Contacts of the helix formed by residues 89 - 97 (chain C) in PDB entry 2I7C
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 GLY 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C GLY 2.9 15.2 + - - -
87C GLY 3.1 1.0 - - - -
88C ASP* 1.3 76.1 + - - +
90C GLY* 1.3 59.9 + - - +
91C ILE 3.3 2.5 - - - -
92C ILE* 3.1 13.6 + - - +
93C ARG 2.8 26.9 + - - -
124C ILE 3.2 13.6 - - - +
125C SER* 4.4 0.9 - - - -
127C GLY 5.4 0.9 + - - -
128C TYR* 3.9 17.3 - - - -
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Residues in contact with GLY 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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64C HIS* 3.7 21.3 - - - +
86C GLY 4.6 0.4 + - - -
88C ASP* 2.8 17.8 + - - -
89C GLY* 1.3 76.5 - - - +
91C ILE* 1.3 62.4 + - - +
93C ARG* 3.3 9.6 + - - +
94C GLU* 3.2 24.4 + - - +
124C ILE* 3.5 18.4 - - - +
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C HIS* 3.7 19.5 - - + +
67C MET* 3.6 28.9 - - + -
68C THR* 3.4 22.7 - - - +
83C VAL* 3.7 30.1 - - + -
86C GLY* 5.5 1.7 + - - -
88C ASP* 4.7 0.4 + - - -
89C GLY 3.3 0.2 - - - -
90C GLY* 1.3 74.6 - - - +
92C ILE* 1.3 64.3 + - - +
94C GLU* 3.0 3.8 + - - +
95C LEU* 2.9 23.9 + - + +
155C ILE* 3.7 26.2 - - + -
157C ASP* 3.7 34.0 + - + +
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Residues in contact with ILE 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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83C VAL* 4.3 7.4 - - + -
86C GLY 5.1 0.6 + - - +
89C GLY* 3.1 13.2 + - - +
91C ILE* 1.3 76.6 - - - +
93C ARG* 1.3 63.9 + - - +
95C LEU* 3.2 9.0 + - - +
96C CYS* 2.9 25.9 + - - -
104C ILE* 4.3 16.8 - - + -
106C ILE* 3.4 41.1 - - + -
127C GLY* 3.9 20.4 - - - +
128C TYR* 3.7 27.8 - - + +
133C VAL* 3.7 29.2 - - + -
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Residues in contact with ARG 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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60C GLU* 2.8 44.2 + - - -
61C PHE* 4.3 9.1 - - - +
64C HIS* 4.0 11.3 - - - +
89C GLY 2.8 15.6 + - - +
90C GLY* 3.4 9.8 + - - +
91C ILE 3.2 0.2 - - - -
92C ILE* 1.3 76.0 - - - +
94C GLU* 1.3 89.6 + - - +
96C CYS* 3.4 10.8 + - - +
97C LYS* 3.6 21.6 + - - +
123C ASN* 3.0 29.5 + - - +
124C ILE* 3.6 17.5 - - - +
126C CYS* 3.8 19.5 - - - -
127C GLY* 4.7 8.0 - - - +
256C ASP* 6.1 0.4 - - - -
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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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64C HIS* 3.6 23.8 - - + +
65C GLU* 3.7 17.5 - - - +
68C THR* 3.4 26.0 - - + +
69C HIS* 2.8 29.3 + - - +
90C GLY 3.2 11.4 + - - +
91C ILE 3.0 3.3 + - - +
93C ARG* 1.3 108.2 + - - +
95C LEU* 1.3 62.8 + - - +
97C LYS* 2.9 48.2 + - - +
98C TYR* 3.6 8.5 - - - -
257C LEU* 3.8 0.2 - - - +
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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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68C THR* 3.6 19.7 - - + +
72C MET* 3.7 33.7 - - + -
81C VAL* 3.8 24.9 - - + -
83C VAL* 3.6 31.6 - - + -
91C ILE* 2.9 20.7 + - + +
92C ILE* 3.6 6.3 - - - +
94C GLU* 1.3 78.3 - - - +
96C CYS* 1.3 61.8 + - - +
98C TYR* 3.0 26.4 + - - +
101C VAL* 4.3 6.0 - - + +
104C ILE* 3.9 27.3 - - + +
155C ILE* 4.1 3.6 - - + -
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Residues in contact with CYS 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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92C ILE* 2.9 30.6 + - - +
93C ARG* 3.8 7.4 - - - +
94C GLU 3.3 0.6 - - - -
95C LEU* 1.3 77.0 - - - +
97C LYS* 1.3 60.5 + - - +
98C TYR 3.1 3.8 + - - +
99C LYS* 4.4 2.9 + - - +
104C ILE* 3.9 15.5 - - - -
127C GLY* 4.1 8.1 - - - -
130C ASP* 3.5 37.5 - - - +
132C ARG* 3.0 26.2 + - - +
133C VAL* 4.2 0.2 - - - -
253C GLU* 5.8 0.2 - - - +
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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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65C GLU* 5.1 2.0 + - - -
69C HIS* 4.8 0.2 - - - +
93C ARG* 3.6 23.8 - - - +
94C GLU* 2.9 49.9 + - - +
95C LEU 3.1 1.2 - - - -
96C CYS* 1.3 76.8 - - - +
98C TYR* 1.3 56.3 + - - +
99C LYS* 3.4 6.5 + - - +
253C GLU* 3.4 47.9 - - - +
254C PHE* 3.5 31.1 - - + -
256C ASP* 2.7 35.9 + - - +
257C LEU* 4.0 5.9 - - - +
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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