Contacts of the helix formed by residues 104 - 121 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLY 3.4 0.8 + - - -
103B THR* 1.3 71.5 - - - +
105B ASN* 1.3 61.4 + - - +
106B TYR* 3.5 9.0 + - - +
107B GLN* 3.3 32.2 + - + +
108B ALA* 2.8 30.1 + - - +
140B GLN* 5.6 1.9 + - - -
276B VAL* 5.9 3.0 - - - +
278B ASP* 3.0 39.6 + - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 3.3 21.6 + - - +
104B ASP* 1.3 68.8 + - - +
106B TYR* 1.3 68.7 + - - +
108B ALA* 3.7 3.9 - - - +
109B GLY* 2.8 22.9 + - - -
137B ASN* 3.7 28.9 - - - +
140B GLN* 3.7 27.9 + - + +
141B ARG* 3.0 39.8 + - + +
215B PHE* 5.0 0.2 - - - -
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 3.5 7.9 + - - +
105B ASN* 1.3 78.3 - - - +
107B GLN* 1.3 82.1 + - + +
109B GLY* 3.1 1.0 + - - -
110B TYR* 2.8 45.2 + + - +
140B GLN* 3.3 30.4 - - + +
143B GLN* 3.9 13.5 - - + -
144B GLY* 3.6 27.7 - - - -
147B ASP* 2.6 38.2 + - - +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 3.3 35.6 + - + +
105B ASN 3.2 0.6 - - - -
106B TYR* 1.3 100.4 - - + +
108B ALA* 1.3 61.0 + - - +
110B TYR* 3.2 15.4 + - - +
111B THR* 2.9 26.4 + - - -
278B ASP* 4.0 10.8 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 4.3 6.1 - - + -
104B ASP 2.8 20.4 + - - +
105B ASN* 3.7 4.7 - - - +
107B GLN* 1.3 71.8 - - - +
109B GLY* 1.3 64.2 + - - +
111B THR* 2.8 22.3 + - - -
112B ALA* 3.0 10.9 + - - +
215B PHE* 3.9 22.0 - - + -
234B MET* 3.9 3.2 - - + +
281B VAL* 3.8 28.9 - - + -
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN 2.8 17.2 + - - -
106B TYR 3.5 3.6 - - - -
108B ALA* 1.3 72.0 - - - +
110B TYR* 1.3 61.7 + - - +
112B ALA* 3.2 7.7 + - - +
113B GLY 3.0 16.6 + - - -
141B ARG* 3.3 24.9 - - - -
145B PHE* 3.3 16.6 + - - +
187B PHE* 5.2 0.2 - - - -
215B PHE* 4.0 9.5 - - - -
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 2.8 40.3 + + + +
107B GLN* 3.2 21.5 - - - +
109B GLY* 1.3 74.6 - - - +
111B THR* 1.3 55.3 + - - +
113B GLY* 2.7 22.3 + - - -
114B LEU* 2.9 48.3 + - + +
144B GLY 3.6 19.8 - - - +
147B ASP* 4.1 7.4 + - + -
148B ALA* 3.5 25.7 + - + +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLN* 2.9 17.8 + - - -
108B ALA* 2.8 15.1 + - - -
110B TYR* 1.3 73.2 - - - +
112B ALA* 1.3 61.7 + - - -
114B LEU* 3.3 10.0 + - + +
115B ILE* 3.1 34.0 + - + +
234B MET* 3.1 20.0 - - + -
281B VAL* 5.6 4.8 - - + +
283B VAL* 3.7 18.6 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.0 7.6 + - - +
109B GLY 3.5 9.2 - - - +
111B THR* 1.3 75.8 - - - +
113B GLY* 1.3 57.0 + - - +
115B ILE* 3.3 7.0 + - - +
116B MET* 2.8 28.8 + - - +
145B PHE* 4.2 2.9 - - + -
187B PHE* 3.9 26.7 - - + -
213B VAL* 3.9 14.3 - - + +
215B PHE* 4.4 1.8 - - + -
234B MET* 3.3 26.6 - - + +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY 3.0 7.3 + - - -
110B TYR 2.7 15.2 + - - -
112B ALA* 1.3 68.5 - - - +
