Contacts of the helix formed by residues 102 - 113 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D LEU* 3.6 12.0 - - + +
100D PHE* 3.2 25.4 + - + -
101D PRO* 1.3 98.2 - - + +
103D LYS* 1.3 65.9 + - - +
104D GLY 3.2 2.2 - - - +
105D ARG* 3.2 27.1 + - + -
106D LEU* 3.1 15.8 + - - +
83E ARG* 2.6 46.4 + - - -
84E TYR* 4.4 0.3 + - - -
97E PRO* 4.0 16.2 - - + +
98E ASP* 3.7 2.9 - - - +
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LEU* 3.9 25.8 - - + -
100D PHE* 3.7 18.6 - - + +
102D GLU* 1.3 75.8 - - - +
104D GLY* 1.3 61.6 + - - +
106D LEU* 3.5 4.5 + - - +
107D LYS* 3.1 22.5 + - - +
122D LEU* 4.6 31.0 + - + +
124D PRO* 5.3 13.2 - - - +
98E ASP* 3.2 11.0 + - - +
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLU 3.2 0.8 - - - -
103D LYS* 1.3 80.5 - - - +
105D ARG* 1.3 60.3 + - - +
107D LYS* 3.4 11.3 + - - +
108D ARG* 3.3 15.6 + - - +
95E VAL* 3.6 17.5 - - - +
96E LEU 5.4 0.9 - - - -
98E ASP* 3.5 14.5 + - - -
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Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASP* 3.3 14.5 + - - +
81D LEU* 3.7 17.0 - - + +
102D GLU* 3.2 30.6 + - + +
103D LYS 3.3 0.4 - - - -
104D GLY* 1.3 75.0 - - - +
106D LEU* 1.3 65.3 + - - +
108D ARG* 3.1 7.9 + - - +
109D GLU* 3.0 27.3 + - - +
83E ARG* 3.0 36.3 - - - +
84E TYR* 3.9 12.4 - - - -
87E ASP* 2.5 36.2 + - - +
95E VAL* 3.2 33.7 + - + +
96E LEU 3.7 15.7 + - - +
97E PRO* 3.8 17.0 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 3.7 36.7 - - + +
84D TYR* 4.0 24.0 - - + -
85D ILE* 3.8 20.6 - - + +
94D VAL* 5.4 1.1 - - + -
96D LEU* 4.2 16.2 - - + -
100D PHE* 4.4 10.3 - - + -
102D GLU 3.1 16.2 + - - +
103D LYS 3.8 4.5 - - - +
104D GLY 3.4 0.2 - - - -
105D ARG* 1.3 75.9 - - - +
107D LYS* 1.3 56.2 + - - +
109D GLU* 3.1 7.2 + - + +
110D ALA* 2.8 28.1 + - - +
118D LEU* 5.3 4.9 - - + -
122D LEU* 3.7 28.0 - - + -
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS 3.1 13.2 + - - +
104D GLY* 3.4 12.8 - - - +
106D LEU* 1.3 76.2 - - - +
108D ARG* 1.3 58.8 + - - +
110D ALA* 3.3 4.6 + - - +
111D GLU* 3.0 47.4 + - - +
119D VAL* 4.1 13.0 - - + +
122D LEU* 3.6 28.1 - - + +
123D THR* 3.3 35.9 - - + +
124D PRO* 5.8 2.0 - - + +
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ARG* 4.1 5.2 - - - +
104D GLY 3.3 9.3 + - - +
105D ARG* 3.1 11.1 + - - +
107D LYS* 1.3 77.9 - - - +
109D GLU* 1.3 67.5 + - - +
111D GLU* 3.0 40.9 + - - +
112D TYR* 3.1 38.9 + - - +
91E ASP* 3.1 41.8 + - - +
93E GLN* 3.9 23.0 + - - +
95E VAL* 4.0 22.4 - - + -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ARG* 2.8 52.7 + - - +
78D ASP* 4.3 16.0 + - - +
81D LEU* 3.8 27.2 - - + +
85D ILE* 4.1 16.4 - - + -
105D ARG* 3.0 17.8 + - - +
106D LEU* 3.1 7.8 + - + +
108D ARG* 1.3 75.4 - - - +
110D ALA* 1.3 66.5 + - - +
112D TYR* 3.1 2.1 + - - +
113D PHE* 3.0 36.5 + - + -
87E ASP* 4.6 8.5 - - - +
91E ASP* 5.0 0.3 - - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ILE* 3.8 8.9 - - - +
106D LEU 2.8 13.0 + - - +
107D LYS* 3.5 12.6 - - - +
109D GLU* 1.3 77.9 - - - +
111D GLU* 1.3 55.2 + - - +
113D PHE 3.5 1.3 + - - +
114D GLN 3.0 7.8 + - - -
115D LEU* 2.9 31.1 + - + +
118D LEU* 3.6 35.0 - - + -
119D VAL* 3.7 15.0 - - + +
122D LEU* 4.4 0.4 - - + -
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS* 3.0 42.6 + - - +
108D ARG* 3.0 39.1 + - - +
109D GLU 3.2 0.2 - - - -
110D ALA* 1.3 74.5 - - - +
112D TYR* 1.3 60.6 + - - +
114D GLN* 2.9 25.5 + - - +
119D VAL* 3.8 21.1 - - + +
93E GLN* 5.8 0.7 + - - -
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Residues in contact with TYR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 3.2 39.0 - - + +
54D MET* 5.8 2.4 - - - -
75D ILE* 4.9 5.0 - - + +
76D ASP* 5.4 2.9 + - - +
77D ARG* 3.6 66.3 - - + +
108D ARG* 3.1 23.1 + - - +
109D GLU 3.1 7.2 + - - +
111D GLU* 1.3 78.4 - - - +
113D PHE* 1.3 75.8 + + - +
114D GLN* 3.0 13.9 + - - +
91E ASP* 4.9 0.7 - - - -
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D SER* 3.8 4.2 - - - -
50D LEU* 3.0 30.1 + - + -
51D LEU* 3.7 28.8 + - + -
54D MET* 6.1 0.7 - - - -
75D ILE* 4.0 19.5 - - + -
77D ARG* 4.0 19.3 - - + -
82D PHE* 3.7 34.3 - + - -
85D ILE* 4.0 21.8 - - + -
109D GLU* 3.0 42.1 + - + +
110D ALA 4.2 0.2 - - - +
112D TYR* 1.3 88.8 - + - +
114D GLN* 1.3 67.1 + - - +
115D LEU* 3.5 20.8 - - + +
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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