Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 5HNH
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 ASP 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LYS* 5.3 0.3 + - - -
96A TYR* 3.8 5.8 - - - +
99A ASP* 2.8 29.3 + - + +
100A SER* 1.3 75.0 - - - +
102A GLN* 1.3 56.0 + - - +
103A PRO* 3.3 14.1 - - - +
104A ALA* 3.0 33.5 + - + +
105A PHE* 3.1 24.9 + - - +
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.6 29.2 + - - +
23A ASP* 3.2 30.5 + - - +
26A LEU* 3.9 13.1 - - + +
27A PRO* 5.8 0.4 - - - +
96A TYR* 4.3 12.6 + - + +
100A SER 3.3 6.3 + - - +
101A ASP* 1.3 71.2 - - - +
103A PRO* 1.4 77.2 - - + +
105A PHE* 3.1 17.1 + - - +
106A PHE* 3.1 29.9 + - + -
219A LEU* 3.8 14.8 - - - +
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Residues in contact with PRO 103 (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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101A ASP* 3.3 9.9 - - - +
102A GLN* 1.4 93.5 - - + +
104A ALA* 1.3 55.0 + - - +
106A PHE 3.3 0.7 + - - -
107A LYS* 2.8 50.8 + - - +
219A LEU 3.4 21.8 - - - +
220A ALA* 3.7 7.1 - - - +
221A ASN* 4.3 9.6 - - + +
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Residues in contact with ALA 104 (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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95A LYS* 3.5 28.6 + - - +
101A ASP* 3.0 34.0 + - - +
103A PRO* 1.3 72.4 - - - +
105A PHE* 1.3 67.1 + - - +
107A LYS* 3.7 12.0 - - - +
108A ASP* 3.0 24.9 + - - +
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Residues in contact with PHE 105 (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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26A LEU* 3.8 32.3 - - + -
77A PHE* 3.7 19.5 - + + -
79A MET* 4.0 20.0 - - + -
92A ARG* 3.5 39.1 - - + -
96A TYR* 4.0 26.7 - + + -
101A ASP 3.1 13.4 + - - +
102A GLN* 3.1 14.3 + - - +
104A ALA* 1.3 78.7 - - - +
106A PHE* 1.3 75.3 + + - +
108A ASP* 3.4 6.2 + - - +
109A ILE* 3.2 43.1 + - + +
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Residues in contact with PHE 106 (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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22A LEU* 3.7 27.4 - - + -
26A LEU* 4.1 2.9 - - + -
77A PHE* 3.9 29.2 - + - -
102A GLN* 3.1 46.5 + - + +
105A PHE* 1.3 87.9 - + - +
107A LYS* 1.3 60.8 + - - +
109A ILE* 3.6 19.4 - - + +
110A CYS* 2.9 33.6 + - - -
216A TYR* 3.8 47.1 - + + +
219A LEU* 3.8 14.8 - - + -
220A ALA* 3.8 12.1 - - - +
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Residues in contact with LYS 107 (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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103A PRO* 2.8 32.1 + - - +
104A ALA* 3.7 10.4 - - - +
106A PHE* 1.3 75.6 - - - +
108A ASP* 1.3 58.1 + - - +
110A CYS* 3.3 4.6 + - - +
111A PHE* 2.9 29.5 + - - +
220A ALA* 2.8 39.1 + - + +
221A ASN* 4.2 0.8 - - - +
222A LEU* 3.6 19.1 - - + -
236A GLU* 3.5 19.3 + - - -
239A ASN* 3.2 37.4 - - + +
243A ILE* 4.2 10.6 - - + +
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ARG* 2.7 41.0 + - + +
95A LYS* 6.3 5.4 - - + -
104A ALA 3.0 16.8 + - - +
105A PHE* 3.5 6.3 - - - +
107A LYS* 1.3 74.7 - - - +
109A ILE* 1.3 64.5 + - - +
111A PHE* 3.2 9.2 + - - +
112A LYS* 3.1 45.6 + - - +
277A TYR 4.5 0.2 - - - +
278A SER 5.6 0.3 - - - +
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Residues in contact with ILE 109 (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 LEU* 4.2 2.2 - - + +
77A PHE* 4.1 20.2 - - + +
92A ARG* 3.5 28.3 - - - +
105A PHE* 3.2 37.3 + - + +
106A PHE* 3.6 27.4 - - + +
107A LYS 3.3 0.2 - - - -
108A ASP* 1.3 78.7 - - - +
110A CYS* 1.3 62.2 + - - +
112A LYS 3.3 1.0 + - - -
113A PHE* 2.9 44.1 + - + +
138A PHE* 5.5 0.2 - - + -
216A TYR* 5.2 8.7 - - + -
277A TYR* 3.3 19.4 - - - +
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Residues in contact with CYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE 2.9 21.4 + - - +
107A LYS* 3.7 5.8 - - - +
109A ILE* 1.3 76.9 - - - +
111A PHE* 1.3 62.6 + - - +
112A LYS 3.5 0.2 + - - -
113A PHE* 3.8 4.2 + - - +
138A PHE* 3.3 52.0 - - + +
139A PRO* 4.0 5.2 - - - +
216A TYR* 3.7 32.5 - - - -
217A LEU* 3.9 21.1 - - + -
220A ALA* 4.5 2.7 - - + -
243A ILE* 4.9 8.1 - - + -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS 2.9 18.0 + - - +
108A ASP* 3.2 11.2 + - - +
110A CYS* 1.3 79.5 - - - +
112A LYS* 1.3 75.3 + - + +
113A PHE 3.9 2.6 + - - +
136A ARG* 5.1 18.3 + - - -
139A PRO* 4.9 8.6 - - + +
242A TYR* 3.4 45.1 - + + -
243A ILE* 4.0 26.9 - - + +
246A PHE* 3.5 36.6 - + - -
276A TYR* 4.6 1.2 + - - -
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Residues in contact with LYS 112 (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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92A ARG* 4.1 5.2 - - - +
108A ASP* 3.1 31.9 + - - +
109A ILE 4.3 0.2 - - - +
111A PHE* 1.3 88.3 - - + +
113A PHE* 1.3 69.1 + - - +
114A GLN* 3.5 3.3 + - - +
273A TRP* 4.3 1.0 - - - -
276A TYR* 2.7 59.8 + - + +
277A TYR* 3.3 36.0 + - + +
278A SER 4.6 0.8 - - - -
279A ASN 2.6 33.7 + - - +
280A VAL* 4.7 3.0 - - - +
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Residues in contact with PHE 113 (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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13A ILE* 3.7 35.2 - - + -
76A LEU* 3.8 18.6 - - + -
109A ILE* 2.9 34.4 + - + +
110A CYS 3.8 2.6 + - - +
111A PHE 3.5 3.4 - - - +
112A LYS* 1.3 80.0 - - - +
114A GLN* 1.3 74.9 + - - +
115A PHE* 4.6 0.4 - + - -
117A ASN* 3.9 18.8 - - - -
119A MET* 3.5 31.9 - - + -
136A ARG* 3.9 14.0 - - - +
137A GLN* 3.3 21.5 + - - +
138A PHE* 3.7 28.8 + + + -
216A TYR* 5.5 3.1 - + - -
273A TRP* 5.0 0.9 - + - -
277A TYR* 3.8 13.7 - + - -
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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
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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