Contacts of the helix formed by residues 87 - 101 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ASP* 2.9 5.9 + - - +
86B ALA* 1.3 76.5 - - - +
88B ASP* 1.3 64.0 + - - +
89B LYS* 3.8 7.2 + - - +
90B MET* 2.6 27.9 + - - +
91B LEU* 2.9 21.0 + - - +
2301B SAH 2.6 25.2 + - - -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ALA 3.7 11.3 + - - +
87B SER* 1.3 64.6 - - - +
89B LYS* 1.3 68.7 + - - +
90B MET 2.6 1.7 + - - -
91B LEU* 2.7 11.5 + - - +
92B LYS* 2.6 31.9 + - + +
114B GLU* 5.5 10.1 - - + +
88D ASP* 5.4 8.9 - - + +
89D LYS* 3.6 30.0 + - - +
92D LYS* 4.4 27.7 + - + +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER* 3.9 8.5 - - - +
88B ASP* 1.3 79.0 - - - +
90B MET* 1.3 64.1 + - + +
92B LYS* 3.2 15.5 - - - +
93B TYR* 3.0 30.2 - - + -
88D ASP* 4.7 12.9 + - - +
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY* 3.2 23.9 - - - +
67B THR* 4.3 19.7 - - + +
87B SER* 2.6 25.8 - - - +
88B ASP 2.6 5.3 + - - -
89B LYS* 1.3 79.5 - - + +
91B LEU* 1.3 68.2 + - - +
92B LYS 3.1 0.2 - - - -
93B TYR* 2.7 27.4 + - + +
94B ALA 3.4 0.3 + - - -
2301B SAH 3.0 33.7 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 3.5 33.0 - - + -
66B GLY* 3.3 3.9 + - - +
84B VAL 4.9 0.2 - - - -
85B ASP* 3.1 48.2 - - + +
87B SER 2.9 12.2 + - - +
88B ASP* 2.7 14.2 + - - +
90B MET* 1.3 72.5 - - - +
92B LYS* 1.3 64.5 + - - +
94B ALA* 2.8 5.4 + - + +
95B LEU* 2.8 26.9 + - + +
112B ILE* 3.5 31.2 - - + -
113B GLU 4.0 9.0 - - - +
114B GLU* 4.1 10.1 - - + +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 2.6 21.1 + - + +
89B LYS* 3.2 26.6 + - - +
91B LEU* 1.3 72.8 - - - +
93B TYR* 1.3 84.3 - - + +
95B LEU* 3.3 14.1 - - - +
96B LYS* 2.9 32.9 + - - +
88D ASP* 2.5 36.7 + - - +
92D LYS* 6.3 2.7 - - + -
114D GLU* 2.9 32.2 + - - +
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Residues in contact with TYR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR* 4.2 20.9 - - + +
89B LYS* 3.0 26.2 - - + -
90B MET* 2.7 18.5 + - + +
92B LYS* 1.3 104.0 - - + +
94B ALA* 1.3 59.0 + - - +
96B LYS* 2.7 57.0 + - - +
97B GLU* 3.3 4.7 + - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 3.8 22.7 - - - -
66B GLY 4.1 2.9 - - - +
67B THR 3.1 32.1 + - - +
68B GLY* 3.8 3.8 - - - +
90B MET 3.4 2.2 + - - -
91B LEU* 2.8 12.4 + - + +
93B TYR* 1.3 74.7 - - - +
95B LEU* 1.3 65.7 + - - +
96B LYS 2.9 1.0 + - - -
97B GLU* 3.2 14.3 + - - +
98B ARG* 3.4 8.5 + - - +
110B TRP* 4.0 9.3 - - + -
112B ILE* 4.0 11.0 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 2.8 11.5 + - + +
92B LYS* 3.3 17.3 - - - +
94B ALA* 1.3 76.3 - - - +
96B LYS* 1.3 65.8 + - - +
98B ARG* 3.5 26.8 - - - +
99B TRP* 3.3 17.7 + - - +
112B ILE* 2.8 54.7 - - + +
92D LYS* 5.9 3.4 - - + +
95D LEU* 5.8 8.7 - - + -
96D LYS* 5.9 9.4 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LYS* 2.9 18.2 + - - +
93B TYR* 2.7 48.6 + - - +
95B LEU* 1.3 76.1 - - - +
97B GLU* 1.3 59.2 + - - +
98B ARG 2.9 1.6 + - - -
99B TRP* 2.9 14.1 + - - +
100B ASN* 2.6 32.6 + - - +
113D GLU* 6.0 0.2 + - - -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 4.1 30.0 - - + +
93B TYR 3.3 3.7 + - - +
94B ALA* 3.2 9.3 + - - +
96B LYS* 1.3 79.7 - - - +
98B ARG* 1.3 52.6 + - - +
100B ASN* 3.2 13.0 + - - +
101B ARG* 2.6 92.4 + - - +
110B TRP* 4.9 0.4 - - + -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 3.4 4.7 + - - +
95B LEU* 3.5 39.2 - - - +
96B LYS 2.9 1.2 + - - -
97B GLU* 1.3 78.2 - - - +
99B TRP* 1.3 53.1 + - - +
101B ARG* 2.9 8.8 - - - +
102B ARG* 2.6 36.4 + - - -
107B PHE* 4.2 9.9 + - - +
110B TRP* 2.9 54.2 + - + +
111B VAL* 4.2 8.7 - - - +
112B ILE* 4.4 9.1 + - + +
99D TRP* 2.7 79.1 - - + +
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Residues in contact with TRP 99 (chain B).
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 3.3 6.6 + - - +
96B LYS* 2.9 14.2 + - - +
98B ARG* 1.3 79.6 - - + +
100B ASN* 1.3 63.8 + - - +
102B ARG* 2.6 80.8 + - - +
98D ARG* 3.3 68.2 - - + +
99D TRP* 3.5 28.7 - + + -
102D ARG* 3.7 20.6 - - + -
107D PHE 4.1 7.2 - - - -
108D ASP* 4.0 19.5 - - - -
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 2.6 47.2 + - - +
97B GLU* 3.2 11.0 + - - +
98B ARG 3.1 0.2 - - - -
99B TRP* 1.3 83.5 - - - +
101B ARG* 1.3 57.5 + - + +
102B ARG* 2.6 23.4 + - - +
103B LYS* 3.7 10.0 + - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 3.7 7.3 - - - +
76B GLU* 2.6 29.7 + - - +
97B GLU* 2.6 63.1 + - - +
98B ARG 2.9 4.0 - - - +
100B ASN* 1.3 71.6 - - + +
102B ARG* 1.3 57.6 + - - +
103B LYS* 3.2 3.7 + - - +
104B GLU* 3.7 21.6 + - - +
107B PHE* 2.7 81.1 - - + +
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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