Contacts of the helix formed by residues 103 - 117 (chain C) in PDB entry 3CUQ
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 ARG 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C LYS* 3.3 26.4 + - - +
85C GLY* 4.0 15.0 - - - +
86C ASN* 4.0 18.1 + - - +
100C MET 4.9 0.4 - - - -
102C ARG* 1.3 83.9 - - - +
104C PRO* 1.3 68.3 - - + +
105C GLU* 3.0 19.1 + - + +
106C GLU* 3.5 34.7 + - + +
107C TRP* 2.9 22.7 + - - -
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Residues in contact with PRO 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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85C GLY 4.2 11.2 - - - +
100C MET* 2.9 34.5 - - + -
102C ARG 3.7 0.8 - - - +
103C ARG* 1.3 93.1 - - + +
105C GLU* 1.3 53.9 + - + +
107C TRP* 3.3 15.3 - - + +
108C GLY* 2.8 28.9 + - - -
148C THR 4.8 0.2 - - - +
151C ARG* 3.7 25.4 - - + +
152C ALA* 3.7 17.0 - - - +
155C ALA* 4.7 6.9 - - + +
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Residues in contact with GLU 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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103C ARG* 3.0 18.7 - - + +
104C PRO* 1.3 77.6 - - - +
106C GLU* 1.3 67.7 + - + +
107C TRP 3.1 0.6 + - - -
108C GLY* 3.4 0.5 + - - -
109C LYS* 2.9 26.5 + - - +
155C ALA* 4.6 15.7 - - + +
156C LEU* 5.0 1.7 - - - +
159C GLU* 3.3 31.1 - - - +
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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 ARG* 4.1 21.8 - - + +
103C ARG* 3.7 42.7 + - + +
105C GLU* 1.3 76.5 - - - +
107C TRP* 1.3 65.1 + - - +
109C LYS* 3.7 10.3 - - - +
110C LEU* 3.1 24.4 + - + +
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Residues in contact with TRP 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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100C MET* 5.5 0.2 - - - +
101C TRP* 3.5 37.2 - + - +
102C ARG* 3.3 42.2 + - + +
103C ARG 2.9 22.4 + - - -
104C PRO* 3.3 12.1 - - + +
105C GLU 3.1 0.6 - - - -
106C GLU* 1.3 73.6 - - - +
108C GLY* 1.3 56.2 + - - +
109C LYS 3.0 0.2 - - - -
110C LEU* 2.7 35.2 + - + +
111C ILE* 3.0 19.7 + - + +
140C GLU* 3.7 42.8 - - + -
141C PHE* 4.0 16.2 - + + -
144C LEU* 3.6 23.9 - - + +
148C THR* 3.2 34.3 - - + +
152C ALA* 3.9 11.9 - - + -
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Residues in contact with GLY 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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104C PRO 2.8 18.9 + - - -
105C GLU 3.9 0.7 - - - -
107C TRP* 1.3 72.2 - - - +
109C LYS* 1.3 55.5 + - - +
111C ILE* 3.9 6.7 - - - -
112C TYR* 2.9 24.4 + - - +
152C ALA* 4.1 11.1 - - - +
155C ALA* 6.3 0.2 - - - -
156C LEU* 3.2 40.7 - - - +
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Residues in contact with LYS 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 GLU* 2.9 20.7 + - - +
106C GLU* 3.7 13.2 - - - +
107C TRP 2.9 0.2 + - - -
108C GLY* 1.3 75.2 - - - +
110C LEU* 1.3 60.7 + - + +
112C TYR* 3.1 13.4 + - + +
113C GLN* 2.9 36.3 + - + +
156C LEU* 4.4 2.9 - - + +
161C LYS* 4.4 23.1 - - - +
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Residues in contact with LEU 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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102C ARG* 2.9 33.2 - - - +
106C GLU* 3.1 15.6 + - + +
107C TRP* 2.7 19.5 + - + +
109C LYS* 1.3 71.9 - - + +
