Contacts of the helix formed by residues 104 - 121 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 3.4 1.0 + - - -
103A THR* 1.3 70.6 - - - +
105A ASN* 1.3 60.7 + - - +
106A TYR* 3.4 9.0 + - - +
107A GLN* 3.2 32.0 + - + +
108A ALA* 2.8 29.3 + - - +
140A GLN* 5.6 1.6 + - - -
276A VAL* 5.9 3.8 - - + +
278A ASP* 3.1 40.2 + - + +
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Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 3.3 21.8 + - - +
104A ASP* 1.3 69.7 + - - +
106A TYR* 1.3 68.4 + - - +
108A ALA* 3.7 3.9 - - - +
109A GLY* 2.8 22.9 + - - -
137A ASN* 3.6 30.2 - - - +
140A GLN* 3.8 27.7 + - + +
141A ARG* 3.0 39.1 + - + +
215A PHE* 5.0 0.2 - - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 3.4 8.1 + - - +
105A ASN* 1.3 78.3 - - - +
107A GLN* 1.3 82.0 + - + +
109A GLY* 3.5 0.9 - - - -
110A TYR* 2.9 45.4 + + - +
140A GLN* 3.3 30.7 - - + +
143A GLN* 4.0 13.9 - - + -
144A GLY* 3.6 26.0 - - - -
147A ASP* 2.6 38.4 + - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 3.2 35.2 + - + +
105A ASN 3.2 0.2 - - - -
106A TYR* 1.3 100.1 - - + +
108A ALA* 1.3 61.0 + - - +
110A TYR* 3.2 15.4 + - - +
111A THR* 2.9 26.1 + - - -
278A ASP* 4.0 10.8 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 4.3 6.3 - - + -
104A ASP 2.8 20.0 + - - +
105A ASN* 3.7 4.7 - - - +
107A GLN* 1.3 71.7 - - - +
109A GLY* 1.3 63.6 + - - +
111A THR* 2.9 22.6 + - - -
112A ALA* 3.0 10.7 + - - +
215A PHE* 3.9 21.8 - - + -
234A MET* 3.9 3.4 - - + +
281A VAL* 3.8 29.4 - - + -
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Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN 2.8 17.2 + - - -
106A TYR 3.5 3.6 - - - -
108A ALA* 1.3 72.0 - - - +
110A TYR* 1.3 62.1 + - - +
112A ALA* 3.2 7.5 + - - +
113A GLY 3.0 16.6 + - - -
141A ARG* 3.4 24.7 - - - -
145A PHE* 3.3 16.1 + - - +
187A PHE* 5.2 0.2 - - - -
215A PHE* 4.0 9.7 - - - -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 2.9 40.9 + + + +
107A GLN* 3.2 21.8 - - - +
109A GLY* 1.3 74.0 - - - +
111A THR* 1.3 55.8 + - - +
113A GLY* 2.7 22.0 + - - -
114A LEU* 2.9 48.0 + - + +
144A GLY* 3.6 19.6 - - - +
147A ASP* 4.1 7.4 + - + -
148A ALA* 3.5 25.4 + - + +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 2.9 17.5 + - - -
108A ALA* 2.9 14.6 + - - -
110A TYR* 1.3 74.1 - - - +
112A ALA* 1.3 62.0 + - - +
114A LEU* 3.4 8.4 + - + +
115A ILE* 3.1 34.4 + - + +
234A MET* 3.1 19.7 - - + -
281A VAL* 5.6 5.0 - - + +
283A VAL* 3.7 18.4 - - + -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 3.0 8.5 + - - +
109A GLY 3.5 9.4 - - - +
111A THR* 1.3 76.7 - - - +
113A GLY* 1.3 56.6 + - - +
115A ILE* 3.4 7.1 + - - +
116A MET* 2.8 28.4 + - - +
145A PHE* 4.2 2.2 - - - -
187A PHE* 3.9 26.5 - - + -
213A VAL* 3.9 13.6 - - + +
215A PHE* 4.4 1.8 - - + -
234A MET* 3.2 25.9 - - + +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY 3.0 7.9 + - - -
