Contacts of the helix formed by residues 87 - 101 (chain D) in PDB entry 1D2H
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 SER 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D ASP* 2.7 8.2 + - - +
86D ALA* 1.3 78.6 - - - +
88D ASP* 1.3 71.6 + - - +
89D LYS* 3.4 3.8 - - - -
90D MET* 2.6 35.3 - - - +
91D LEU* 3.0 16.7 + - - +
114D GLU* 5.6 0.7 - - - -
4301D SAH 2.7 21.0 + - - -
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Residues in contact with ASP 88 (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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88B ASP* 5.4 9.4 - - + +
89B LYS* 4.7 15.1 + - - +
92B LYS* 2.5 26.9 + - - -
86D ALA 4.2 1.2 + - - -
87D SER* 1.3 72.1 - - - +
89D LYS* 1.3 71.7 + - + +
91D LEU* 2.9 4.4 + - - -
92D LYS* 2.7 28.3 + - + +
114D GLU* 2.7 34.6 - - - +
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Residues in contact with LYS 89 (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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88B ASP* 3.6 22.7 + - - -
87D SER* 5.1 3.8 - - - +
88D ASP* 1.3 81.7 - - + +
90D MET* 1.3 75.2 + - + +
92D LYS* 3.1 41.5 + - + +
93D TYR* 3.2 9.4 - - + -
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Residues in contact with MET 90 (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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66D GLY* 3.4 21.7 - - - +
67D THR* 3.6 26.0 - - + -
85D ASP* 3.8 1.8 - - - +
87D SER* 2.6 22.3 + - - +
88D ASP 3.0 2.8 + - - -
89D LYS* 1.3 84.8 - - + +
91D LEU* 1.3 64.9 + - - +
93D TYR* 2.8 21.6 + - + +
94D ALA 3.7 0.2 + - - -
4301D SAH 2.5 44.9 - - - +
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Residues in contact with LEU 91 (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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65D CYS* 3.4 27.4 - - + -
66D GLY 3.5 3.1 + - - -
85D ASP* 3.3 36.1 - - + +
87D SER 3.0 6.8 + - - +
88D ASP* 2.9 12.5 + - - +
90D MET* 1.3 75.5 - - - +
92D LYS* 1.3 53.1 + - - +
93D TYR 2.6 13.2 + - - -
94D ALA* 2.6 16.3 + - - +
95D LEU* 2.9 17.9 + - + +
112D ILE* 3.3 21.8 - - + -
113D GLU 2.7 36.1 - - - +
114D GLU* 3.6 15.7 - - + +
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Residues in contact with LYS 92 (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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88B ASP* 4.4 31.5 + - + +
92B LYS* 6.3 2.9 - - + -
95B LEU* 5.9 3.0 - - + +
114B GLU* 4.7 17.4 + - - -
88D ASP* 2.7 17.2 + - + +
89D LYS* 3.1 40.3 - - - +
90D MET 3.1 0.2 + - - -
91D LEU* 1.3 71.5 - - - +
93D TYR* 1.3 85.1 + - + +
95D LEU* 3.5 15.0 - - - +
96D LYS* 3.0 37.9 + - - +
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Residues in contact with TYR 93 (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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114B GLU* 5.3 2.4 + - - -
67D THR* 4.0 22.9 - - + +
89D LYS* 3.2 20.0 - - + -
90D MET* 2.8 13.3 + - + +
91D LEU 2.6 5.5 + - - -
92D LYS* 1.3 109.4 + - + +
94D ALA* 1.3 64.1 + - - +
95D LEU 3.1 1.3 - - - -
96D LYS* 3.2 24.0 + - + +
97D GLU* 3.0 30.0 + - - +
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Residues in contact with ALA 94 (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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65D CYS* 3.8 18.6 - - - -
66D GLY 4.1 1.3 - - - +
