Contacts of the helix formed by residues 93 - 106 (chain C) in PDB entry 2I6A
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 ASP 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C GLY* 3.2 4.5 + - - -
92C ILE* 1.3 77.9 - - - +
94C LYS* 1.3 70.2 + - - +
95C PHE* 3.7 7.7 + - - +
96C GLY 3.1 7.3 + - - -
97C GLU* 3.0 19.9 + - - +
119C PRO* 3.4 15.3 - - - +
120C THR* 3.0 44.6 + - - -
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Residues in contact with LYS 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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60C TYR* 5.9 4.9 - - - -
93C ASP* 1.3 74.2 - - - +
95C PHE* 1.3 77.1 + - + +
97C GLU* 2.6 31.9 + - - +
98C ILE* 2.9 28.3 + - + +
340C GLU* 3.4 34.0 + - - -
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Residues in contact with PHE 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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17C LEU* 3.0 30.3 - - + +
19C ILE* 4.8 5.8 - - + -
60C TYR* 4.2 22.7 - + - -
93C ASP* 3.5 7.1 + - - +
94C LYS* 1.3 99.1 - - + +
96C GLY* 1.3 56.2 + - - +
98C ILE* 3.4 15.0 + - + +
99C LEU* 2.9 32.7 + - - +
120C THR* 3.9 22.9 - - + -
122C THR* 3.8 28.3 - - + -
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Residues in contact with GLY 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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90C ILE* 4.0 11.0 - - - +
91C GLY 3.8 10.1 - - - -
93C ASP* 3.1 15.8 + - - -
95C PHE* 1.3 74.5 - - - +
97C GLU* 1.3 57.8 + - - +
99C LEU* 3.2 4.0 + - - +
100C LYS* 3.0 38.4 + - - +
114C GLU* 5.7 0.2 - - - -
120C THR* 3.2 18.5 + - - -
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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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100A LYS* 5.5 4.0 + - - -
93C ASP 3.0 11.5 + - - +
94C LYS* 2.6 20.3 + - - +
96C GLY* 1.3 71.6 - - - +
98C ILE* 1.3 54.4 + - + -
100C LYS* 3.1 36.0 + - - +
101C ARG* 3.0 30.7 + - - +
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Residues in contact with ILE 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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17C LEU* 4.3 21.8 - - + -
60C TYR* 6.3 2.0 - - + -
62C ALA* 5.6 1.6 - - + +
94C LYS* 3.4 38.6 - - + +
95C PHE* 3.4 28.7 - - + +
97C GLU* 1.3 73.5 - - + +
99C LEU* 1.3 61.9 + - + +
101C ARG* 3.1 30.1 + - - +
102C LYS* 2.8 46.0 + - + +
340C GLU* 5.7 1.6 - - - +
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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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15C PRO* 3.7 31.9 - - + +
16C LEU 3.5 21.1 - - - +
17C LEU* 4.0 12.1 - - + +
62C ALA* 3.6 26.5 - - + -
63C GLY 4.2 0.4 - - - +
67C GLN* 4.4 8.6 - - - +
71C LYS* 5.1 0.7 + - - -
90C ILE* 3.8 15.9 - - + -
95C PHE 2.9 18.4 + - - +
96C GLY 3.2 7.8 + - - +
98C ILE* 1.3 71.5 - - - +
100C LYS* 1.3 57.0 + - - +
102C LYS* 3.4 3.4 + - - +
103C ALA* 2.9 30.3 + - - +
112C TYR* 3.7 11.5 + - + +
120C THR* 3.7 23.3 - - + -
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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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100A LYS* 5.6 4.8 - - - +
90C ILE* 3.5 15.3 - - + -
96C GLY 3.0 24.7 + - - +
97C GLU* 3.1 36.1 + - - +
99C LEU* 1.3 75.0 - - - +
101C ARG* 1.3 63.6 + - - +
103C ALA* 3.2 2.9 + - - +
104C ALA* 2.9 24.7 + - - +
112C TYR* 3.7 31.9 - - + -
114C GLU* 2.9 31.8 + - - -
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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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97C GLU* 3.0 17.6 + - + +
98C ILE* 3.1 33.5 + - - +
100C LYS* 1.3 75.3 - - - +
102C LYS* 1.3 100.7 + - - +
104C ALA* 3.2 7.2 + - - +
105C GLU* 2.9 42.9 + - + +
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Residues in contact with LYS 102 (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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62C ALA* 4.0 16.8 - - + +
71C LYS* 3.9 18.4 + - - +
98C ILE* 2.8 34.0 + - + +
99C LEU 3.8 3.4 - - - +
101C ARG* 1.3 104.5 - - - +
103C ALA* 1.3 62.5 + - - +
105C GLU* 2.8 25.6 + - - +
106C ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 103 (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 GLN* 4.5 3.1 - - + +
71C LYS* 4.0 12.5 - - - +
99C LEU 2.9 18.3 + - - +
100C LYS* 3.4 6.7 - - - +
102C LYS* 1.3 78.6 - - - +
104C ALA* 1.3 61.2 + - - +
106C ALA* 3.3 7.8 + - - +
108C VAL* 3.1 29.7 + - + +
110C ALA* 3.7 20.2 - - + -
112C TYR* 3.3 18.8 - - - +
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Residues in contact with ALA 104 (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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82C LYS* 6.4 0.4 - - - +
100C LYS 2.9 16.1 + - - +
101C ARG* 3.2 7.8 + - - +
103C ALA* 1.3 73.7 - - - +
105C GLU* 1.3 57.0 + - + +
106C ALA 3.0 1.6 - - - -
107C HIS* 2.6 33.6 + - - -
108C VAL 4.6 5.8 - - - -
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Residues in contact with GLU 105 (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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101C ARG* 2.9 34.0 + - + +
102C LYS* 2.8 43.2 + - - +
104C ALA* 1.3 74.9 - - + +
106C ALA* 1.3 57.3 + - - +
107C HIS* 3.1 22.6 + - - -
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Residues in contact with ALA 106 (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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71C LYS* 3.8 23.9 - - + +
74C GLN* 3.0 22.2 - - - +
75C TRP* 5.1 1.2 + - - -
102C LYS 3.2 13.4 + - - +
103C ALA 3.4 5.2 - - - +
104C ALA 3.0 0.8 - - - -
105C GLU* 1.3 74.3 - - - +
107C HIS* 1.3 69.9 + - - +
108C VAL* 3.3 19.2 + - + -
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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