Contacts of the helix formed by residues 78 - 94 (chain A) in PDB entry 1HMU
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 PRO 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 12.4 - - + +
67A PRO 3.4 16.6 - - - +
68A TYR* 4.1 7.6 - - - +
70A ASP* 3.4 29.4 - - + +
76A TRP* 3.3 36.1 - - + +
77A LEU* 1.3 90.3 - - + +
79A ASN* 1.3 61.6 + - - +
81A HIS* 3.0 14.9 + - - +
116A TRP* 3.1 17.9 - - + -
121A PRO* 3.7 16.2 - - + -
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Residues in contact with ASN 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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76A TRP* 3.3 34.5 + - + +
77A LEU 2.9 0.6 + - - -
78A PRO* 1.3 78.6 - - - +
80A ASN* 1.3 62.9 + - - +
81A HIS 3.0 0.7 - - - -
82A LEU* 2.9 39.0 + - - +
83A LEU* 3.1 32.6 + - + +
116A TRP* 4.4 2.9 - - - -
128A HIS* 6.0 1.8 - - + +
132A ALA* 5.3 10.7 + - - +
133A THR* 5.2 1.4 + - - -
136A ALA* 4.9 5.7 - - - +
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Residues in contact with ASN 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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66A VAL* 4.1 15.0 - - + +
67A PRO* 5.8 1.2 - - - +
77A LEU* 2.9 43.3 + - - +
79A ASN* 1.3 77.6 - - - +
81A HIS* 1.3 57.1 + - - +
83A LEU* 3.8 20.8 - - - +
84A GLN* 3.0 47.6 + - + +
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.2 26.9 - - - -
63A TRP* 3.3 26.3 - + - -
66A VAL* 4.3 5.6 - - + +
68A TYR* 2.7 35.8 + + + +
78A PRO 3.0 13.7 + - - +
79A ASN 3.0 0.6 - - - -
80A ASN* 1.3 79.1 - - - +
82A LEU* 1.3 62.6 + - + +
84A GLN 3.4 0.2 + - - -
85A LEU* 2.9 33.1 + - + +
112A ALA* 3.0 27.7 + - - +
115A TYR* 4.2 5.8 - + - -
116A TRP* 3.5 33.8 - + + +
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Residues in contact with LEU 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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79A ASN* 2.9 26.5 + - - +
81A HIS* 1.3 80.2 - - + +
83A LEU* 1.3 60.7 + - + +
85A LEU* 3.3 3.5 + - + -
86A GLU* 2.9 26.4 + - - +
113A PHE* 5.5 2.0 - - + -
116A TRP* 3.5 48.2 - - + -
133A THR* 4.2 9.6 - - + +
136A ALA* 3.8 20.4 - - + -
137A LEU* 3.4 28.3 - - + -
140A MET* 3.0 29.5 - - + +
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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
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79A ASN* 3.1 33.6 + - + +
80A ASN* 3.9 26.0 - - - +
82A LEU* 1.3 77.9 - - + +
84A GLN* 1.3 64.2 + - + +
86A GLU* 3.1 19.2 + - + +
87A THR* 3.3 17.6 + - - +
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Residues in contact with GLN 84 (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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53A ASN* 3.3 32.1 + - - +
63A TRP* 3.2 47.4 - - + +
66A VAL* 4.4 6.6 - - - +
80A ASN* 3.0 34.4 + - - +
81A HIS 3.9 0.4 - - - +
83A LEU* 1.3 77.7 - - + +
85A LEU* 1.3 61.2 + - - +
87A THR* 2.6 23.7 + - - -
88A ILE* 3.4 9.4 + - - +
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Residues in contact with LEU 85 (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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57A LEU* 6.1 0.2 - - + -
63A TRP* 3.7 13.1 - - + -
81A HIS* 2.9 24.0 + - + +
82A LEU* 5.2 2.2 - - + -
84A GLN* 1.3 76.9 - - - +
86A GLU* 1.3 63.1 + - - +
88A ILE* 3.1 8.6 + - + -
89A ILE* 3.0 25.8 + - + +
109A ILE* 4.1 26.9 - - + -
112A ALA* 3.6 33.0 - - + -
113A PHE* 3.8 33.4 - - + +
116A TRP* 6.1 0.4 - - + -
140A MET* 3.5 21.3 - - + -
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Residues in contact with GLU 86 (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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39A LEU 4.6 0.2 - - - +
41A LYS* 3.5 27.4 + - - +
82A LEU 2.9 14.1 + - - +
83A LEU* 3.1 15.5 + - + +
85A LEU* 1.3 78.3 - - - +
87A THR* 1.3 74.0 + - - +
89A ILE* 3.1 7.0 + - - +
90A GLN* 2.9 51.5 + - - +
140A MET* 3.4 23.3 - - + +
143A LEU* 4.5 8.3 - - + +
