Contacts of the helix formed by residues 93 - 109 (chain C) in PDB entry 7CAL
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 ILE 93 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASP* 4.7 9.9 - - - +
90C ALA 4.2 11.7 - - - +
92C PHE* 1.3 85.5 - - + +
94C ILE* 1.3 73.8 + - + +
95C ASP 3.4 0.2 - - - -
96C ASN* 3.3 4.2 + - - +
97C ILE* 2.9 43.7 + - + +
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 3.4 31.0 - - + +
90C ALA 5.2 1.8 - - - +
91C ILE* 3.2 28.8 + - + +
93C ILE* 1.3 90.4 - - + +
95C ASP* 1.3 57.1 + - - +
96C ASN 3.1 0.2 - - - -
97C ILE* 4.1 9.1 - - + +
98C VAL* 3.0 34.6 + - + +
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Residues in contact with ASP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.8 3.0 + - - -
76C ILE* 4.7 10.5 - - + -
80C GLN* 5.3 8.1 - - - +
91C ILE* 3.3 14.3 + - + +
92C PHE* 3.8 6.0 + - + +
93C ILE 3.4 0.2 - - - -
94C ILE* 1.3 77.2 - - - +
96C ASN* 1.3 61.4 + - - +
98C VAL* 4.7 5.6 - - - +
99C ASN* 3.4 21.8 + - - +
150C PRO* 5.2 6.7 - - + +
171C ARG* 4.4 25.5 + - - +
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 3.2 50.4 + - - +
93C ILE* 3.3 5.5 + - - +
94C ILE 3.1 0.4 - - - -
95C ASP* 1.3 80.6 - - - +
97C ILE* 1.3 59.4 + - - +
98C VAL 3.3 0.4 - - - -
99C ASN* 3.7 10.0 - - - +
100C GLY* 3.1 21.1 + - - -
147C PRO* 4.6 8.5 - - - +
150C PRO* 3.4 26.6 - - - +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 2.9 31.9 + - + +
94C ILE* 4.1 8.5 - - + +
96C ASN* 1.3 76.8 - - + +
98C VAL* 1.3 66.1 + - + +
100C GLY* 3.1 10.4 + - - -
101C PHE* 3.1 38.4 + - + -
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.0 40.6 - - + +
72C TYR* 4.2 19.1 - - + -
73C SER* 4.5 7.4 - - - -
94C ILE* 3.0 25.6 + - + +
95C ASP* 4.7 4.7 - - - +
97C ILE* 1.3 81.0 - - + +
99C ASN* 1.3 60.9 + - + +
101C PHE* 3.1 17.1 + - - +
102C PHE* 3.2 24.8 - - + -
171C ARG* 6.1 1.8 - - - +
174C ARG* 3.9 20.9 - - - +
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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
----------------------------------------------------------
95C ASP 3.4 19.7 + - - +
96C ASN* 3.6 11.9 + - - +
97C ILE 3.3 0.4 - - - -
98C VAL* 1.3 80.1 - - + +
100C GLY* 1.3 58.2 + - - +
102C PHE* 4.0 4.8 + - - +
103C ALA* 3.8 15.4 + - - +
144C SER 5.1 0.4 + - - -
145C THR* 3.0 34.1 + - - +
146C ALA 4.6 0.4 + - - -
147C PRO* 3.8 25.7 - - + +
150C PRO* 5.6 2.2 - - - +
171C ARG* 5.4 10.0 - - - +
174C ARG* 3.4 24.6 + - - +
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Residues in contact with GLY 100 (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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96C ASN 3.1 10.3 + - - -
97C ILE* 3.1 7.2 + - - -
98C VAL 3.1 1.0 - - - -
99C ASN* 1.3 75.8 - - - +
101C PHE* 1.3 64.9 + - - +
102C PHE 3.2 2.0 - - - -
103C ALA* 3.2 16.6 + - - +
104C ILE* 3.3 19.0 + - - +
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TRP* 4.0 18.1 - + - -
65C TRP* 3.4 40.8 - + + -
66C LEU* 3.9 15.3 - - + +
69C LEU* 4.0 18.2 - - + -
97C ILE* 3.1 41.2 + - + -
98C VAL* 3.1 8.3 + - + +
100C GLY* 1.3 77.6 - - - +
102C PHE* 1.3 60.2 + - - +
103C ALA 3.4 0.2 - - - -
104C ILE* 4.1 23.5 - - + +