67D THR 3.1 29.2 + - - +
68D GLY* 3.8 3.8 - - - -
90D MET 3.7 0.8 + - - -
91D LEU* 2.6 14.7 + - - +
93D TYR* 1.3 74.9 - - - +
95D LEU* 1.3 61.2 + - - +
97D GLU* 3.5 4.2 + - - +
98D ARG 3.3 6.2 + - - -
110D TRP* 3.2 25.9 - - + -
112D ILE* 3.4 18.6 - - + -
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Residues in contact with LEU 95 (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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95B LEU* 5.8 8.1 - - + -
91D LEU* 2.9 43.4 + - + +
92D LYS* 3.5 13.7 - - - +
94D ALA* 1.3 78.3 - - - +
96D LYS* 1.3 63.2 + - + +
98D ARG* 3.1 27.3 + - - +
99D TRP* 3.0 20.7 + - - +
112D ILE* 2.8 47.8 - - + +
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Residues in contact with LYS 96 (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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95B LEU* 5.9 10.3 - - + -
113B GLU* 5.1 7.3 + - - -
114B GLU* 3.3 26.1 + - - +
92D LYS* 3.0 39.5 + - - +
93D TYR* 3.2 30.7 + - + +
95D LEU* 1.3 78.1 - - - +
97D GLU* 1.3 67.6 + - - +
99D TRP* 2.8 14.9 + - - +
100D ASN* 2.7 27.9 - - - +
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Residues in contact with GLU 97 (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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67D THR 5.5 1.6 - - - +
72D ILE* 3.4 33.4 - - + -
93D TYR* 3.0 27.0 + - - +
94D ALA* 3.8 4.5 - - - +
95D LEU 3.4 0.2 - - - -
96D LYS* 1.3 80.8 - - - +
98D ARG* 1.3 58.6 + - - +
100D ASN* 2.7 23.9 + - - +
101D ARG* 2.9 39.3 + - + +
110D TRP* 4.6 0.4 - - + -
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Residues in contact with ARG 98 (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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99B TRP* 3.3 61.7 - - + +
94D ALA 3.3 2.7 + - - +
95D LEU* 3.1 33.0 + - - +
97D GLU* 1.3 78.9 - - - +
99D TRP* 1.3 55.6 + - - +
101D ARG 3.4 0.9 - - - -
102D ARG* 2.6 33.6 + - - -
107D PHE* 3.8 18.7 - - + +
110D TRP* 2.6 66.1 + - + -
111D VAL* 3.8 7.1 - - - +
112D ILE* 3.9 17.4 + - + +
113D GLU* 5.3 1.0 + - - -
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Residues in contact with TRP 99 (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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98B ARG* 2.7 71.5 - - + +
99B TRP* 3.5 27.8 - + + -
102B ARG* 4.2 10.1 - - + -
107B PHE 4.2 9.4 - - - -
108B ASP* 4.3 13.9 - - - -
95D LEU 3.0 9.7 + - - +
96D LYS* 2.8 13.4 + - - +
98D ARG* 1.3 78.2 - - + +
100D ASN* 1.3 65.8 + - - +
102D ARG* 2.6 97.5 + - - +
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Residues in contact with ASN 100 (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 LYS* 2.7 17.7 + - - +
97D GLU* 2.7 33.6 + - - +
99D TRP* 1.3 80.1 - - - +
101D ARG* 1.3 62.5 + - + +
102D ARG* 2.9 14.8 + - - +
103D LYS* 3.8 12.8 + - - +
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Residues in contact with ARG 101 (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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72D ILE* 4.4 5.4 - - - +
76D GLU* 2.6 31.3 + - - +
97D GLU* 2.9 23.9 + - + +
98D ARG 3.4 0.9 - - - -
100D ASN* 1.3 73.8 - - + +
102D ARG* 1.3 53.5 + - - +
103D LYS* 2.5 19.1 + - - -
104D GLU* 2.8 59.2 + - + +
107D PHE* 2.9 52.5 - - + +
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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