Contacts of the helix formed by residues 82 - 99 (chain C) in PDB entry 2IHU
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 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 1.3 71.6 - - - +
83C PRO* 1.3 65.7 - - - +
85C MET* 3.1 30.3 + - - +
86C THR 3.1 9.5 + - - -
108C GLN* 5.3 0.8 + - - -
121C GLN 3.2 17.4 + - - -
123C LEU* 3.6 27.0 - - - +
125C SER* 5.2 3.0 + - - -
97D LEU* 5.7 0.2 - - - -
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU 3.2 7.0 - - - +
82C GLY* 1.3 81.0 - - - +
84C GLY* 1.3 60.0 + - - +
85C MET 3.3 0.2 - - - -
86C THR* 3.2 12.8 + - - +
87C ASN* 3.0 33.8 + - - -
121C GLN* 4.1 9.4 - - + +
123C LEU* 4.4 0.8 - - + -
90D THR* 3.9 4.7 - - + -
435D CYS* 3.3 42.6 - - - +
437D SER* 3.5 37.9 - - - +
600D TP9 3.8 10.8 - - + +
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 3.6 21.6 - - - +
79C ALA* 3.2 16.8 - - - +
80C THR* 3.6 20.1 - - - +
81C LEU 3.2 6.7 + - - -
83C PRO* 1.3 80.1 - - - +
85C MET* 1.3 56.4 + - - +
87C ASN* 3.6 2.4 - - - +
88C LEU 2.9 23.9 + - - -
600D TP9 4.0 1.5 - - - +
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Residues in contact with MET 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 4.3 6.3 - - - -
80C THR 3.1 13.9 + - - +
81C LEU* 5.0 0.7 - - - -
82C GLY* 3.1 22.3 + - - +
84C GLY* 1.3 76.2 - - - +
86C THR* 1.3 73.4 + - + +
88C LEU* 3.3 6.4 + - + +
89C SER* 2.9 27.5 + - - -
92C ILE* 5.1 2.2 - - + +
106C ALA* 3.9 9.9 - - + -
107C ALA 5.4 0.2 - - - +
123C LEU* 3.8 17.3 - - + -
125C SER* 3.6 38.6 - - - +
128C ILE* 4.0 13.9 - - + -
129C VAL* 3.9 20.6 - - + -
165C PHE* 4.0 18.4 - - + -
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY 3.1 1.6 + - - -
83C PRO* 3.2 19.6 - - - +
85C MET* 1.3 86.9 - - + +
87C ASN* 1.3 59.6 + - - +
89C SER* 2.6 26.0 + - - -
90C THR* 4.0 2.3 + - - -
123C LEU* 3.7 22.4 - - + -
128C ILE* 4.9 1.8 - - + -
86D THR 4.0 7.4 - - - +
89D SER* 3.9 9.6 - - - +
90D THR* 2.8 29.4 + - - +
93D ALA* 4.4 3.7 - - + +
132D MET* 3.6 30.1 - - + -
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Residues in contact with ASN 87 (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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56C HIS* 3.3 31.0 + - + -
57C GLU* 3.2 24.2 + - + +
58C PHE* 3.9 15.6 + - - +
83C PRO 3.0 16.9 + - - +
84C GLY 3.6 1.6 - - - +
86C THR* 1.3 74.7 + - - +
88C LEU* 1.3 64.5 + - - +
89C SER 3.3 0.5 + - - -
90C THR* 3.5 13.8 + - - -
56D HIS* 5.7 1.7 - - - -
58D PHE* 5.2 5.4 - - - +
87D ASN* 5.4 0.3 - - - +
90D THR* 2.7 31.8 + - - +
437D SER* 4.5 3.2 + - - -
438D PHE* 4.5 3.0 + - - -
600D TP9 3.1 27.1 - - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 3.5 30.0 - - + +
60C ALA* 4.6 1.1 - - + -
61C GLY* 4.0 7.0 - - - +
77C CYS* 3.7 37.2 - - + -
78C TRP 4.3 9.0 - - - +
79C ALA* 3.9 16.8 - - + +
84C GLY 2.9 17.2 + - - +
85C MET* 3.6 6.1 - - + +
87C ASN* 1.3 76.2 - - - +
89C SER* 1.3 57.2 + - - +
91C GLY* 2.8 21.5 + - - -
92C ILE* 2.9 19.2 + - + -
104C ALA* 4.0 14.8 - - + -
105C LEU 4.0 16.6 - - - +
106C ALA* 5.0 4.0 - - + -
165C PHE* 5.4 1.1 - - + -
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 2.9 15.1 + - - -
86C THR* 2.6 24.4 + - - -
87C ASN 3.1 0.4 - - - -
88C LEU* 1.3 76.8 - - - +
90C THR* 1.3 56.0 + - - +
92C ILE* 4.0 13.5 - - - -
93C ALA* 2.7 30.1 + - - +
128C ILE* 5.4 4.0 - - - +
129C VAL* 5.0 6.7 - - - -
132C MET* 3.4 24.5 - - - +
86D THR* 3.9 14.1 - - - -
89D SER* 4.2 5.0 + - - -
128D ILE* 5.8 0.7 - - - +
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.6 25.1 - - + -
86C THR 4.5 1.2 + - - -
87C ASN* 3.5 9.3 + - - -
88C LEU 3.1 1.0 + - - -
89C SER* 1.3 77.7 + - - +
91C GLY* 1.3 57.7 + - - +
93C ALA* 3.6 2.6 - - - +
94C THR* 3.0 29.5 + - - -
435C CYS* 4.4 0.2 - - - -
437C SER* 4.0 4.0 - - - +
83D PRO* 3.8 21.8 - - + -
86D THR* 2.7 31.7 + - - +
87D ASN* 2.7 29.5 + - - +
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Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.9 7.0 - - - +