114B LEU* 1.3 59.2 + - - -
116B MET* 2.9 4.4 + - - +
117B LYS* 2.7 30.1 + - - +
145B PHE* 3.7 22.3 - - - -
148B ALA* 3.5 17.7 - - - -
149B ILE* 4.0 4.5 - - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 2.9 55.0 + - + +
111B THR* 3.9 10.8 - - + +
113B GLY* 1.3 71.0 - - - -
115B ILE* 1.3 68.7 + - + +
117B LYS* 3.3 16.6 + - + +
118B GLU* 3.0 24.9 + - - +
148B ALA* 3.7 15.5 - - + +
268C LYS* 6.2 2.0 - - - +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR* 3.1 26.8 + - + +
112B ALA* 3.4 11.7 - - - +
113B GLY 3.1 0.4 - - - -
114B LEU* 1.3 83.4 - - + +
116B MET* 1.3 59.9 + - - +
118B GLU* 3.1 10.9 + - - +
119B LEU* 2.6 48.2 + - + +
213B VAL* 4.0 10.5 - - + -
232B ALA* 3.8 21.3 - - + -
234B MET* 5.2 1.6 - - + -
283B VAL* 3.8 27.4 - - + -
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 2.8 17.6 + - - +
113B GLY 2.9 6.9 + - - +
115B ILE* 1.3 75.4 - - - +
117B LYS* 1.3 65.8 + - - +
119B LEU* 3.0 7.5 + - - +
120B LEU* 2.9 42.2 + - + +
126B VAL* 4.3 6.7 - - + -
145B PHE* 3.8 24.5 - - + -
149B ILE* 5.0 1.8 - - + -
154B ILE* 4.7 4.5 - - + -
185B ALA* 3.5 26.9 - - + -
186B PHE 3.4 26.5 - - - +
187B PHE* 3.7 19.7 - - + -
211B LYS* 5.0 4.0 - - - -
213B VAL* 4.0 19.3 - - + -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY 2.7 15.2 + - - +
114B LEU* 3.4 20.3 - - + +
116B MET* 1.3 73.9 - - - +
118B GLU* 1.3 61.1 + - - +
120B LEU 3.6 0.2 + - - -
121B GLY* 3.1 4.3 + - - -
122B GLY* 3.1 33.6 + - - -
148B ALA 3.7 18.9 + - - +
149B ILE* 4.6 4.9 - - + +
151B ASP* 3.5 29.0 + - - +
152B SER* 4.3 26.2 - - - +
154B ILE* 3.7 12.1 - - + +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU 3.0 14.3 + - - +
115B ILE* 3.6 13.9 - - - +
117B LYS* 1.3 76.7 - - - +
119B LEU* 1.3 65.1 + - + +
121B GLY* 3.4 11.0 + - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 2.6 52.3 + - + +
116B MET* 3.0 9.0 + - - +
118B GLU* 1.3 79.9 - - + +
120B LEU* 1.3 64.5 + - + +
121B GLY 3.6 0.3 + - - -
211B LYS* 4.3 34.7 + - + -
213B VAL* 4.5 9.0 - - + -
231B GLN* 3.4 39.0 - - + +
232B ALA* 5.1 2.5 - - + -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B MET* 2.9 40.8 + - + +
119B LEU* 1.3 76.8 - - + +
121B GLY* 1.3 61.6 + - - +
123B LYS* 2.9 33.0 + - - +
124B GLY* 4.6 2.2 - - - -
126B VAL* 3.9 20.0 - - + -
154B ILE* 3.9 16.8 - - + -
184B ASP* 4.1 27.1 - - + +
185B ALA* 3.9 4.7 - - + -
211B LYS* 3.9 29.4 - - + +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LYS 3.1 6.6 + - - -
118B GLU* 3.4 7.0 + - - -
119B LEU 3.3 4.4 + - - -
120B LEU* 1.3 74.4 - - - +
122B GLY* 1.3 57.0 + - - +
123B LYS* 3.1 23.4 + - - +
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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
------------------------------------------------------------
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