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Residues in contact with THR 87 (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 MET* 4.7 3.1 - - - +
49A VAL* 3.5 32.4 + - + +
50A ALA* 3.8 11.6 + - - +
53A ASN* 3.0 17.1 + - - +
83A LEU 3.5 13.5 - - - +
84A GLN* 2.6 20.3 + - - +
86A GLU* 1.3 85.8 + - - +
88A ILE* 1.3 64.1 + - - +
90A GLN* 3.7 7.4 + - - +
91A ALA* 3.7 12.5 + - - +
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Residues in contact with ILE 88 (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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50A ALA* 4.1 19.5 - - + +
53A ASN* 4.1 1.6 - - + -
54A LEU* 3.8 37.0 - - + +
57A LEU* 4.7 6.1 - - + -
63A TRP* 3.7 33.0 - - + -
84A GLN 3.5 9.0 - - - +
85A LEU* 3.1 11.0 + - + +
86A GLU 3.1 0.4 - - - -
87A THR* 1.3 85.4 + - - +
89A ILE* 1.3 64.9 + - - +
91A ALA* 3.4 5.3 + - + +
92A TYR* 3.1 19.8 + - - +
105A VAL* 3.8 24.7 - - + +
108A GLN* 6.0 0.2 - - + -
109A ILE* 3.9 13.0 - - + +
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Residues in contact with ILE 89 (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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85A LEU* 3.0 22.8 + - + +
86A GLU* 3.6 7.4 - - - +
88A ILE* 1.3 75.3 - - - +
90A GLN* 1.3 67.7 + - - +
92A TYR* 3.3 3.3 + - - +
93A ILE* 3.3 20.7 + - + +
109A ILE* 4.1 25.6 - - + -
113A PHE* 3.8 21.5 - - + -
140A MET* 3.7 38.8 - - + +
143A LEU* 3.8 33.0 - - + -
144A MET* 3.8 17.3 - - + +
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Residues in contact with GLN 90 (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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39A LEU 3.1 22.6 + - - -
40A LYS* 3.8 11.3 + - - +
41A LYS* 3.0 35.0 + - + +
46A MET* 3.9 23.2 - - + +
86A GLU* 2.9 43.6 + - - +
87A THR* 3.7 9.9 - - - +
89A ILE* 1.3 77.2 - - - +
91A ALA* 1.3 63.5 + - - +
93A ILE* 3.3 9.5 - - - +
94A GLU* 3.1 21.8 + - - +
143A LEU* 3.4 19.9 - - - +
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Residues in contact with ALA 91 (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 MET* 3.7 12.5 - - + -
47A ASP* 3.9 5.6 - - - +
50A ALA* 3.8 27.1 - - + -
87A THR 3.7 1.6 + - - +
88A ILE* 3.4 9.1 + - + +
89A ILE 3.3 0.4 - - - -
90A GLN* 1.3 79.1 - - - +
92A TYR* 1.3 64.8 + - - +
94A GLU 2.9 12.6 + - - +
97A SER* 3.1 32.9 - - - +
99A TYR* 4.1 9.4 - - + -
100A TYR* 3.8 1.7 - - - -
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Residues in contact with TYR 92 (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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88A ILE 3.1 5.8 + - - +
89A ILE 3.3 7.6 + - - +
91A ALA* 1.3 78.7 - - - +
93A ILE* 1.3 63.7 + - + +
99A TYR* 4.0 8.2 - - - +
100A TYR* 3.4 4.5 - - - -
101A GLY* 2.8 42.9 + - - -
102A ASP 3.4 27.5 - - - -
103A ASP* 5.6 0.2 + - - -
105A VAL* 4.0 14.6 - - + -
106A PHE* 3.4 12.7 - + + +
109A ILE* 3.7 18.8 - - + -
144A MET* 3.8 35.2 - - + -
147A GLY* 3.9 5.6 - - - -
148A LYS* 3.3 24.0 + - + +
149A LYS* 3.1 38.9 + - - +
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Residues in contact with ILE 93 (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 MET* 5.3 2.5 - - + -
40A LYS* 4.2 25.0 + - + +
89A ILE 3.6 12.3 - - - +
90A GLN* 3.3 18.4 - - - +
92A TYR* 1.3 86.0 - - + +
94A GLU* 1.3 62.2 + - - +
95A LYS* 3.5 6.4 + - - +
100A TYR* 3.5 13.9 - - - -
143A LEU* 3.8 49.8 - - + +
144A MET* 4.6 4.7 - - - -
146A TYR* 3.9 16.7 - - + +
147A GLY* 3.6 26.5 - - - +
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Residues in contact with GLU 94 (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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40A LYS* 3.1 27.4 + - - +
41A LYS 5.4 0.7 - - - +
43A LEU* 3.5 32.3 - - + +
46A MET* 3.6 18.5 - - - +
90A GLN 3.1 15.7 + - - +
91A ALA 2.9 6.1 + - - +
93A ILE* 1.3 74.2 - - - +
95A LYS* 1.3 68.8 + - - +
96A ASP* 2.9 33.3 + - - +
97A SER* 3.0 15.1 + - - +
100A TYR* 3.0 22.1 - - - +
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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