114B PHE* 3.6 17.2 - + + -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.8 27.0 - - + +
60B TYR 3.1 9.2 + - - +
61B THR* 3.3 32.5 - - - +
62B LYS 4.8 0.2 - - - +
63B HIS 3.4 0.2 - - - -
64B HIS* 1.3 75.1 - - - +
66B ALA* 1.3 58.0 + - - +
68B VAL* 3.1 5.7 + - - +
69B ASP* 2.8 64.5 + - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 2.9 20.7 + - - +
63B HIS* 3.6 4.9 - - - +
65B LYS* 1.3 77.6 - - - +
67B TYR* 1.3 58.2 + - + +
69B ASP* 3.8 8.3 - - - +
70B LYS* 2.9 32.4 + - - +
103B GLN* 4.6 0.9 - - - -
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 4.1 15.0 - + - -
63B HIS* 3.1 35.3 + - + -
64B HIS* 3.0 8.3 + - - +
66B ALA* 1.3 76.3 - - + +
68B VAL* 1.3 59.5 + - - +
71B LEU* 2.9 30.2 + - - +
103B GLN* 3.2 38.2 - - - +
106B GLN* 3.1 40.8 + - + -
107B HIS* 4.3 8.3 - - - +
110B HIS* 3.3 35.0 - + - -
196B TRP* 3.6 22.3 - - - -
198B HIS* 4.1 4.8 - + - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.3 30.3 - - + +
35B GLU 4.1 9.9 - - - -
36B LEU* 4.0 24.0 - - + +
64B HIS* 3.0 17.2 + - + +
65B LYS* 3.6 8.5 - - - +
67B TYR* 1.3 77.3 - - - +
69B ASP* 1.3 67.6 + - - +
71B LEU* 3.3 8.5 + - - +
72B ASN* 3.0 28.0 + - - +
107B HIS* 3.6 32.8 - - + +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 2.8 53.3 + - - +
66B ALA* 3.8 7.1 - - - +
68B VAL* 1.3 82.2 - - - +
70B LYS* 1.3 57.2 + - - +
72B ASN* 3.4 8.7 + - - +
73B ALA* 3.1 26.5 + - - +
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Residues in contact with LYS 70 (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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152A ASN* 4.2 16.2 + - - -
66B ALA 2.9 12.7 + - - +
69B ASP* 1.3 72.6 - - - +
71B LEU* 1.3 66.6 + - - +
73B ALA* 3.3 10.3 + - + +
74B LEU* 2.9 46.3 + - + +
103B GLN* 3.3 38.5 - - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 5.8 2.9 - - + -
34B ALA* 4.7 9.9 - - + -
67B TYR 2.9 19.8 + - - +
68B VAL* 3.3 6.3 + - - +
70B LYS* 1.3 77.0 - - - +
72B ASN* 1.3 60.9 + - - +
74B LEU* 3.7 0.7 - - - +
75B ALA* 2.8 40.5 + - + +
84B ILE* 3.9 15.0 - - + -
87B ILE* 5.0 8.3 - - + -
100B LEU* 3.5 25.6 - - + -
103B GLN* 3.8 13.1 - - + +
104B ALA* 3.9 20.4 - - + +
107B HIS* 3.6 36.6 - - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 3.5 16.6 - - - +
33B PRO* 3.5 17.5 - - + +
34B ALA* 2.8 52.0 + - - +
68B VAL* 3.0 26.5 + - - +
69B ASP* 3.7 10.7 + - - +
71B LEU* 1.3 76.5 - - - +
73B ALA* 1.3 63.2 + - - +
75B ALA* 4.1 3.3 - - - +
76B GLY* 3.2 23.2 + - - +
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Residues in contact with ALA 73 (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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69B ASP 3.1 16.8 + - - +
70B LYS* 3.3 13.9 + - + +
72B ASN* 1.3 76.7 - - - +
74B LEU* 1.3 63.1 + - + +
76B GLY* 3.8 6.1 + - - -
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Residues in contact with LEU 74 (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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70B LYS* 2.9 43.7 + - + +
71B LEU 4.0 1.8 - - - +
73B ALA* 1.3 77.0 - - + +
75B ALA* 1.3 61.5 + - - +
76B GLY 3.6 0.2 + - - -
79B TYR* 5.1 1.4 - - - -
99B GLY* 3.6 14.1 - - - +
100B LEU* 3.6 46.5 - - + +
103B GLN* 4.0 10.1 - - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 4.7 10.5 - - + -
71B LEU* 2.8 28.9 + - + +
72B ASN* 4.1 4.0 - - - +
74B LEU* 1.3 75.0 - - - +
76B GLY* 1.3 69.6 + - - +
77B THR 4.0 0.2 - - - -
78B THR* 3.1 27.3 + - - -
79B TYR* 3.9 28.7 - - + -
87B ILE* 5.6 0.7 - - + -
100B LEU* 4.1 9.6 - - + +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 3.8 15.2 + - - -
72B ASN 3.2 13.3 + - - +
73B ALA 3.8 5.3 + - - -
74B LEU 3.4 2.8 + - - -
75B ALA* 1.3 77.7 - - - +
77B THR* 1.3 62.6 + - - +
78B THR* 5.0 0.9 - - - -
79B TYR 4.9 0.2 + - - -
80B ASP* 3.6 9.2 - - - +
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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
------------------------------------------------------------
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