Contacts of the helix formed by residues 64 - 78 (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 GLY 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ASN 3.0 25.6 - - - -
16C LEU* 3.8 5.0 + - - +
63C GLY* 1.3 71.1 - - - -
65C SER* 1.3 59.8 + - - -
66C THR 3.5 2.2 - - - -
67C GLN* 3.9 3.6 - - - -
68C ASN* 3.0 32.7 + - - -
500C 5I5 2.9 25.8 + - - -
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Residues in contact with SER 65 (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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14C ASN 4.6 0.4 + - - +
64C GLY* 1.3 67.2 - - - +
66C THR* 1.3 67.0 + - - +
68C ASN* 3.1 14.6 + - - +
69C SER* 3.1 14.7 + - - -
166C TYR* 4.6 5.1 + - - -
168C ALA* 4.0 11.5 - - - +
170C PHE* 3.7 34.2 - - - -
196C ASN* 5.4 2.6 + - - -
198C SER* 5.1 0.7 + - - -
300C ASP* 2.8 35.5 + - - -
500C 5I5 3.2 16.1 + - - -
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C MET 3.2 27.4 + - - +
13C GLY* 4.3 6.2 - - - -
14C ASN 5.3 1.4 - - - +
65C SER* 1.3 76.9 + - - +
67C GLN* 1.3 64.7 + - - +
69C SER* 3.1 2.4 + - - -
70C ILE* 2.9 27.4 + - + +
86C PHE* 3.7 14.8 - - + -
166C TYR* 3.8 35.8 - - + +
168C ALA* 2.9 32.4 + - - +
171C PHE* 6.0 0.2 - - - +
500C 5I5 5.7 0.4 - - - -
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Residues in contact with GLN 67 (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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14C ASN 4.9 0.4 - - - +
15C PRO* 3.5 19.5 - - - +
16C LEU 4.0 1.6 - - - +
63C GLY 2.6 32.2 + - - +
64C GLY* 3.6 5.0 + - - +
65C SER 3.2 0.2 - - - -
66C THR* 1.3 79.6 - - - +
68C ASN* 1.3 62.5 + - - +
70C ILE* 3.4 3.0 + - + +
71C LYS* 3.0 50.0 + - + +
86C PHE* 3.4 39.1 - - + -
99C LEU* 4.4 16.0 - - - +
103C ALA* 4.5 0.5 - - - +
108C VAL* 6.6 0.4 - - + -
112C TYR* 2.6 30.7 + - - -
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Residues in contact with ASN 68 (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 3.6 7.0 - - - +
63C GLY* 3.4 17.3 - - - +
64C GLY 3.0 19.6 + - - +
65C SER 3.3 7.6 - - - +
67C GLN* 1.3 74.8 - - - +
69C SER* 1.3 57.7 + - - +
71C LYS* 3.1 14.6 + - - +
72C VAL* 2.9 36.0 + - + +
297C GLY* 5.6 3.6 - - - -
300C ASP* 3.7 22.9 + - + +
332C ARG* 4.6 7.7 - - - +
500C 5I5 3.0 26.7 + - - +
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Residues in contact with SER 69 (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 3.1 6.5 + - - -
66C THR 3.5 7.4 - - - -
68C ASN* 1.3 74.7 - - - +
70C ILE* 1.3 60.0 + - - +
72C VAL* 3.2 2.6 + - - -
73C ALA* 2.9 27.4 + - - +
166C TYR* 3.8 24.1 + - - -
300C ASP* 2.6 36.1 + - - -
303C VAL* 3.6 17.8 - - - +
304C GLY* 3.3 10.5 - - - -
307C LEU* 4.6 1.3 - - - -
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Residues in contact with ILE 70 (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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9C LEU* 3.7 30.1 - - + -
10C PHE 4.3 0.2 - - - -
11C GLY* 3.9 30.5 - - - +
66C THR* 2.9 22.8 + - + +
67C GLN* 3.7 5.6 - - + +
69C SER* 1.3 76.4 - - - +
71C LYS* 1.3 56.4 + - - +
73C ALA* 3.7 4.6 - - - +
74C GLN* 3.1 26.0 + - - +
84C ALA* 3.6 12.3 - - + +
85C THR 3.9 13.2 - - - +
86C PHE* 4.2 12.6 - - + -
108C VAL* 3.4 30.5 - - + -
166C TYR* 5.0 8.5 - - + -
307C LEU* 5.2 0.9 - - + -
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Residues in contact with LYS 71 (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* 3.4 34.4 + - - +
67C GLN* 3.0 43.6 + - + +
68C ASN* 3.1 14.1 + - - +
70C ILE* 1.3 75.0 - - - +
72C VAL* 1.3 65.7 + - + +
74C GLN* 3.2 2.8 + - - +
75C TRP* 2.9 23.4 + - - +
99C LEU 5.1 0.2 + - - -
102C LYS* 3.9 14.8 + - - +
103C ALA* 4.0 22.8 - - - +
106C ALA* 3.8 12.6 - - + +
108C VAL* 3.8 23.8 - - + -
