Contacts of the helix formed by residues 101 - 115 (chain C) in PDB entry 1C3Q
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 THR 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 39.2 + - - +
54A ASP* 3.8 20.0 - - + -
55A MET* 3.9 30.5 - - + +
97C GLY 4.1 1.4 + - - -
99C GLY 4.7 1.6 - - - -
100C ALA* 1.3 83.3 - - - +
102C PRO* 1.3 73.9 - - - +
103C PHE 4.2 0.9 - - - -
104C ARG* 3.3 16.6 + - - +
105C THR* 3.2 22.4 + - - -
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Residues in contact with PRO 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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54A ASP* 3.2 29.6 - - + +
100C ALA 4.8 0.4 - - - +
101C THR* 1.3 83.7 - - - +
103C PHE* 1.3 56.7 + - - +
105C THR* 3.3 6.9 + - - +
106C GLU* 2.8 39.9 + - + +
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Residues in contact with PHE 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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48A ALA* 3.9 18.2 - - + -
50A GLU* 3.7 49.4 - - + +
51A GLU* 3.9 21.1 - - + -
54A ASP* 5.3 0.2 + - - -
69C LEU* 3.4 33.4 - - + -
70C SER 4.2 1.6 - - - -
71C LYS* 4.1 27.6 - - + -
74C VAL* 4.9 1.6 - - + -
101C THR 3.2 0.4 - - - -
102C PRO* 1.3 80.9 - - - +
104C ARG* 1.3 56.9 + - - +
106C GLU* 3.9 4.8 - - + +
107C SER* 2.8 48.8 + - - -
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Residues in contact with ARG 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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44A VAL* 4.8 2.5 - - - +
45A MET 3.1 17.4 + - - -
46A ALA* 3.6 7.1 - - - +
51A GLU* 2.6 40.1 + - - +
55A MET* 3.6 16.3 - - - +
301A TZE 4.7 2.4 - - - -
66C ILE* 3.5 15.3 + - + +
67C GLY* 2.9 31.8 + - - -
68C THR* 4.5 0.8 - - - +
69C LEU* 3.6 24.5 - - + +
96C VAL* 3.2 25.0 + - - +
97C GLY* 3.5 30.9 - - - +
98C ALA* 4.2 4.9 - - - -
100C ALA* 4.9 0.2 - - - -
101C THR* 3.3 10.3 + - - +
103C PHE* 1.3 75.1 - - - +
105C THR* 1.3 65.4 + - - +
107C SER 3.3 0.2 + - - -
108C ALA* 2.9 25.5 + - - +
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Residues in contact with THR 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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98C ALA* 4.5 6.5 - - - +
99C GLY* 2.8 34.8 + - - +
101C THR 3.2 6.9 + - - -
102C PRO* 3.6 10.4 - - - +
104C ARG* 1.3 80.5 - - - +
106C GLU* 1.3 68.2 + - - +
108C ALA* 3.4 2.9 + - - +
109C ARG* 3.1 52.2 + - - +
129C HIS* 3.9 17.8 - - + +
130C THR* 5.1 1.0 - - - -
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Residues in contact with GLU 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 PRO* 2.8 24.1 + - + +
103C PHE* 4.1 4.9 - - + +
105C THR* 1.3 79.7 - - - +
107C SER* 1.3 59.9 + - - +
109C ARG* 3.0 35.1 + - - +
110C ASP* 2.8 38.6 + - - +
113C ARG* 3.7 20.3 + - - -
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Residues in contact with SER 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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66C ILE* 4.9 4.3 - - - -
69C LEU* 3.3 27.4 - - - +
74C VAL* 3.8 18.6 - - - +
103C PHE* 2.8 39.3 + - - -
104C ARG 3.3 2.2 + - - -
106C GLU* 1.3 76.0 - - - +
108C ALA* 1.3 62.3 + - - +
110C ASP* 3.2 12.3 + - - +
111C ILE* 3.1 30.7 + - - +
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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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66C ILE* 4.2 8.4 - - + +
93C LEU* 4.2 6.2 - - + +
