Contacts of the helix formed by residues 72 - 83 (chain A) in PDB entry 1HJV
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 3.4 23.0 + - - -
34A TYR* 3.9 0.2 + - - -
42A PHE* 4.9 1.8 - - - -
70A GLU* 4.3 1.4 - - - +
71A TRP* 1.3 130.7 + - + +
73A ASP* 1.3 66.8 + - - +
74A VAL* 3.2 3.6 - - - -
75A THR* 2.8 26.1 + - - +
76A LEU* 2.9 45.9 + - - +
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.9 0.9 - - - -
56A TYR* 2.4 39.4 + - - -
58A PHE 4.3 1.9 - - - +
68A THR* 3.7 14.0 - - + -
69A TRP* 2.7 34.5 + - - +
70A GLU* 2.8 36.1 + - - +
71A TRP 3.6 0.8 + - - -
72A ASN* 1.3 75.8 - - - +
74A VAL* 1.3 52.5 + - - +
76A LEU* 2.7 6.3 + - - +
77A TYR* 2.6 51.2 + - + -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 4.1 20.0 - - + +
71A TRP 5.8 2.5 - - - +
72A ASN* 3.2 1.7 - - - -
73A ASP* 1.3 77.3 - - - +
75A THR* 1.3 61.2 + - - +
77A TYR* 3.6 10.2 + - - +
78A GLY* 3.1 16.5 + - - -
130A HIS* 4.2 27.8 - - + +
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 2.8 21.0 + - - +
74A VAL* 1.3 79.6 - - - +
76A LEU* 1.3 66.4 + - + +
78A GLY* 2.8 16.6 + - - -
79A MET* 2.9 22.6 + - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.0 19.1 - - + +
30A SER 4.7 2.7 - - - +
33A GLN* 3.8 26.9 - - - +
42A PHE* 4.1 17.7 - - + -
43A PRO* 3.5 18.0 - - + +
56A TYR* 3.4 34.5 - - + +
72A ASN* 2.9 28.7 + - - +
73A ASP* 2.7 9.5 + - - +
75A THR* 1.3 75.0 - - + +
77A TYR* 1.3 62.3 + - - +
78A GLY 2.7 6.4 + - - -
79A MET* 2.8 21.0 + - - +
80A LEU* 2.9 15.1 + - - +
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Residues in contact with TYR 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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56A TYR* 3.5 34.3 - + - -
58A PHE 5.5 0.2 + - - -
59A ALA* 4.5 4.2 - - - +
68A THR* 3.2 43.7 - - + +
73A ASP* 2.6 27.9 + - + +
74A VAL* 3.8 12.3 - - - +
76A LEU* 1.3 71.0 - - - +
78A GLY* 1.3 56.7 + - - +
80A LEU* 4.1 3.8 - - - -
81A ASN* 2.9 41.0 + - - +
94A LEU* 3.8 19.5 - - + +
126A PHE* 3.7 23.7 - + - -
130A HIS* 3.8 31.1 - + + +
132A PHE* 3.7 24.9 - + + -
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Residues in contact with GLY 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 VAL 3.1 10.5 + - - -
75A THR* 2.8 9.3 + - - -
76A LEU 2.7 2.6 - - - -
77A TYR* 1.3 78.2 - - - +
79A MET* 1.3 63.3 + - - -
80A LEU 3.2 0.2 + - - -
81A ASN* 3.9 2.1 - - - +
82A THR* 3.1 27.1 + - - -
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Residues in contact with MET 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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42A PHE* 4.1 14.4 - - + -
43A PRO* 3.4 31.3 - - + +
44A ASP* 2.9 50.7 + - + +
75A THR* 2.9 22.6 + - + +
76A LEU* 2.8 13.5 + - - +
78A GLY* 1.3 72.4 - - - +
80A LEU* 1.3 63.0 + - - +
82A THR* 3.6 16.5 - - - +
83A LEU* 3.8 9.5 + - - +
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Residues in contact with LEU 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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28A TYR* 5.9 1.8 - - + -
43A PRO* 3.4 13.6 - - + +
46A LEU* 4.6 5.6 - - + -
54A ILE* 3.5 37.5 - - + +
56A TYR* 3.9 23.8 - - + -
76A LEU 2.9 14.6 + - - +
77A TYR* 4.1 2.2 - - - +
79A MET* 1.3 77.7 - - - +
81A ASN* 1.3 59.3 + - - +
83A LEU* 2.8 48.7 + - + +
84A LYS* 4.2 1.9 + - - +
90A LEU* 5.5 0.4 - - + -
92A THR* 4.0 19.1 - - + -
132A PHE* 3.8 28.7 - - + -
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Residues in contact with ASN 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 TYR 2.9 23.3 + - - +
78A GLY* 4.1 2.7 - - - +
80A LEU* 1.3 78.0 - - - +
82A THR* 1.3 61.0 + - - +
83A LEU 3.2 0.2 - - - -
84A LYS* 3.0 31.3 + - + +
85A ASN* 4.3 3.6 + - - -
92A THR* 2.9 20.4 + - - -
130A HIS 2.7 29.2 + - - +
131A GLY* 2.8 29.2 - - - +
132A PHE* 4.1 14.7 - - - -
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Residues in contact with THR 82 (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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48A ARG* 3.4 12.4 + - - +
78A GLY 3.1 13.4 + - - -
79A MET* 3.6 14.9 - - - +
80A LEU 3.0 0.4 + - - -
81A ASN* 1.3 71.0 - - - +
83A LEU* 1.3 60.3 + - + +
84A LYS 2.8 12.1 + - - -
85A ASN* 2.8 37.8 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.3 24.0 - - - +
44A ASP* 5.0 7.4 - - - +
46A LEU* 3.5 28.5 - - + +
48A ARG* 3.0 67.2 + - + +
54A ILE* 4.3 8.5 - - + -
79A MET 4.0 6.7 - - - +
80A LEU* 2.8 32.9 + - + +
82A THR* 1.3 78.9 - - + +
84A LYS* 1.3 57.9 + - - +
85A ASN 3.2 1.3 - - - -
87A ASN* 3.9 4.7 + - - +
90A LEU* 3.9 12.6 - - + +
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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