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Residues in contact with VAL 72 (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 ASN* 2.9 17.8 + - + +
69C SER 3.6 6.5 - - - +
71C LYS* 1.3 75.4 - - + +
73C ALA* 1.3 57.3 + - - +
75C TRP* 3.2 11.4 + - + +
76C MET* 2.9 28.7 + - + +
301C ALA* 3.4 45.8 - - + +
304C GLY* 4.0 2.7 - - - -
305C GLY* 3.8 7.2 - - - +
326C ALA* 3.8 18.2 - - + -
330C ILE* 4.2 24.7 - - + -
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Residues in contact with ALA 73 (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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9C LEU* 3.6 30.1 - - + -
69C SER 2.9 16.8 + - - +
70C ILE 3.7 2.0 - - - +
72C VAL* 1.3 73.8 - - - +
74C GLN* 1.3 59.8 + - - +
76C MET* 3.1 2.8 + - - +
77C ILE* 2.8 40.3 + - + +
304C GLY* 3.4 24.8 + - - +
307C LEU* 4.4 1.3 - - + -
308C SER* 4.1 5.8 - - - +
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Residues in contact with GLN 74 (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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70C ILE 3.1 15.4 + - - +
71C LYS 3.5 8.3 - - - +
73C ALA* 1.3 72.0 - - - +
75C TRP* 1.3 61.4 + - - +
77C ILE* 2.9 6.7 + - - +
78C GLN* 2.8 38.2 + - - +
80C PRO 3.2 23.2 + - - -
81C HIS* 3.7 5.9 + - - +
82C LYS 3.7 5.9 + - - +
83C ALA* 3.0 25.7 + - - +
84C ALA* 3.1 15.1 + - + +
106C ALA 3.0 26.7 - - - +
107C HIS* 3.5 21.6 + - + +
108C VAL* 4.3 5.6 - - + -
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Residues in contact with TRP 75 (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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338B PHE* 5.5 0.8 - - + +
339B PRO* 3.0 25.5 + - + -
340B GLU* 3.1 23.7 + - - +
341B LYS 3.6 2.0 - - - -
342B PRO* 3.5 45.6 - - + +
71C LYS 2.9 13.4 + - - +
72C VAL* 3.2 16.4 - - + +
74C GLN* 1.3 79.8 - - - +
76C MET* 1.3 84.4 + - + +
78C GLN* 3.0 29.6 + - - +
106C ALA 5.1 1.1 + - - -
325C TYR* 4.1 8.3 - + - -
326C ALA* 5.1 2.5 - - - -
329C ILE* 3.9 20.6 - - + -
330C ILE* 3.8 34.3 - - + -
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Residues in contact with MET 76 (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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342B PRO* 3.9 13.5 - - - +
344B PHE* 4.4 8.1 - - + -
72C VAL* 2.9 20.1 + - + +
73C ALA 3.5 1.3 - - - +
75C TRP* 1.3 103.4 - - + +
77C ILE* 1.3 60.3 + - - +
78C GLN* 3.1 3.9 - - - +
305C GLY* 4.2 8.7 - - - -
308C SER* 3.1 33.7 - - - +
309C GLN* 5.1 8.1 + - - +
322C ALA* 3.5 37.0 - - + +
325C TYR* 3.2 33.7 - - + -
326C ALA* 4.3 3.8 - - + -
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Residues in contact with ILE 77 (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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4C VAL* 4.1 12.1 - - + -
8C ILE* 5.5 0.7 - - + -
9C LEU* 4.7 11.7 - - + -
73C ALA* 2.8 40.6 + - + +
74C GLN* 2.9 9.2 + - - +
76C MET* 1.3 77.0 - - - +
78C GLN* 1.3 52.6 - - - +
79C GLN* 2.1 41.9 + - + +
80C PRO* 3.9 15.9 - - + +
83C ALA* 3.6 30.7 - - + -
84C ALA* 5.2 1.8 - - + -
308C SER* 4.0 26.7 - - - +
311C VAL* 4.5 14.6 - - + -
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Residues in contact with GLN 78 (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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340B GLU 4.3 4.2 + - - +
341B LYS* 2.9 40.2 - - + +
342B PRO* 4.3 9.4 - - + +
74C GLN* 2.8 14.9 + - - +
75C TRP* 3.0 34.8 - - - +
76C MET 3.1 4.6 - - - +
77C ILE* 1.3 72.1 - - - +
79C GLN* 1.3 78.1 + - - +
80C PRO 3.7 3.5 - - - +
81C HIS* 4.0 25.4 + - - -
107C HIS* 5.4 6.3 + - - -
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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
------------------------------------------------------------
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