Contacts of the helix formed by residues 96 - 110 (chain C) in PDB entry 3CQ6
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 ASN 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASN* 4.2 24.4 + - - +
100A GLU* 6.3 0.4 - - - -
255A LEU* 5.3 1.4 - - + +
257A TYR 5.6 0.2 - - - +
258A HIS* 4.5 14.3 - - - +
260A SER* 5.7 2.9 - - - -
95C ALA* 1.3 71.4 - - - +
97C GLY* 1.3 64.2 + - - +
99C ASN* 4.7 1.4 - - - +
100C GLU* 2.8 39.9 + - + +
236C ARG* 3.4 29.2 + - + +
258C HIS 2.5 31.2 + - - +
259C LEU* 3.6 12.3 - - - +
260C SER 5.3 0.7 + - - -
263C SER* 4.6 9.4 + - - -
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Residues in contact with GLY 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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95C ALA 2.9 9.7 + - - -
96C ASN* 1.3 76.3 - - - +
98C SER* 1.3 66.1 + - - -
99C ASN 3.1 2.5 - - - -
100C GLU 3.2 6.6 + - - -
101C ILE* 3.3 13.7 + - - +
228C LLP 3.5 8.5 - - - -
236C ARG* 3.3 20.0 + - - -
237C LEU 3.9 5.2 - - - -
238C GLY* 3.3 18.3 - - - +
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Residues in contact with SER 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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97C GLY* 1.3 68.5 - - - -
99C ASN* 1.3 66.1 + - - +
101C ILE* 3.9 10.1 - - - -
102C LEU* 2.9 33.6 + - - +
123C TYR* 5.8 0.2 - - - -
197C ASP* 5.2 0.5 + - - -
223C SER* 4.0 12.5 + - - -
224C ARG 3.3 22.3 + - - -
225C THR* 3.6 6.4 - - - -
228C LLP 2.8 44.4 + - - -
238C GLY* 3.6 2.0 - - - -
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Residues in contact with ASN 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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63A TYR* 6.1 0.2 - - - -
255A LEU* 4.0 21.8 - - + -
256A PRO* 3.4 28.7 - - - +
257A TYR* 5.0 2.8 - - - -
96C ASN 4.7 1.3 - - - +
97C GLY 3.1 1.0 - - - -
98C SER* 1.3 77.7 - - - +
100C GLU* 1.3 57.8 + - - +
102C LEU* 5.7 0.2 - - - +
103C GLN* 3.0 26.0 + - - +
123C TYR* 4.1 10.4 + - - -
125C MET* 3.5 39.7 - - - +
129C LEU* 3.7 17.7 - - - +
228C LLP 3.2 13.3 + - - +
236C ARG* 3.9 9.1 + - - +
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 4.6 10.0 - - - +
255A LEU* 3.7 18.2 - - + -
95C ALA* 4.0 1.6 - - + -
96C ASN* 2.8 59.7 + - + +
97C GLY 3.2 3.3 + - - +
99C ASN* 1.3 76.3 - - - +
101C ILE* 1.3 67.1 + - - +
103C GLN* 3.5 9.7 - - - +
104C GLN* 2.9 46.5 + - + +
255C LEU* 4.5 15.1 + - - +
258C HIS* 3.5 18.1 - - - +
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C TRP* 3.5 41.7 - - + +
95C ALA* 3.5 22.3 - - + +
97C GLY 3.3 8.2 + - - +
98C SER* 3.6 9.9 - - - +
100C GLU* 1.3 76.7 - - - +
102C LEU* 1.3 59.9 + - + +
104C GLN* 3.4 6.0 + - - +
105C LEU* 3.1 44.3 + - + +
223C SER* 4.0 19.3 - - - +
238C GLY* 3.6 25.4 - - - +
239C TYR* 3.7 3.1 - - - +
240C PHE* 4.0 15.4 - - + -
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Residues in contact with LEU 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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98C SER* 2.9 29.9 + - - +
99C ASN* 5.7 0.2 - - - +
101C ILE* 1.3 74.2 - - + +
103C GLN* 1.3 67.2 + - - +
105C LEU* 3.2 13.3 + - + +
106C LEU* 2.9 34.9 + - + +
123C TYR* 5.2 4.0 - - + -
126C HIS* 3.8 32.8 - - + +
129C LEU* 3.9 18.8 - - + -
166C PHE* 4.4 11.2 - - + -
195C ILE* 3.8 30.3 - - + -
197C ASP* 4.2 8.7 - - - +
223C SER* 3.9 15.9 - - - +
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Residues in contact with GLN 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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100A GLU* 5.4 1.2 - - - +
103A GLN* 3.6 23.9 + - - +
107A GLN* 4.1 22.4 + - - +
253A VAL 5.1 2.0 + - - -
255A LEU* 3.8 34.9 - - + +
99C ASN 3.0 20.2 + - - +
100C GLU* 3.3 15.5 + - - +
102C LEU* 1.3 77.4 - - - +
104C GLN* 1.3 58.4 + - - +
106C LEU* 3.3 6.2 + - - +