61C GLY* 4.1 30.7 - - - +
62C VAL* 4.3 7.6 - - - -
65C ASP* 5.0 0.3 - - - +
87C ASN 4.3 1.0 + - - -
88C LEU 2.8 8.9 + - - -
90C THR* 1.3 75.3 - - - +
92C ILE* 1.3 58.8 + - - +
94C THR* 3.2 11.0 + - - +
95C SER* 3.0 26.9 + - - -
102C VAL* 6.5 0.7 - - - -
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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
----------------------------------------------------------
61C GLY* 5.2 0.2 - - - -
77C CYS* 5.4 1.8 - - - -
85C MET 5.1 1.6 - - - +
88C LEU* 2.9 25.6 + - + +
89C SER* 3.6 21.1 - - - +
91C GLY* 1.3 73.5 - - - +
93C ALA* 1.3 57.5 + - - +
95C SER* 3.0 5.1 + - - -
96C VAL* 2.9 24.8 + - - +
102C VAL* 6.1 2.2 - - + -
104C ALA* 3.8 31.4 - - + -
129C VAL* 4.0 28.7 - - + -
132C MET* 3.6 30.3 - - + +
133C SER* 4.6 0.9 - - - -
163C PRO* 3.4 22.1 - - + +
165C PHE* 4.3 7.2 - - + -
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Residues in contact with ALA 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 SER 2.7 20.2 + - - +
90C THR* 3.6 9.4 - - - +
92C ILE* 1.3 74.3 - - - +
94C THR* 1.3 62.7 + - - +
96C VAL* 3.4 11.4 - - - +
97C LEU* 3.2 26.5 + - - +
132C MET* 4.0 7.4 - - - -
435C CYS* 3.9 11.6 - - - +
86D THR* 4.4 4.5 - - + +
123D LEU* 3.7 29.8 - - + -
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 4.1 5.9 - - - -
62C VAL* 4.0 16.3 - - + +
65C ASP* 3.9 19.5 - - + +
90C THR 3.0 14.7 + - - -
91C GLY* 3.2 13.2 + - - -
93C ALA* 1.3 76.8 - - - +
95C SER* 1.3 56.8 + - - +
98C ASP* 2.8 54.5 + - - +
432C SER* 4.5 1.7 + - - +
435C CYS* 3.7 18.3 - - - +
437C SER* 4.6 2.9 - - - -
440C TYR* 4.0 17.1 - - + -
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 3.5 12.1 - - - -
91C GLY 3.0 12.9 + - - -
92C ILE* 3.0 9.2 + - - -
94C THR* 1.3 78.3 - - - +
96C VAL* 1.3 57.4 + - - +
99C ARG* 3.0 22.0 + - - -
100C SER* 2.7 41.8 + - - -
102C VAL* 3.7 13.5 - - - +
162C GLY* 3.9 2.1 - - - -
163C PRO* 3.2 20.9 - - - +
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Residues in contact with VAL 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 7.2 + - - +
93C ALA* 3.4 17.7 - - - +
95C SER* 1.3 76.7 - - - +
97C LEU* 1.3 57.9 + - - +
99C ARG* 2.7 37.1 + - - +
132C MET* 3.3 35.0 - - + +
133C SER* 4.1 6.5 - - - +
134C LYS* 4.9 9.0 - - + -
161C VAL 4.5 1.9 - - - +
162C GLY* 4.5 1.3 - - - -
163C PRO* 3.5 15.7 - - + +
117D ASN* 3.6 36.8 - - + +
123D LEU* 4.1 8.3 - - + -
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Residues in contact with LEU 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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93C ALA 3.2 10.6 + - - +
96C VAL* 1.3 82.1 - - + +
98C ASP* 1.3 62.0 + - - +
99C ARG* 3.3 7.5 + - - +
299C ALA* 3.5 28.6 - - + +
434C GLY* 3.7 20.3 - - - +
435C CYS* 3.7 25.8 - - + +
82D GLY* 5.6 0.7 - - - -
117D ASN* 3.6 30.5 - - - +
119D THR 3.6 22.0 - - - +
121D GLN* 4.2 2.5 - - - -
122D CYS 4.0 10.3 - - - +
123D LEU* 3.6 34.5 - - + -
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 4.2 1.3 - - - +
69C ARG* 3.2 25.8 + - - +
94C THR* 2.8 35.5 + - - +
97C LEU* 1.3 69.4 - - - +
99C ARG* 1.3 75.0 + - - +
229C ARG* 4.9 2.1 + - - -
252C ILE* 5.7 4.3 - - - +
300C GLU* 6.1 0.5 - - - +
431C THR 4.7 1.0 - - - +
432C SER* 2.6 31.6 + - - -
433C ALA 4.4 1.3 - - - -
434C GLY* 3.0 13.5 + - - +
435C CYS 2.9 28.1 + - - -
440C TYR* 4.1 5.4 + - - -
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 3.5 9.0 + - - +
95C SER 3.0 9.1 + - - -
96C VAL* 2.7 31.6 + - - +
97C LEU 3.3 6.2 + - - +
98C ASP* 1.3 84.3 - - - +
100C SER* 1.3 62.5 + - - +
160C PRO* 3.8 25.7 - - + +
161C VAL* 3.2 34.0 - - + +
229C ARG* 3.9 25.6 + - - +
297C ASP* 2.8 43.5 + - - +
299C ALA* 3.5 11.4 - - + +
300C GLU* 6.2 2.2 - - + -
117D ASN* 2.7 31.0 + - - +
118D ASP* 3.1 15.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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