Contacts of the helix formed by residues 84 - 95 (chain C) in PDB entry 4I6N
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 ALA 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TRP* 3.8 34.5 - - + -
79C GLN* 4.8 0.7 - - - -
81C ILE* 3.9 21.7 - - + +
82C GLN 3.0 2.8 + - - -
83C ASN* 1.3 76.2 - - - +
85C CYS* 1.3 64.0 + - - +
86C ALA 3.0 3.1 + - - -
87C SER* 3.0 5.5 + - - -
88C GLN* 2.9 38.8 + - - +
127C LEU* 4.4 7.2 - - + -
128C THR* 5.1 2.0 - - - +
137C HIS* 4.2 0.9 - - - -
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Residues in contact with CYS 85 (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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79C GLN* 3.3 22.7 - - - +
82C GLN 3.3 2.0 + - - -
83C ASN 3.1 4.4 - - - -
84C ALA* 1.3 76.9 - - - +
86C ALA* 1.3 59.2 + - - +
88C GLN* 3.9 1.5 - - - +
89C ALA* 2.8 32.9 + - - +
161C HIS* 3.7 8.3 - - + +
162C PHE* 3.7 19.0 - - - +
75D GLY 3.6 4.3 - - - -
101D GVE 1.8 80.8 - - + +
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Residues in contact with ALA 86 (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 ILE* 3.7 28.9 - - + -
16C PHE* 3.8 18.0 - - + -
19C MSE 4.6 3.8 - - + -
83C ASN 4.6 0.6 + - - -
84C ALA 3.0 1.4 + - - -
85C CYS* 1.3 80.9 - - - +
87C SER* 1.3 59.3 + - - +
89C ALA* 3.8 1.9 - - - +
90C LEU* 3.0 27.9 + - - +
137C HIS* 4.3 2.7 - - + +
162C PHE* 3.5 34.3 - - + -
75D GLY 4.9 1.5 + - - +
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Residues in contact with SER 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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6C TRP* 4.0 13.0 - - - -
19C MSE 3.2 20.2 - - - +
23C PHE* 3.5 13.0 - - - -
84C ALA 3.0 5.1 + - - -
86C ALA* 1.3 75.4 - - - +
88C GLN* 1.3 62.3 + - - +
90C LEU* 3.8 3.0 - - - +
91C ILE* 2.8 36.2 + - - +
127C LEU* 4.7 1.8 - - - -
133C ILE* 4.3 7.9 - - - -
137C HIS* 2.7 33.9 + - - +
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Residues in contact with GLN 88 (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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77C SER* 2.9 37.4 + - - +
78C GLN 3.3 20.6 + - - -
79C GLN* 3.2 39.6 - - + +
80C VAL 4.6 1.7 + - - -
84C ALA* 2.9 21.8 + - - +
85C CYS* 3.9 3.4 - - - +
87C SER* 1.3 78.2 - - - +
89C ALA* 1.3 56.0 + - - +
91C ILE* 3.8 0.7 - - - +
92C ASN* 2.8 39.0 + - - +
124C GLY* 3.5 11.8 - - - +
127C LEU* 3.8 27.9 - - + +
128C THR* 4.8 1.0 + - - -
177C GLY* 5.0 1.8 - - - -
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Residues in contact with ALA 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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50C ILE* 4.5 5.6 - - + -
85C CYS 2.8 17.7 + - - +
86C ALA 3.8 3.6 - - - +
88C GLN* 1.3 76.2 - - - +
90C LEU* 1.3 63.1 + - - +
92C ASN* 3.4 5.2 + - - +
93C LEU 3.0 12.5 + - - -
162C PHE* 3.8 30.3 - - + +
163C VAL* 4.2 6.7 - - - +
164C THR* 2.6 32.7 + - - +
175C LEU 5.2 2.0 - - - +
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Residues in contact with LEU 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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16C PHE* 4.1 15.9 - - + +
19C MSE 3.8 23.1 - - + -
20C ILE* 3.6 39.3 - - + -
23C PHE* 3.8 21.1 - - + -
30C VAL* 5.9 0.2 - - + -
50C ILE* 3.9 23.7 - - + +
86C ALA 3.0 16.4 + - - +
87C SER* 3.8 5.2 - - - +
88C GLN 3.3 0.2 - - - -
89C ALA* 1.3 78.6 - - - +
91C ILE* 1.3 58.0 + - - +
93C LEU* 3.2 5.2 + - + +
94C LEU* 2.8 44.1 + - + +
221C VAL* 4.8 6.5 - - + -
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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
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23C PHE* 3.7 28.3 - - + -
75C TYR* 5.2 2.7 - - + -
77C SER* 5.3 1.6 - - - +
87C SER 2.8 21.7 + - - +
88C GLN 4.1 0.2 - - - +
90C LEU* 1.3 76.9 - - - +
92C ASN* 1.3 56.4 + - - +
94C LEU* 4.3 3.6 - - + +
95C LEU* 2.9 55.1 + - + +
108C LEU* 4.0 17.5 - - + -
111C PHE* 4.4 10.3 - - + -
127C LEU* 3.9 22.9 - - + -
133C ILE* 3.8 33.4 - - + -
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Residues in contact with ASN 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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75C TYR* 4.0 7.6 - - - -
76C PHE* 3.6 21.1 - - - -
77C SER* 2.7 55.6 + - - +
88C GLN* 2.8 28.2 + - - +
89C ALA* 3.7 6.7 - - - +
91C ILE* 1.3 75.9 - - - +
93C LEU* 1.3 58.3 + - - +
95C LEU* 4.4 0.5 - - - +
96C ASN* 2.8 32.4 + - - +
175C LEU* 3.5 24.6 + - + +
177C GLY* 4.7 5.1 - - - -
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Residues in contact with LEU 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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47C HIS* 4.2 12.8 - - + +
48C GLY* 3.8 24.0 - - - -
49C PHE 3.9 11.7 - - - +
50C ILE* 4.0 8.1 - - + -
89C ALA 3.0 13.1 + - - +
90C LEU* 3.4 9.9 - - + +
92C ASN* 1.3 76.0 - - - +
94C LEU* 1.3 75.9 + - + +
96C ASN* 3.0 16.3 + - - +
97C CYS* 3.6 22.7 + - - -
164C THR* 3.6 26.1 - - + +
165C TYR 4.7 0.9 - - - +
166C VAL* 4.3 7.0 - - + +
175C LEU* 4.8 0.9 - - - -
221C VAL* 3.8 31.2 - - + -
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Residues in contact with LEU 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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20C ILE* 4.4 14.4 - - + -
23C PHE* 4.4 9.4 - - + -
25C CYS* 4.0 13.5 - - + -
28C LEU* 3.4 33.9 - - + -
90C LEU* 2.8 42.7 + - + +
91C ILE* 4.1 3.1 - - - +
93C LEU* 1.3 85.6 - - + +
95C LEU* 1.3 63.8 + - + +
97C CYS* 3.1 30.2 + - - +
102C VAL* 4.8 1.6 - - + -
104C LEU* 3.6 20.0 - - + +
108C LEU* 3.8 21.8 - - + -
221C VAL* 5.1 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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75C TYR* 3.6 49.5 - - + +
91C ILE* 2.9 29.9 + - + +
94C LEU* 1.3 78.6 - - + +
96C ASN* 1.3 60.2 + - - +
97C CYS 3.4 0.9 - - - -
104C LEU* 3.6 33.7 - - + -
108C LEU* 4.1 17.3 - - + +
111C PHE* 3.9 20.2 - - + -
112C LYS* 2.9 47.7 + - + +
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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