Contacts of the helix formed by residues 104 - 121 (chain C) in PDB entry 3C6Q
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 ASP 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C THR* 1.3 72.9 - - - +
105C ASN* 1.3 58.0 + - - +
106C TYR* 3.8 5.7 + - - +
107C GLN* 3.2 41.8 + - + +
108C ALA* 2.9 30.0 + - - +
278C ASP* 3.9 27.7 + - - +
281C VAL* 5.7 4.2 - - + +
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Residues in contact with ASN 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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89C ASP 3.9 1.0 + - - -
90C THR* 4.9 1.0 - - - +
91C ASP 5.8 0.2 - - - +
100C TYR* 3.3 23.4 + - - -
103C THR* 3.1 16.0 + - - +
104C ASP* 1.3 68.8 + - - +
106C TYR* 1.3 59.9 + - - +
108C ALA* 3.2 3.7 + - - +
109C GLY* 2.8 25.8 + - - -
137C ASN* 3.1 29.8 - - - +
140C GLN* 2.9 39.5 + - + +
141C ARG* 2.9 40.1 + - + +
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Residues in contact with TYR 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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104C ASP* 3.8 5.3 + - - +
105C ASN* 1.3 77.5 - - - +
107C GLN* 1.3 72.1 + - - +
109C GLY* 2.9 1.9 + - - -
110C TYR* 2.7 56.6 + + + +
140C GLN* 3.8 22.8 - - + +
143C GLN* 3.7 11.9 - - + -
144C GLY* 3.3 31.0 - - - -
147C ASP* 2.6 37.3 + - - +
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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
----------------------------------------------------------
104C ASP* 3.2 38.2 + - + +
106C TYR* 1.3 93.0 - - - +
108C ALA* 1.3 53.4 + - - +
110C TYR* 3.5 6.4 - - - +
111C THR* 2.7 40.6 + - - +
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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
----------------------------------------------------------
103C THR* 4.3 11.0 - - + -
104C ASP 2.9 18.5 + - - +
105C ASN 3.6 4.0 - - - +
107C GLN* 1.3 75.5 - - - +
109C GLY* 1.3 65.4 + - - +
111C THR* 3.4 0.8 + - - -
112C ALA* 3.0 24.3 + - - +
215C PHE* 3.8 24.7 - - + -
234C MET* 3.6 21.7 - - + +
281C VAL* 4.4 10.8 - - + -
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Residues in contact with GLY 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASN 2.8 14.3 + - - -
106C TYR 3.5 2.5 - - - -
108C ALA* 1.3 74.4 - - - +
110C TYR* 1.3 63.0 + - - +
112C ALA* 3.2 5.7 + - - +
113C GLY 2.9 18.0 + - - -
141C ARG* 3.4 27.8 - - - -
145C PHE* 3.4 16.6 - - - +
187C PHE* 4.9 0.7 - - - -
215C PHE* 4.1 5.3 - - - -
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Residues in contact with TYR 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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106C TYR* 2.7 49.3 + + + +
107C GLN* 3.5 11.4 - - - +
109C GLY* 1.3 70.2 - - - +
111C THR* 1.3 66.1 + - - +
113C GLY* 2.7 14.9 + - - -
114C LEU* 2.9 45.2 + - + +
144C GLY 3.3 22.1 - - - +
147C ASP* 4.0 6.8 + - + -
148C ALA* 3.5 26.8 + - + +
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Residues in contact with THR 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 GLN* 2.7 28.5 + - - +
108C ALA* 3.6 5.0 - - - -
110C TYR* 1.3 74.4 - - - +
112C ALA* 1.3 60.5 + - - +
114C LEU* 3.3 17.0 + - + +
115C ILE* 2.9 32.2 + - + +
234C MET* 3.8 8.2 - - + +
283C VAL* 3.8 28.5 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.8 + - - +
109C GLY* 3.6 5.2 - - - +
111C THR* 1.3 73.2 - - - +
113C GLY* 1.3 61.6 + - - +
115C ILE* 3.0 13.3 + - - +
116C MET* 2.8 27.5 + - - +
145C PHE* 4.5 2.0 - - - -
187C PHE* 4.0 17.0 - - + -
213C VAL* 4.0 18.1 - - + +
215C PHE* 4.6 0.7 - - + -
234C MET* 3.7 22.4 - - + -