105C ASP* 3.9 12.3 + - - +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.9 20.4 - - + -
69C LEU* 3.6 31.2 - - + -
70C VAL* 3.6 25.4 - - + -
98C VAL* 3.2 24.1 + - + +
99C ASN* 4.4 5.6 - - - +
100C GLY 3.2 0.8 - - - -
101C PHE* 1.3 81.2 - - + +
103C ALA* 1.3 58.3 + - - +
104C ILE 3.5 0.4 - - - -
105C ASP* 4.0 7.4 - - + +
106C ILE* 3.3 23.7 + - - +
145C THR* 3.7 16.4 + - - +
174C ARG* 3.7 44.4 - - + +
177C ARG* 3.8 32.4 + - - -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASN 3.8 8.1 + - - +
100C GLY* 3.2 12.3 + - - +
102C PHE* 1.3 76.7 - - - +
104C ILE* 1.3 65.1 + - + +
105C ASP 3.3 0.2 - - - -
106C ILE* 3.6 13.1 + - - +
107C ILE* 3.7 14.0 + - - +
145C THR* 3.8 19.5 - - + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TRP* 4.1 18.6 - - + -
100C GLY 3.3 15.4 + - - +
101C PHE* 4.1 29.1 + - + +
102C PHE 3.5 0.2 - - - -
103C ALA* 1.3 78.3 - - + +
105C ASP* 1.3 57.7 + - - +
107C ILE* 3.0 12.7 + - + +
108C LEU* 2.9 29.5 + - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 5.0 2.8 + - - -
62C TRP* 2.4 39.0 + - + -
63C GLU* 5.8 1.0 - - - +
66C LEU* 3.4 23.6 - - + +
101C PHE 3.9 7.1 + - - +
102C PHE* 4.0 6.4 + - - +
103C ALA 3.3 0.6 - - - -
104C ILE* 1.3 76.6 - - - +
106C ILE* 1.3 63.5 - - - +
108C LEU* 3.8 9.6 - - - +
109C THR* 3.2 35.6 + - - +
133C TYR* 4.5 1.6 + - - -
177C ARG* 3.5 26.4 + - - +
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Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE 3.3 14.4 - - - +
103C ALA* 3.6 8.0 + - - +
104C ILE 3.2 1.0 - - - -
105C ASP* 1.3 79.4 - - - +
107C ILE* 1.3 64.0 + - + +
109C THR* 3.8 6.4 + - - -
110C PHE* 3.4 19.4 - - + -
133C TYR* 3.9 14.2 - - - +
138C PHE* 3.6 33.4 - - + -
141C ASP* 3.3 28.7 - - + +
142C VAL* 4.0 16.6 - - + -
145C THR* 3.4 22.9 - - + +
177C ARG* 6.0 2.7 - - - +
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Residues in contact with ILE 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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103C ALA 3.7 10.5 + - - +
104C ILE* 3.0 11.8 + - + +
106C ILE* 1.3 82.4 - - + +
108C LEU* 1.3 64.0 + - + +
110C PHE* 3.2 22.4 + - + +
111C PHE* 3.6 19.9 - - + -
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Residues in contact with LEU 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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52C ILE* 5.0 15.9 - - + -
59C TYR* 4.1 18.6 - - + -
62C TRP* 3.4 42.2 - - + +
104C ILE* 2.9 21.3 + - + +
105C ASP* 3.8 8.5 + - - +
106C ILE 3.4 0.2 - - - -
107C ILE* 1.3 79.4 - - + +
109C THR* 1.3 57.7 + - + +
110C PHE 3.1 0.2 - - - -
111C PHE* 3.1 31.4 + - + +
112C VAL* 4.3 1.7 - - - +
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Residues in contact with THR 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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59C TYR* 3.8 20.6 - - - +
105C ASP* 3.2 34.5 + - - +
106C ILE 3.8 0.3 + - - -
107C ILE 3.3 0.6 - - - -
108C LEU* 1.3 75.6 - - + +
110C PHE* 1.3 57.1 + - - +
111C PHE 3.3 4.0 - - - -
112C VAL* 3.8 20.8 - - + +
129C ILE* 4.4 2.8 - - - +
133C TYR* 3.1 52.7 - - + +
177C ARG* 5.6 2.2 - - - +
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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