110A TYR 2.7 14.6 + - - -
112A ALA* 1.3 67.8 - - - +
114A LEU* 1.3 54.2 + - - -
116A MET* 2.9 4.4 + - - +
117A LYS* 2.7 35.7 + - - +
145A PHE* 3.7 22.3 - - - -
148A ALA* 3.5 17.5 - - - -
149A ILE* 4.1 4.3 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 2.9 54.7 + - + +
111A THR* 3.9 10.3 - - + +
113A GLY* 1.3 70.7 - - - +
115A ILE* 1.3 68.8 + - + +
117A LYS* 3.3 15.9 + - + +
118A GLU* 3.0 25.5 + - - +
148A ALA* 3.7 15.5 - - + +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR* 3.1 26.8 + - + +
112A ALA* 3.4 11.9 - - - +
114A LEU* 1.3 82.0 - - + +
116A MET* 1.3 59.5 + - - +
118A GLU* 3.1 11.2 + - - +
119A LEU* 2.6 47.9 + - + +
213A VAL* 4.0 11.2 - - + -
232A ALA* 3.8 21.3 - - + -
234A MET* 5.2 1.6 - - + -
283A VAL* 3.8 27.6 - - + -
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Residues in contact with MET 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA 2.8 17.8 + - - +
113A GLY 2.9 6.7 + - - +
115A ILE* 1.3 72.4 - - - +
117A LYS* 1.3 65.6 + - - +
119A LEU* 3.0 9.1 + - - +
120A LEU* 3.0 42.3 + - + +
126A VAL* 4.3 6.3 - - + -
145A PHE* 3.8 23.6 - - + -
149A ILE* 5.0 2.0 - - + -
154A ILE* 4.7 4.5 - - + -
185A ALA* 3.4 27.6 - - + -
186A PHE 3.4 26.5 - - - +
187A PHE* 3.7 19.7 - - + -
211A LYS* 5.0 3.8 - - - -
213A VAL* 3.9 19.5 - - + -
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 2.7 15.5 + - - +
114A LEU* 3.4 20.3 - - + +
116A MET* 1.3 72.8 - - - +
118A GLU* 1.3 63.0 + - - +
120A LEU 3.5 0.3 + - - -
121A GLY* 3.1 17.8 + - - -
122A GLY* 3.1 18.2 + - - -
148A ALA 3.8 18.2 + - - +
149A ILE* 4.6 4.7 - - + +
151A ASP* 3.5 29.2 + - - +
152A SER* 4.3 26.2 - - - +
154A ILE* 3.8 11.9 - - + +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 3.0 14.3 + - - +
115A ILE* 3.6 13.9 - - - +
117A LYS* 1.3 76.7 - - - +
119A LEU* 1.3 64.9 + - + +
121A GLY* 3.4 11.0 + - - -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 2.6 51.9 + - + +
116A MET* 3.0 9.0 + - - +
118A GLU* 1.3 80.5 - - + +
120A LEU* 1.3 63.8 + - + +
121A GLY 3.6 0.3 + - - -
211A LYS* 4.3 34.4 + - + -
213A VAL* 4.5 8.7 - - + -
231A GLN* 3.4 39.3 - - + +
232A ALA* 5.1 2.2 - - + -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A MET* 3.0 41.7 + - + +
119A LEU* 1.3 76.5 - - + +
121A GLY* 1.3 60.9 + - - +
123A LYS* 2.8 32.6 + - - +
124A GLY* 4.6 2.2 - - - -
126A VAL* 3.9 20.0 - - + -
154A ILE* 3.9 17.9 - - + -
184A ASP* 4.0 26.0 - - + +
185A ALA* 3.9 4.5 - - + -
211A LYS* 4.0 28.5 - - + +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS 3.1 6.8 + - - -
118A GLU* 3.4 7.4 + - - -
119A LEU 3.3 4.4 + - - -
120A LEU* 1.3 74.1 - - - +
122A GLY* 1.3 56.3 + - - +
123A LYS* 3.1 22.5 + - - +
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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