Contacts of the helix formed by residues 87 - 101 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ASP* 2.9 7.6 + - - +
86C ALA* 1.3 75.9 - - - +
88C ASP* 1.3 69.7 + - - +
89C LYS* 3.8 8.5 + - - +
90C MET* 3.5 18.7 + - - +
91C LEU* 2.8 25.2 + - - +
3301C SAH 2.6 27.5 + - - -
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Residues in contact with ASP 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 4.6 16.6 - - - +
92A LYS* 2.6 26.3 + - - +
86C ALA 3.9 3.0 + - - +
87C SER* 1.3 73.9 + - - +
89C LYS* 1.3 69.9 + - - +
90C MET 2.7 0.5 + - - -
91C LEU* 2.7 14.6 + - - -
92C LYS* 2.8 18.9 + - + +
114C GLU* 2.6 41.2 - - - +
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASP* 5.1 4.7 - - - +
87C SER* 3.9 7.6 - - - +
88C ASP* 1.3 78.8 - - - +
90C MET* 1.3 58.3 + - + +
92C LYS* 3.6 16.5 - - - +
93C TYR* 2.6 51.4 - - + +
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLY* 3.5 14.3 - - - +
67C THR* 3.2 44.6 - - + +
87C SER* 3.3 13.5 + - - +
88C ASP 2.7 4.4 + - - -
89C LYS* 1.3 77.1 - - + +
91C LEU* 1.3 66.7 + - - +
92C LYS 3.1 1.6 - - - -
93C TYR* 2.9 22.4 + - + +
94C ALA 3.6 0.5 + - - -
3301C SAH 3.5 44.9 - - - +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C CYS* 3.5 27.8 - - + -
66C GLY 3.7 3.1 - - - +
85C ASP* 2.6 63.7 + - + +
87C SER 2.8 14.9 + - - +
88C ASP* 2.7 9.2 + - - +
90C MET* 1.3 71.3 - - - +
92C LYS* 1.3 56.7 + - - +
94C ALA* 2.9 23.6 + - - +
95C LEU* 3.0 18.8 + - + +
112C ILE* 4.0 13.0 - - + -
113C GLU* 3.4 15.3 - - - +
114C GLU* 3.5 17.0 - - + +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASP* 2.6 44.4 + - - +
114A GLU* 3.9 15.4 + - - -
88C ASP* 2.8 17.9 + - + +
89C LYS* 3.6 19.6 + - - +
91C LEU* 1.3 74.0 - - - +
93C TYR* 1.3 94.3 + - + +
94C ALA 3.0 0.2 - - - -
95C LEU* 3.2 19.8 + - + +
96C LYS* 3.1 35.7 + - - +
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 3.9 24.9 - - + +
89C LYS* 2.6 41.9 - - + +
90C MET* 2.9 11.0 + - + +
92C LYS* 1.3 112.9 + - + +
94C ALA* 1.3 59.1 + - - +
96C LYS* 3.4 31.3 - - + +
97C GLU* 3.7 9.5 - - - +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C CYS* 3.9 13.9 - - - -
66C GLY 3.7 4.5 - - - +
67C THR 2.6 32.1 + - - +
68C GLY* 3.9 4.3 - - - +
72C ILE* 5.4 0.2 - - - -
90C MET 3.6 0.4 + - - -
91C LEU 2.9 11.0 + - - +
93C TYR* 1.3 75.5 - - - +
95C LEU* 1.3 54.9 + - - +
96C LYS 2.7 16.0 + - - -
97C GLU* 2.8 19.5 + - - +
98C ARG 3.3 6.4 + - - -
110C TRP* 3.9 14.0 - - + -
112C ILE* 4.4 5.6 - - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 6.6 0.2 - - - -
91C LEU* 3.0 12.5 + - + +
92C LYS* 3.4 29.4 - - + +
94C ALA* 1.3 75.4 - - - +
96C LYS* 1.3 61.9 + - - +
98C ARG* 3.3 29.2 + - - +
99C TRP* 3.4 7.4 + - - +
112C ILE* 3.0 55.6 - - + +
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 4.9 10.5 + - - -
92C LYS* 3.1 25.3 + - - +
93C TYR* 3.4 32.5 - - + +
94C ALA 2.7 1.0 + - - -
95C LEU* 1.3 73.7 - - - +
97C GLU* 1.3 71.3 + - - +
98C ARG 3.0 2.4 + - - -
99C TRP* 3.1 8.0 + - - +
100C ASN* 3.1 33.1 + - - +
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 3.4 34.8 - - + -
93C TYR 3.7 7.9 - - - +
94C ALA 2.8 12.3 + - - +
96C LYS* 1.3 82.9 - - - +
98C ARG* 1.3 56.1 + - - +
100C ASN* 4.2 13.5 + - - -
101C ARG* 2.8 48.2 + - + +
107C PHE* 3.6 2.4 - - + -
110C TRP* 4.4 2.9 - - + -
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TRP* 2.8 58.3 - - + +
94C ALA 3.3 3.0 + - - -
95C LEU* 3.3 23.3 + - - +
96C LYS 3.0 0.6 - - - -
97C GLU* 1.3 74.8 - - - +
99C TRP* 1.3 55.3 + - - +
101C ARG 3.3 0.9 - - - -
102C ARG* 2.5 38.7 + - - +
107C PHE* 3.4 26.2 - - + +
110C TRP* 2.5 62.0 + - + -
111C VAL* 3.1 19.6 - - - +
112C ILE* 3.3 25.9 + - - +
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Residues in contact with TRP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 2.6 60.0 - - + +
99A TRP* 3.7 22.6 - + + -
102A ARG* 3.5 30.3 - - + -
108A ASP* 3.1 24.7 + - - -
110A TRP 4.6 1.2 + - - -
111A VAL* 5.4 4.0 - - - +
95C LEU 3.4 7.3 + - - +
96C LYS* 3.1 10.1 + - - +
98C ARG* 1.3 76.8 - - - +
100C ASN* 1.3 60.5 + - - +
102C ARG* 2.6 86.3 + - - +
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Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LYS* 3.1 30.5 + - - +
97C GLU* 3.7 16.6 + - - +
99C TRP* 1.3 85.8 - - - +
101C ARG* 1.3 62.0 + - + +
102C ARG* 3.1 6.6 + - - +
103C LYS* 4.0 11.8 + - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 5.0 2.1 - - - +
76C GLU* 2.5 39.0 + - - +
97C GLU* 2.8 30.1 + - + +
98C ARG 3.3 1.6 - - - -
100C ASN* 1.3 72.8 - - + +
102C ARG* 1.3 51.1 + - - +
103C LYS* 2.8 6.7 - - - +
104C GLU* 2.4 81.5 + - - +
107C PHE* 2.9 39.9 - - + +
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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