95C PRO* 4.2 15.9 - - + -
98C ALA* 4.6 1.1 - - + -
104C ARG 2.9 18.1 + - - +
105C THR* 3.6 6.5 - - - +
107C SER* 1.3 77.6 - - - +
109C ARG* 1.3 60.7 + - - +
111C ILE* 3.4 10.6 + - - +
112C ILE* 3.1 28.3 + - - +
130C THR* 4.0 25.4 - - + +
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Residues in contact with ARG 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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105C THR* 3.1 24.2 + - - +
106C GLU* 3.0 33.3 + - - +
108C ALA* 1.3 74.4 - - - +
110C ASP* 1.3 60.8 + - - +
112C ILE* 3.6 9.5 - - + +
113C ARG* 2.8 59.0 + - - +
129C HIS 2.9 23.0 + - - -
130C THR* 3.2 25.0 + - + +
131C VAL 5.0 0.4 - - - -
132C GLY* 3.5 20.2 - - - +
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Residues in contact with ASP 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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74C VAL* 5.1 6.3 - - + +
78C ILE* 4.3 14.8 - - + -
106C GLU* 2.8 26.6 + - - +
107C SER* 3.2 16.9 + - - +
109C ARG* 1.3 76.6 - - - +
111C ILE* 1.3 56.8 - - + +
113C ARG* 3.3 24.4 + - - +
114C GLU* 2.9 36.4 + - + +
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Residues in contact with ILE 111 (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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64C LEU* 4.0 21.5 - - + -
66C ILE* 4.1 11.2 - - + -
74C VAL* 4.8 2.0 - - + -
77C MET* 3.4 41.1 - - + -
78C ILE* 4.2 22.0 - - + -
93C LEU* 4.1 21.1 - - + -
107C SER 3.1 15.7 + - - +
108C ALA* 3.6 7.2 - - - +
110C ASP* 1.3 78.5 - - - +
112C ILE* 1.3 53.7 + - - +
115C VAL* 2.7 45.2 + - + +
117C LEU* 4.4 10.5 - - + -
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Residues in contact with ILE 112 (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 LEU* 4.1 5.4 - - + -
108C ALA 3.1 12.0 + - - +
109C ARG* 3.6 10.1 - - + +
111C ILE* 1.3 76.6 - - - +
113C ARG* 1.3 65.1 + - + +
115C VAL 3.2 18.2 - - - +
117C LEU* 3.7 23.8 - - + -
120C ILE* 4.0 16.2 - - + -
130C THR* 3.3 36.3 - - + +
161C LEU* 4.0 32.3 - - + +
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Residues in contact with ARG 113 (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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106C GLU* 3.7 20.4 + - - -
109C ARG* 2.8 41.8 + - - +
110C ASP* 3.4 28.2 + - - +
112C ILE* 1.3 82.0 - - + +
114C GLU* 1.3 68.8 + - + +
115C VAL 3.9 0.2 + - - -
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Residues in contact with GLU 114 (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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78C ILE* 3.7 33.0 - - + -
82C LYS* 2.9 41.7 + - - +
85C ASN* 4.4 1.6 + - - -
110C ASP* 2.9 21.1 + - + +
111C ILE 4.3 0.9 - - - +
113C ARG* 1.3 86.8 - - + +
115C VAL* 1.3 62.5 + - + +
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Residues in contact with VAL 115 (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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64C LEU* 5.1 0.7 - - + -
77C MET 4.7 0.9 - - - +
78C ILE* 4.1 24.7 - - + +
81C GLY* 3.8 33.2 - - - +
82C LYS 4.3 0.2 - - - +
85C ASN* 3.5 13.2 - - - +
91C VAL* 4.2 6.5 - - + -
111C ILE* 2.7 31.6 + - + +
112C ILE 3.2 16.1 - - - +
113C ARG 3.6 0.8 + - - -
114C GLU* 1.3 81.4 - - + +
116C ARG* 1.3 74.7 + - - +
117C LEU* 3.4 21.6 + - + +
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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