Contacts of the helix formed by residues 102 - 113 (chain A) in PDB entry 5A15
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 GLU 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 4.0 11.7 - - + -
81A LEU* 3.7 10.8 - - + +
100A PHE* 3.2 25.1 - - + -
101A PRO* 1.3 98.9 - - + +
103A LYS* 1.3 63.0 + - - +
104A GLY 3.3 2.7 - - - +
105A ARG* 3.5 26.0 + - + +
106A LEU* 3.1 15.8 + - - +
83B ARG* 3.1 41.5 + - - -
84B TYR* 4.4 0.3 + - - -
96B LEU 5.8 0.2 - - - -
97B PRO* 3.9 17.4 - - + +
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Residues in contact with LYS 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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96A LEU* 3.6 19.1 - - + -
100A PHE* 3.6 34.5 + - + +
101A PRO 3.8 2.2 + - - -
102A GLU* 1.3 74.3 - - - +
104A GLY* 1.3 60.6 + - - +
106A LEU* 3.2 5.2 + - - +
107A LYS* 2.9 31.3 + - - +
122A LEU* 4.7 25.1 + - + +
124A PRO* 6.3 1.4 - - - +
98B ASP* 4.3 6.5 + - - +
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Residues in contact with GLY 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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102A GLU* 3.3 0.6 - - - +
103A LYS* 1.3 78.1 - - - +
105A ARG* 1.3 60.2 + - - +
107A LYS* 3.5 13.1 + - - +
108A ARG* 3.2 21.3 + - - +
95B VAL* 3.7 20.2 - - - +
96B LEU 5.8 0.4 - - - -
98B ASP* 5.2 5.6 + - - -
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Residues in contact with ARG 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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78A ASP* 3.8 21.0 + - - +
81A LEU* 3.7 14.2 - - + +
102A GLU* 3.5 39.7 + - + +
103A LYS 3.2 0.2 - - - -
104A GLY* 1.3 75.2 - - - +
106A LEU* 1.3 64.5 + - - +
108A ARG* 3.2 7.5 + - - +
109A GLU* 3.1 27.8 + - - +
83B ARG* 3.8 13.5 - - - +
84B TYR* 3.9 17.2 - - - -
87B ASP* 2.5 37.4 + - - +
94B VAL* 5.4 1.2 - - - +
95B VAL* 2.6 60.7 + - + +
96B LEU 4.2 3.8 + - - +
97B PRO* 4.0 16.2 - - - -
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Residues in contact with LEU 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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81A LEU* 3.9 33.4 - - + +
84A TYR* 3.9 23.8 - - + +
85A ILE* 3.8 24.0 - - + +
94A VAL* 5.6 1.1 - - + -
96A LEU* 4.3 22.4 - - + -
100A PHE* 4.5 5.8 - - + -
102A GLU 3.1 18.1 + - - +
103A LYS* 3.2 6.2 + - - +
105A ARG* 1.3 76.0 - - - +
107A LYS* 1.3 57.9 + - - +
109A GLU* 3.2 3.3 + - + +
110A ALA* 3.0 25.6 + - - +
118A LEU* 5.4 6.1 - - + -
122A LEU* 4.0 25.6 - - + -
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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 LYS 2.9 16.3 + - - +
104A GLY* 3.8 11.8 - - - +
106A LEU* 1.3 75.4 - - - +
108A ARG* 1.3 62.3 + - - +
110A ALA* 3.3 3.6 + - - +
111A GLU* 3.1 32.2 + - - +
119A VAL* 4.0 26.9 - - + +
122A LEU* 3.1 50.7 + - + +
123A THR* 4.2 3.7 + - - +
124A PRO* 4.1 13.3 - - - +
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Residues in contact with ARG 108 (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 ARG* 4.1 8.8 - - - +
104A GLY 3.2 13.5 + - - +
105A ARG* 3.2 13.1 + - - +
107A LYS* 1.3 77.4 - - - +
109A GLU* 1.3 63.3 + - - +
111A GLU* 3.3 40.3 + - - +
112A TYR* 3.2 37.6 + - - +
91B ASP* 3.5 35.1 + - - +
93B GLN* 4.5 25.7 + - + +
95B VAL* 4.4 16.8 - - + -
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Residues in contact with GLU 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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77A ARG* 2.9 53.6 + - - +
78A ASP* 4.4 13.0 + - - +
81A LEU* 3.6 29.2 - - + +
85A ILE* 4.1 16.6 - - + -
105A ARG* 3.1 16.4 + - - +
106A LEU* 3.2 7.8 + - - +
108A ARG* 1.3 75.1 - - - +
110A ALA* 1.3 67.5 + - - +
112A TYR* 3.1 2.5 + - - +
113A PHE* 3.0 37.7 + - + -
87B ASP* 4.7 6.8 - - - +
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Residues in contact with ALA 110 (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 ILE* 3.8 9.3 - - + +
106A LEU 3.0 12.9 + - - +
107A LYS* 3.5 13.0 - - - +
109A GLU* 1.3 77.0 - - - +
111A GLU* 1.3 58.2 + - - +
113A PHE 3.5 1.2 + - - -
114A GLN 3.0 8.1 + - - -
115A LEU* 2.9 31.6 + - - +
118A LEU* 3.7 32.5 - - + -
119A VAL* 3.7 17.7 - - + +
122A LEU* 4.5 0.4 - - + -
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Residues in contact with GLU 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* 3.1 32.2 + - - +
108A ARG* 3.3 37.4 + - - +
109A GLU 3.2 0.2 - - - -
110A ALA* 1.3 74.3 - - - +
112A TYR* 1.3 64.5 + - - +
114A GLN* 3.1 17.9 + - - +
115A LEU 4.9 0.4 - - - +
119A VAL* 3.8 23.0 - - + +
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Residues in contact with TYR 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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50A LEU* 3.3 35.9 - - + +
75A ILE* 5.2 3.6 - - + +
76A ASP* 5.1 3.8 + - - +
77A ARG* 3.5 63.5 - - + +
108A ARG* 3.2 24.1 + - - +
109A GLU 3.1 7.9 + - - +
111A GLU* 1.3 80.5 - - - +
113A PHE* 1.3 72.6 + + - +
114A GLN* 3.2 13.0 + - - +
39B ARG* 4.8 15.6 + - - -
91B ASP* 5.0 1.1 - - - -
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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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49A SER* 3.9 4.0 - - - -
50A LEU* 3.0 36.4 + - + -
51A LEU* 3.8 30.9 + - + -
54A MET* 6.0 0.7 - - - -
75A ILE* 4.1 22.0 - - + -
77A ARG* 4.2 8.5 - - + -
82A PHE* 3.6 38.8 - + - -
85A ILE* 3.9 20.4 - - + -
109A GLU* 3.0 44.4 + - + +
112A TYR* 1.3 84.8 - + - +
114A GLN* 1.3 68.5 + - - +
115A LEU* 3.9 19.9 - - + +
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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