Contacts of the helix formed by residues 102 - 113 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81N LEU* 3.4 12.5 - - + +
100N PHE* 3.1 29.1 - - + -
101N PRO* 1.3 98.4 - - + +
103N LYS* 1.3 63.3 + - - +
104N GLY 3.3 3.1 - - - +
105N ARG* 3.3 27.9 + - + +
106N LEU* 3.2 15.8 + - - +
83O ARG* 2.7 47.1 + - - -
84O TYR* 4.2 0.5 + - - -
97O PRO* 4.0 17.1 - - + +
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Residues in contact with LYS 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N LEU* 4.8 11.0 - - + -
100N PHE* 3.8 16.8 + - + +
101N PRO 3.7 2.6 + - - -
102N GLU* 1.3 76.4 - - - +
104N GLY* 1.3 62.7 + - - +
106N LEU* 3.5 5.2 + - - +
107N LYS* 3.1 23.6 + - - +
122N LEU* 4.4 17.8 - - + +
98O ASP* 4.0 8.8 + - - +
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Residues in contact with GLY 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N GLU* 3.3 0.8 - - - +
103N LYS* 1.3 81.1 - - - +
105N ARG* 1.3 58.7 + - - +
107N LYS* 3.3 12.9 - - - +
108N ARG* 3.2 18.7 + - - +
95O VAL* 3.9 17.7 - - - +
96O LEU 5.8 0.4 - - - -
98O ASP* 4.9 8.2 + - - -
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Residues in contact with ARG 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N ASP* 3.0 9.7 + - - +
81N LEU* 3.6 18.0 - - + +
102N GLU* 3.3 23.6 + - + +
103N LYS 3.3 0.4 - - - -
104N GLY* 1.3 74.7 - - - +
106N LEU* 1.3 66.7 + - - +
108N ARG* 3.0 16.6 + - - +
109N GLU* 3.1 18.8 + - - +
83O ARG* 3.0 44.5 - - - +
84O TYR* 3.7 15.4 - - - -
87O ASP* 2.2 37.8 + - - +
95O VAL* 3.0 35.1 + - + +
96O LEU 3.9 10.5 - - - +
97O PRO* 4.0 14.6 - - - -
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Residues in contact with LEU 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N LEU* 3.7 32.0 - - + +
84N TYR* 4.0 26.0 - - + -
85N ILE* 3.9 18.4 - - + +
94N VAL* 5.2 5.2 - - + -
96N LEU* 4.3 16.6 - - + -
100N PHE* 4.4 13.7 - - + -
102N GLU 3.2 16.4 + - - +
103N LYS 3.7 4.7 - - - +
104N GLY 3.4 0.2 - - - -
105N ARG* 1.3 78.2 - - - +
107N LYS* 1.3 57.8 + - - +
109N GLU* 3.2 8.0 + - + +
110N ALA* 2.9 26.7 + - - +
118N LEU* 5.5 2.7 - - + -
122N LEU* 3.8 25.8 - - + -
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Residues in contact with LYS 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N LYS 3.1 13.5 + - - +
104N GLY* 3.3 15.3 - - - +
106N LEU* 1.3 77.3 - - - +
108N ARG* 1.3 61.3 + - - +
110N ALA* 3.3 4.6 + - - +
111N GLU* 3.1 39.1 + - - +
119N VAL* 4.2 12.4 - - + +
122N LEU* 3.5 31.9 + - + +
123N THR* 3.5 35.1 - - + +
124N PRO* 5.2 4.4 - - - +
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Residues in contact with ARG 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N ARG* 4.1 6.1 - - - +
104N GLY 3.2 8.5 + - - +
105N ARG* 3.0 13.5 + - - +
107N LYS* 1.3 77.5 - - - +
109N GLU* 1.3 65.7 + - - +
111N GLU* 2.8 47.7 + - - +
112N TYR* 3.2 34.7 + - - +
91O ASP* 3.5 40.0 + - - +
93O GLN* 4.5 25.9 + - + +
95O VAL* 4.5 16.8 - - + -
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Residues in contact with GLU 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N ARG* 2.8 55.4 + - - +
78N ASP* 4.3 17.1 + - - +
81N LEU* 4.1 24.6 - - + +
85N ILE* 4.2 16.6 - - + -
105N ARG* 3.1 15.3 + - - +
106N LEU* 3.2 9.2 + - + +
108N ARG* 1.3 74.8 - - - +
110N ALA* 1.3 65.5 + - - +
112N TYR* 3.1 2.1 + - - +
113N PHE* 3.0 39.0 + - + -
87O ASP* 4.5 7.4 - - - +
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Residues in contact with ALA 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N ILE* 4.0 8.7 - - - +
106N LEU 2.9 15.3 + - - +
107N LYS* 3.4 13.2 - - - +
108N ARG 3.3 0.2 - - - -
109N GLU* 1.3 75.5 - - - +
111N GLU* 1.3 57.1 + - - +
113N PHE* 3.6 1.6 + - - -
114N GLN 3.0 21.1 + - - -
115N LEU* 3.0 17.2 + - - +
118N LEU* 3.9 30.5 - - + -
119N VAL* 3.6 18.6 - - + +
122N LEU* 4.5 0.7 - - + -
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Residues in contact with GLU 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N LYS* 3.1 36.0 + - - +
108N ARG* 2.8 40.0 + - - +
109N GLU 3.2 0.2 - - - -
110N ALA* 1.3 77.2 - - - +
112N TYR* 1.3 62.1 + - - +
114N GLN* 3.1 20.5 + - - +
119N VAL* 4.0 21.0 - - + +
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Residues in contact with TYR 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N LEU* 3.3 37.9 - - + +
54N MET* 6.1 0.7 - - - -
75N ILE* 4.8 6.2 - - + +
76N ASP* 5.1 4.2 + - - +
77N ARG* 3.5 67.1 - - + +
108N ARG* 3.2 18.1 + - - +
109N GLU 3.1 7.5 + - - +
111N GLU* 1.3 80.7 - - - +
113N PHE* 1.3 78.3 + + - +
114N GLN* 3.2 11.1 + - - +
39O ARG* 5.6 6.8 + - - -
91O ASP* 5.0 0.4 - - - -
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Residues in contact with PHE 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N SER* 3.9 4.2 - - - -
50N LEU* 3.1 26.9 + - + -
51N LEU* 3.8 30.1 + - + -
54N MET* 6.5 0.2 - - - -
75N ILE* 4.0 14.1 - - + -
77N ARG* 4.0 17.9 - - + -
82N PHE* 3.6 38.1 - + - -
85N ILE* 4.1 19.3 - - + -
109N GLU* 3.0 46.4 + - - +
110N ALA 4.3 2.7 - - - +
112N TYR* 1.3 90.0 - + - +
114N GLN* 1.3 71.3 + - - +
115N LEU* 3.6 18.3 - - + +
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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