Contacts of the helix formed by residues 69 - 81 (chain A) in PDB entry 2H7B
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 ASN 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 2.6 30.4 - - - +
7A LEU* 3.0 47.0 - - + +
8A LYS 4.2 1.0 + - - -
65A PHE* 2.7 26.5 + - - +
66A LEU* 3.1 7.0 + - - -
68A ALA* 1.3 82.2 - - - +
70A LEU* 1.3 55.8 + - - +
71A PRO* 3.2 3.6 - - - -
72A LEU* 2.7 10.8 + - + +
73A LEU* 2.7 41.6 + - + +
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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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36A LEU* 3.3 56.3 - - + +
37A VAL* 4.5 6.1 - - - +
43A ILE* 3.7 21.5 - - + +
66A LEU* 2.7 23.2 + - + +
67A LYS 4.4 5.2 - - - +
69A ASN* 1.3 79.5 - - - +
71A PRO* 1.3 67.8 - - + +
73A LEU* 3.2 2.6 + - - +
74A GLN* 3.2 21.9 + - + +
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Residues in contact with PRO 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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4A LEU* 5.8 1.3 - - + -
67A LYS 4.6 3.8 - - - +
68A ALA 4.2 5.8 - - - +
69A ASN 3.3 5.6 - - - +
70A LEU* 1.3 99.0 - - + +
72A LEU* 1.3 71.2 + - + +
74A GLN* 3.2 16.8 - - + +
75A ARG* 2.8 35.1 + - - +
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Residues in contact with LEU 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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0A SER 4.3 2.2 - - - +
1A ALA* 3.3 26.5 - - + +
4A LEU* 3.8 14.6 - - + -
5A SER* 3.0 34.8 - - - +
8A LYS* 3.3 23.1 - - + +
68A ALA 3.8 20.4 - - - +
69A ASN* 2.7 15.6 + - + +
71A PRO* 1.3 90.6 - - + +
73A LEU* 1.3 59.2 + - + +
74A GLN 3.4 0.4 - - - -
75A ARG* 3.3 31.2 + - - +
76A GLU* 3.3 11.8 + - - +
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Residues in contact with LEU 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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7A LEU* 4.1 2.5 - - + -
8A LYS* 4.3 5.4 - - - -
11A LEU* 3.4 46.9 - - + -
15A GLN* 3.7 9.9 - - - +
33A VAL* 4.1 4.7 - - + -
37A VAL* 3.9 14.6 - - + -
66A LEU* 4.0 12.1 - - + -
69A ASN* 2.7 31.8 + - + +
70A LEU* 3.8 4.5 - - - +
72A LEU* 1.3 78.1 - - - +
74A GLN* 1.3 57.6 + - - +
75A ARG 3.0 8.6 + - - -
76A GLU* 2.9 55.5 - - - +
77A LEU* 3.5 11.4 + - - +
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Residues in contact with GLN 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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37A VAL* 3.6 29.8 - - + +
70A LEU* 3.2 17.4 + - + +
71A PRO* 3.2 20.1 + - + +
73A LEU* 1.3 76.4 - - - +
75A ARG* 1.3 97.9 + - - +
77A LEU* 3.9 10.0 - - - +
78A LEU* 4.5 7.8 + - - +
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Residues in contact with ARG 75 (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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1A ALA* 5.6 5.8 - - - +
8A LYS* 5.5 3.6 - - + -
71A PRO* 2.8 30.7 + - - +
72A LEU* 3.3 29.2 - - - +
74A GLN* 1.3 109.5 + - - +
76A GLU* 1.3 66.0 + - - +
77A LEU 3.0 1.3 - - - -
78A LEU* 3.1 25.0 + - - +
79A HIS* 4.1 1.2 + - - +
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Residues in contact with GLU 76 (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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8A LYS* 2.9 41.5 - - + +
12A THR* 2.6 48.7 + - + +
15A GLN* 3.6 6.5 + - - +
72A LEU 3.3 6.2 + - - +
73A LEU* 2.9 40.5 - - + +
75A ARG* 1.3 76.9 - - - +
77A LEU* 1.3 60.6 + - + +
79A HIS* 2.7 32.5 + - + +
80A ALA* 3.1 11.3 + - - +
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Residues in contact with LEU 77 (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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15A GLN* 4.7 7.2 - - - +
34A LEU* 3.6 26.9 - - + -
37A VAL* 3.4 25.6 - - + -
38A ASN* 3.4 30.7 - - - +
73A LEU 3.5 11.2 + - - +
74A GLN 3.9 8.3 - - - +
75A ARG 3.0 0.2 - - - -
76A GLU* 1.3 83.8 - - + +
78A LEU* 1.3 60.2 + - + +
79A HIS 3.3 0.5 + - - -
80A ALA* 3.4 13.1 + - + +
81A ALA* 3.5 11.3 + - - +
88A PRO* 3.8 15.2 - - - +
91A TYR* 3.6 28.7 - - + -
92A LEU 5.6 0.2 - - - +
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Residues in contact with LEU 78 (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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74A GLN 4.5 7.4 + - - +
75A ARG* 3.1 15.1 + - - +
76A GLU 3.0 0.6 - - - -
77A LEU* 1.3 79.7 - - + +
79A HIS* 1.3 58.4 + - - +
81A ALA* 4.2 4.4 + - - +
82A ARG* 3.5 21.0 + - - +
88A PRO* 3.3 34.5 - - + +
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Residues in contact with HIS 79 (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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75A ARG 4.1 0.4 + - - +
76A GLU* 2.7 17.4 + - + +
78A LEU* 1.3 77.9 - - - +
80A ALA* 1.3 65.4 + - - +
81A ALA 3.2 1.8 - - - -
82A ARG* 3.0 28.2 + - + +
83A LEU* 3.2 21.5 + - + +
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Residues in contact with ALA 80 (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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12A THR* 6.4 1.6 - - + -
15A GLN* 5.7 2.5 - - - +
16A GLN* 5.0 10.5 - - - +
76A GLU* 3.1 10.1 + - + +
77A LEU* 3.4 14.1 + - + +
79A HIS* 1.3 77.1 - - - +
81A ALA* 1.3 50.8 + - - +
83A LEU* 2.8 10.1 + - - +
84A ALA* 2.7 37.5 + - - +
91A TYR* 3.9 30.3 - - + +
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Residues in contact with ALA 81 (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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77A LEU 3.5 4.6 + - - +
78A LEU 4.2 3.8 - - - +
79A HIS 3.2 0.6 - - - -
80A ALA* 1.3 78.1 - - - +
82A ARG* 1.3 64.4 + - - +
84A ALA* 4.1 6.3 - - - -
85A LYS* 3.1 17.7 + - - -
86A GLN 2.9 32.2 + - - +
87A ASN 3.2 26.0 - - - +
88A PRO* 3.2 18.8 - - + -
91A TYR* 4.6 4.8 - - + -
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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