Contacts of the helix formed by residues 88 - 100 (chain C) in PDB entry 2I62
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 THR 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C TYR* 3.3 28.0 - - - +
13C LEU* 4.0 6.1 - - - -
16C PHE* 4.4 4.3 - - + -
86C ASP* 3.0 12.8 + - - +
87C TYR* 1.3 76.8 - - - +
89C ASP* 1.3 63.7 + - - +
90C GLN* 3.2 40.6 - - + +
91C ASN* 3.1 29.9 + - - +
92C LEU* 3.4 9.7 + - - +
4003C SAH 2.7 18.8 + - - -
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Residues in contact with ASP 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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13C LEU* 4.0 8.8 - - + +
87C TYR 3.7 0.6 - - - +
88C THR* 1.3 72.5 - - - +
90C GLN* 1.3 66.0 + - - +
92C LEU* 3.1 18.0 + - - +
93C TRP* 3.1 21.7 + - - +
141C LYS* 3.3 32.4 + - - +
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Residues in contact with GLN 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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12C TYR 3.3 11.5 + - - -
13C LEU* 3.0 30.8 + - - +
14C SER 4.7 1.4 + - - -
15C HIS 4.7 0.8 - - - +
16C PHE 3.0 21.8 + - - +
18C PRO* 3.6 24.9 - - + +
88C THR* 3.2 16.3 - - + +
89C ASP* 1.3 82.7 + - - +
91C ASN* 1.3 58.7 + - - +
93C TRP* 3.6 9.0 + - + +
94C GLU* 3.1 27.4 + - - +
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Residues in contact with ASN 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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16C PHE* 3.4 22.5 - - - -
18C PRO* 3.2 27.0 - - - +
66C GLY* 3.6 13.2 - - - +
67C PRO* 3.5 14.2 - - - +
86C ASP* 3.0 23.6 + - - +
88C THR* 3.1 24.0 + - - +
90C GLN* 1.3 76.3 - - - +
92C LEU* 1.3 58.6 + - - +
94C GLU* 3.3 5.0 + - - +
95C LEU* 2.9 28.6 + - - +
4003C SAH 3.1 17.8 + - - -
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Residues in contact with LEU 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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85C SER* 4.2 2.7 - - - -
86C ASP* 3.7 30.1 - - + +
87C TYR 5.5 0.4 - - - -
88C THR 3.4 12.1 + - - +
89C ASP* 3.1 17.6 + - - +
91C ASN* 1.3 77.4 - - - +
93C TRP* 1.3 56.0 + - - +
95C LEU* 3.2 16.0 - - + +
96C GLN* 2.9 34.4 + - - +
139C VAL* 3.6 25.1 - - + +
140C LEU* 3.5 35.4 - - - +
141C LYS* 3.9 8.5 - - + +
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Residues in contact with TRP 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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89C ASP 3.1 12.3 + - - +
90C GLN* 3.7 12.8 - - + +
92C LEU* 1.3 74.1 - - - +
94C GLU* 1.3 64.4 + - - +
96C GLN* 3.2 8.8 + - - +
97C LYS* 3.0 34.4 + - - +
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Residues in contact with GLU 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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18C PRO* 3.9 13.1 - - + +
19C ARG* 3.3 42.4 + - - +
22C LEU* 3.9 15.1 - - + +
67C PRO* 3.8 23.8 - - + +
90C GLN 3.1 17.4 + - - +
91C ASN 3.3 5.1 + - - +
93C TRP* 1.3 74.6 - - - +
95C LEU* 1.3 64.2 + - - +
97C LYS* 3.2 45.7 + - - +
98C TRP* 3.4 7.4 + - - +
104C GLY 4.2 2.1 - - - +
105C ALA* 4.6 0.7 - - - +
106C PHE* 4.1 8.2 + - + -
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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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65C SER* 3.2 24.7 - - - +
66C GLY 3.4 6.1 - - - +
67C PRO* 3.4 31.6 - - - +
68C THR 3.6 15.0 - - - +
69C ILE* 3.9 17.2 - - + +
84C VAL* 3.4 31.0 - - + -
91C ASN 2.9 8.1 + - - +
92C LEU* 3.2 24.0 - - + +
94C GLU* 1.3 75.2 - - - +
96C GLN* 1.3 57.8 + - - +
98C TRP* 3.2 10.5 + - - +
99C LEU* 3.0 26.2 + - - +
136C ILE* 6.5 0.9 - - + -
139C VAL* 4.4 4.7 - - + -
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Residues in contact with GLN 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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211B LYS* 5.0 12.1 - - - +
92C LEU 2.9 19.4 + - - +
93C TRP* 3.2 8.0 + - - +
95C LEU* 1.3 73.8 - - - +
97C LYS* 1.3 60.0 + - - +
99C LEU* 3.4 19.1 - - - +
100C LYS* 2.9 50.5 + - + +
102C GLU* 4.5 3.5 - - - +
139C VAL* 4.1 31.8 - - + +
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Residues in contact with LYS 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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19C ARG* 5.7 0.2 - - - +
93C TRP* 3.0 25.0 + - - +
94C GLU* 3.2 38.6 + - - +
96C GLN* 1.3 75.3 - - - +
98C TRP* 1.3 61.9 + - - +
101C LYS 3.1 2.3 + - - -
102C GLU* 2.8 54.6 + - + +
103C PRO 4.7 4.9 - - - +
104C GLY 4.4 15.2 + - - +
105C ALA* 3.4 13.8 - - + +
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Residues in contact with TRP 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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69C ILE* 4.1 28.3 - - + -
73C LEU* 5.8 0.2 - - + -
94C GLU 3.4 5.5 + - - +
95C LEU* 3.2 10.5 + - - +
97C LYS* 1.3 78.6 - - - +
99C LEU* 1.3 80.4 + - + +
101C LYS 3.1 5.2 + - - -
105C ALA* 3.5 12.5 - - + +
106C PHE* 3.3 26.7 + - + +
108C TRP* 3.4 33.7 - + + +
112C VAL* 5.2 0.4 - - + -
129C GLU* 4.0 29.1 + - + -
132C LEU* 3.8 32.8 - - + -
133C ARG* 2.8 73.0 + - + +
136C ILE* 4.8 0.9 - - + -
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Residues in contact with LEU 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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204B TYR* 6.5 1.3 - - + -
95C LEU 3.0 15.5 + - - +
96C GLN* 3.3 26.9 + - - +
98C TRP* 1.3 85.3 - - + +
100C LYS* 1.3 63.8 + - + +
101C LYS* 4.5 3.1 + - - -
133C ARG* 3.3 61.3 + - + +
136C ILE* 3.9 33.0 - - + +
139C VAL* 4.0 21.1 - - + -
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Residues in contact with LYS 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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204B TYR* 3.8 28.6 + - - +
206B MET* 3.6 34.4 - - - +
211B LYS* 4.5 15.2 - - - +
96C GLN* 2.9 34.7 + - + +
99C LEU* 1.3 81.2 - - + +
101C LYS* 1.3 73.4 + - - +
102C GLU* 3.2 24.0 + - + +
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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