111C ILE* 1.3 57.6 + - - +
113C GLN* 3.1 31.5 + - + +
114C TRP* 2.8 27.5 + - - +
140C GLU* 3.7 31.6 - - + +
141C PHE* 4.0 13.0 - - + -
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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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107C TRP* 3.2 21.5 - - + +
108C GLY* 3.8 7.2 - - - +
110C LEU* 1.3 77.0 - - - +
112C TYR* 1.3 58.2 + - - +
114C TRP* 3.4 2.3 + - - +
115C VAL* 2.9 30.7 + - - +
130C LEU* 4.0 19.1 - - + -
141C PHE* 3.5 44.2 - - + -
144C LEU* 5.7 1.3 - - + -
149C LEU* 3.8 28.7 - - + -
152C ALA* 4.8 4.7 - - + -
153C LEU* 4.6 9.6 - - + -
156C LEU* 5.0 0.2 - - + -
175C PHE* 3.9 26.0 - - + -
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Residues in contact with TYR 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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108C GLY 2.9 19.8 + - - +
109C LYS* 3.1 16.8 + - + +
111C ILE* 1.3 75.1 - - - +
113C GLN* 1.3 61.7 + - - +
115C VAL* 3.1 7.0 + - + +
116C SER* 2.8 54.6 + - - -
121C ASN* 3.8 8.7 + - - -
156C LEU* 4.8 4.0 - - + +
161C LYS* 3.9 59.4 - - + +
175C PHE* 4.3 18.8 - + - -
176C PHE 3.6 29.4 + - - -
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Residues in contact with GLN 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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109C LYS* 2.9 21.3 + - - +
110C LEU* 3.1 32.0 + - + +
112C TYR* 1.3 78.6 - - - +
114C TRP* 1.3 84.2 + - - +
116C SER* 3.2 5.0 + - - -
117C ARG* 2.9 69.2 + - + +
139C GLU* 4.9 2.6 + - - +
141C PHE* 5.4 0.4 - - - -
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Residues in contact with TRP 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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110C LEU 2.8 9.5 + - - +
111C ILE 3.7 3.1 - - - +
113C GLN* 1.3 87.4 - - - +
115C VAL* 1.3 82.6 + - + +
117C ARG* 3.6 24.7 + - - +
118C SER* 3.1 25.9 + - - -
120C GLN* 3.2 23.8 - - - -
125C PHE* 3.9 23.8 - + - -
130C LEU* 4.1 17.5 - - + -
135C ASP* 3.8 45.1 + - + -
136C THR* 4.4 8.9 - - - +
139C GLU* 3.7 23.7 + - + +
141C PHE* 3.5 27.6 - + + -
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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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111C ILE* 2.9 23.7 + - + +
112C TYR* 3.1 7.6 + - + +
114C TRP* 1.3 94.3 - - + +
116C SER* 1.3 63.9 + - - +
118C SER* 3.2 17.8 + - - -
120C GLN 3.3 33.8 + - - +
121C ASN* 4.5 6.5 - - - +
125C PHE* 4.2 8.5 - - + -
130C LEU* 4.7 1.6 - - + -
175C PHE* 3.6 52.9 - - + -
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Residues in contact with SER 116 (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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112C TYR* 2.8 51.7 + - - -
113C GLN* 3.2 5.4 + - - -
115C VAL* 1.3 73.7 - - - +
117C ARG* 1.3 57.7 + - - +
118C SER 3.1 4.9 + - - -
119C GLY* 3.9 6.9 + - - -
121C ASN* 3.6 28.4 + - - +
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Residues in contact with ARG 117 (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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113C GLN* 2.9 63.2 + - + +
114C TRP* 3.6 23.7 + - - +
116C SER* 1.3 73.3 - - - +
118C SER* 1.3 58.3 + - - +
139C GLU* 3.3 22.4 + - - -
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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