107C GLN* 2.9 39.6 + - - +
129C LEU* 4.4 5.0 - - + +
132C GLY 5.6 1.0 + - - -
133C THR* 3.7 21.7 - - + +
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Residues in contact with GLN 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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93C TRP* 2.9 30.2 + - - -
95C ALA* 4.1 3.2 - - - +
100C GLU* 2.9 37.7 + - + +
101C ILE* 3.6 5.2 - - - +
103C GLN* 1.3 75.4 - - + +
105C LEU* 1.3 64.2 + - - +
107C GLN* 3.3 18.1 + - - +
108C ALA* 3.1 19.8 + - - +
250C VAL* 4.4 9.6 - - + +
253C VAL* 3.4 22.4 - - + +
254C ARG* 3.5 28.4 - - - +
255C LEU 4.7 1.0 - - - +
258C HIS* 3.6 24.4 - - - -
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Residues in contact with LEU 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 ILE* 3.1 37.3 + - + +
102C LEU* 3.2 11.4 + - + +
104C GLN* 1.3 75.5 - - - +
106C LEU* 1.3 53.9 + - - +
108C ALA 3.3 0.7 + - - -
109C PHE* 2.8 59.3 + - + +
164C ILE* 4.9 2.7 - - - -
193C ILE* 4.9 2.5 - - + -
195C ILE* 4.1 25.6 - - + -
221C VAL* 3.9 35.4 - - + -
223C SER* 5.8 0.2 - - - +
240C PHE* 4.2 12.6 - - + -
246C PHE* 4.7 1.3 - - + -
250C VAL* 3.9 21.5 - - + -
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Residues in contact with LEU 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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102C LEU* 2.9 24.8 + - + +
103C GLN 3.5 3.8 - - - +
105C LEU* 1.3 74.3 - - + +
107C GLN* 1.3 61.0 + - - +
110C GLY* 2.7 34.6 + - - +
111C GLY 3.4 2.3 + - - -
116C ALA* 4.5 3.1 - - + -
129C LEU* 3.7 41.1 - - + +
130C ALA* 3.8 6.1 - - - +
133C THR* 3.3 17.0 - - + +
135C THR* 3.8 25.8 - - + +
164C ILE* 3.7 22.4 - - + -
166C PHE* 4.3 24.7 - - + -
195C ILE* 5.8 0.9 - - + -
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Residues in contact with GLN 107 (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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12A ARG* 3.2 25.3 - - - -
15A LEU* 4.2 4.2 - - - +
103A GLN* 4.1 18.9 + - - +
132A GLY* 3.6 28.0 + - - +
133A THR* 5.8 0.8 - - - +
134A HIS* 5.0 8.2 + - - +
103C GLN* 2.9 27.1 + - + +
104C GLN* 3.5 28.0 + - - +
105C LEU 3.3 0.4 - - - -
106C LEU* 1.3 75.6 - - - +
108C ALA* 1.3 57.5 + - - +
111C GLY* 5.3 2.0 - - - +
133C THR* 4.4 13.9 - - + +
253C VAL* 3.9 35.1 + - + +
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Residues in contact with ALA 108 (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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11A LEU* 3.7 18.2 - - + +
12A ARG* 3.0 29.3 + - - +
15A LEU* 3.9 9.4 - - - -
104C GLN 3.1 14.7 + - - +
105C LEU* 4.7 0.2 - - - -
107C GLN* 1.3 80.5 - - - +
109C PHE* 1.3 80.3 + - + +
249C ALA 4.4 8.1 - - - +
250C VAL* 4.9 1.6 - - + -
253C VAL* 4.1 14.6 - - + -
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Residues in contact with PHE 109 (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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9A LEU* 3.8 16.8 - - + -
10A PRO* 3.6 27.8 - - + +
11A LEU* 3.6 22.7 - - + -
105C LEU* 2.8 31.8 + - + +
108C ALA* 1.3 87.1 - - + +
110C GLY* 1.3 59.0 + - - +
114C ARG* 3.0 26.1 + - - +
163C ASP* 4.0 6.0 - - - +
164C ILE* 3.9 13.8 - - + +
193C ILE* 3.8 30.7 - - + -
246C PHE* 3.6 29.4 - + - -
249C ALA* 3.5 27.1 - - + -
250C VAL* 5.0 0.7 - - + -
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Residues in contact with GLY 110 (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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12A ARG* 3.0 27.5 + - - -
106C LEU 2.7 21.2 + - - -
109C PHE* 1.3 72.3 - - - +
111C GLY* 1.3 61.7 + - - -
114C ARG* 3.4 16.4 - - - -
135C THR* 4.0 7.9 - - - -
163C ASP* 5.3 0.2 - - - -
164C ILE* 3.8 14.7 - - - +
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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