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY 2.9 8.1 + - - -
110C TYR 2.7 12.7 + - - -
112C ALA* 1.3 68.2 - - - +
114C LEU* 1.3 58.3 + - - -
116C MET* 3.2 2.4 + - - +
117C LYS* 2.9 31.0 + - - +
145C PHE* 3.5 26.6 - - - -
148C ALA* 4.0 13.9 - - - -
149C ILE* 3.8 7.3 - - - +
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Residues in contact with LEU 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 TYR* 2.9 49.7 + - + +
111C THR* 3.4 15.5 - - + +
113C GLY* 1.3 74.6 - - - +
115C ILE* 1.3 63.2 + - + +
117C LYS* 3.5 16.2 + - + +
118C GLU* 3.0 23.4 + - - +
148C ALA* 3.7 15.5 - - + +
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Residues in contact with ILE 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 THR* 2.9 23.7 + - + +
112C ALA* 3.0 14.1 + - - +
114C LEU* 1.3 74.7 - - + +
116C MET* 1.3 65.8 + - - +
118C GLU* 3.2 6.0 + - - +
119C LEU* 3.0 40.2 + - + +
213C VAL* 4.3 4.7 - - + -
232C ALA* 3.8 26.9 - - + -
234C MET* 5.1 4.3 - - - -
283C VAL* 4.3 26.7 - - + -
285C THR* 6.2 0.4 - - + -
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA 2.8 11.2 + - - +
113C GLY 3.4 7.2 - - - +
115C ILE* 1.3 72.7 - - - +
117C LYS* 1.3 68.1 + - - +
119C LEU* 2.9 7.0 + - - +
120C LEU* 2.8 43.4 + - + +
126C VAL* 4.2 6.1 - - + -
145C PHE* 3.9 23.1 - - + -
149C ILE* 5.1 1.1 - - + -
154C ILE* 4.9 3.6 - - + -
185C ALA* 3.4 27.1 - - + -
186C PHE 3.3 28.0 - - - +
187C PHE* 3.9 15.7 - - + -
211C LYS* 5.0 3.4 - - - -
213C VAL* 3.4 32.4 - - + +
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Residues in contact with LYS 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 GLY 2.9 21.0 + - - +
114C LEU* 3.6 16.2 - - + +
116C MET* 1.3 72.2 - - - +
118C GLU* 1.3 64.9 + - - +
120C LEU 3.4 0.2 + - - -
121C GLY* 2.9 4.2 + - - -
122C GLY* 2.8 40.2 + - - -
148C ALA 4.4 11.7 + - - +
149C ILE* 4.7 6.3 - - + +
151C ASP* 2.8 40.0 + - - +
152C SER* 4.6 8.3 - - - +
154C ILE* 3.8 16.5 - - + +
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Residues in contact with GLU 118 (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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114C LEU 3.0 13.1 + - - +
115C ILE* 3.4 11.2 - - - +
116C MET 3.1 0.2 - - - -
117C LYS* 1.3 78.1 - - - +
119C LEU* 1.3 80.3 + - + +
121C GLY* 2.9 15.3 + - - -
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Residues in contact with LEU 119 (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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115C ILE* 3.0 25.1 + - + +
116C MET* 2.9 7.8 + - - +
118C GLU* 1.3 96.0 - - + +
120C LEU* 1.3 63.8 + - + +
211C LYS* 3.9 41.2 + - + +
213C VAL* 3.8 28.5 - - + -
231C GLN* 3.8 28.7 - - + -
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Residues in contact with LEU 120 (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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116C MET* 2.8 23.6 + - + +
119C LEU* 1.3 78.1 - - + +
121C GLY* 1.3 61.2 - - - +
123C LYS* 3.6 25.6 - - - +
124C GLY* 4.7 2.9 - - - -
126C VAL* 3.8 26.2 - - + -
154C ILE* 3.6 28.3 - - + -
184C ASP* 3.9 36.1 - - + +
185C ALA* 4.0 7.9 - - + -
211C LYS* 4.1 14.8 - - + -
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Residues in contact with GLY 121 (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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117C LYS 2.9 5.4 + - - -
118C GLU* 2.9 9.6 + - - -
120C LEU* 1.3 76.5 - - - +
122C GLY* 1.3 58.9 + - - +
123C LYS* 3.0 19.3 + - - +
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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