Contacts of the helix formed by residues 135 - 150 (chain D) 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 ALA 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D LYS* 4.2 13.0 - - - -
65D PRO 4.4 2.9 - - - +
66D SER* 3.6 14.6 - - - +
68D PRO* 4.5 0.4 - - - -
90D THR* 4.3 3.8 - - - +
132D SER* 3.2 13.0 + - - +
134D THR* 1.3 79.9 + - - +
136D MET* 1.3 66.7 + - - +
137D ASN* 3.3 17.7 - - - +
138D SER* 3.1 12.5 + - - -
139D LEU* 3.2 11.8 + - - +
190D TYR* 3.4 15.7 - - - +
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Residues in contact with MET 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PRO* 3.4 19.4 - - + +
90D THR* 3.3 8.2 + - - +
91D ASP* 3.1 23.3 - - - +
93D PRO* 3.3 39.3 - - + -
134D THR 3.3 2.9 + - - +
135D ALA* 1.3 70.5 - - - +
137D ASN* 1.3 58.7 + - - +
138D SER 3.2 0.2 + - - -
139D LEU* 3.3 12.3 + - + +
140D GLN* 2.8 70.1 + - + +
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Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 3.5 12.6 + - - +
90D THR* 3.3 15.7 + - - +
105D ASN* 3.1 34.6 - - - +
135D ALA* 3.3 11.1 - - - +
136D MET* 1.3 74.6 - - - +
138D SER* 1.3 61.4 + - - -
140D GLN* 3.6 0.8 + - - -
141D ARG* 3.0 57.0 + - - +
190D TYR* 3.2 17.3 + - - -
501D XYP 2.8 32.1 + - - -
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Residues in contact with SER 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 2.7 25.1 + - - -
132D SER 3.4 16.0 + - - -
133D LEU* 5.2 0.2 - - - -
135D ALA* 3.1 7.8 + - - -
137D ASN* 1.3 78.6 + - - +
139D LEU* 1.3 69.2 + - - +
141D ARG* 3.3 1.9 + - - +
142D ILE* 3.1 30.9 + - - +
189D VAL* 3.8 13.1 - - - +
190D TYR* 3.4 26.5 - - - -
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PRO* 6.0 0.2 - - + -
133D LEU* 3.9 33.7 - - + +
134D THR* 3.7 24.7 - - - +
135D ALA 3.2 8.3 + - - +
136D MET* 3.6 13.7 - - + +
138D SER* 1.3 78.6 - - - +
140D GLN* 1.3 63.7 + - + +
142D ILE* 3.1 9.4 + - + +
143D GLN* 2.9 24.3 + - - +
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ASP* 5.3 5.3 + - - +
100D TYR* 5.8 0.7 - - - -
105D ASN* 2.9 42.5 + - + +
106D TYR* 3.7 20.7 - - + +
136D MET* 2.8 58.2 + - + +
137D ASN* 3.6 0.9 + - - -
139D LEU* 1.3 73.6 - - + +
141D ARG* 1.3 58.2 + - - +
142D ILE 3.1 0.2 + - - -
143D GLN* 3.2 6.4 + - - +
144D GLY* 2.9 28.1 + - - -
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 4.3 1.2 + - - -
105D ASN* 2.9 43.9 + - + +
109D GLY* 3.4 6.3 - - - -
137D ASN* 3.0 37.4 + - - +
138D SER 3.3 3.3 + - - +
140D GLN* 1.3 74.0 - - - +
142D ILE* 1.3 58.3 + - - +
145D PHE* 3.0 28.1 + - - +
187D PHE* 4.1 3.9 - - + -
189D VAL* 2.9 36.8 + - + -
190D TYR* 4.6 0.6 - - - -
215D PHE* 3.2 48.8 - - + -
236D GLN* 2.9 19.2 + - - +
501D XYP 2.9 37.3 + - - -
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.1 29.6 - - + -
130D THR* 4.4 6.1 - - + -
133D LEU* 5.1 6.3 - - + -
138D SER* 3.1 32.8 + - - +
139D LEU* 3.6 7.0 - - + +
141D ARG* 1.3 76.5 - - - +
143D GLN* 1.3 61.0 + - - +
145D PHE* 3.8 4.3 - - - +
146D LYS* 2.8 54.1 + - + +
159D ILE* 4.2 18.6 - - + -
187D PHE* 4.8 0.7 - - + -
189D VAL* 3.8 24.5 - - + -
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Residues in contact with GLN 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR* 3.7 11.0 - - + -
139D LEU 2.9 12.8 + - - +
140D GLN* 3.7 9.2 - - - +
142D ILE* 1.3 77.3 - - - +
144D GLY* 1.3 56.4 + - - +
146D LYS* 3.3 16.8 + - - +
147D ASP* 2.9 67.1 + - - +
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Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR* 3.4 27.2 - - - -
110D TYR* 3.3 29.6 - - - -
140D GLN 2.9 13.4 + - - -
141D ARG 4.1 0.4 - - - -
143D GLN* 1.3 77.5 - - - +
145D PHE* 1.3 62.1 + - - +
147D ASP 3.4 0.2 + - - -
148D ALA* 3.1 18.9 + - - +
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Residues in contact with PHE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLY 3.4 11.9 - - - +
112D ALA 4.7 0.4 - - - -
113D GLY* 3.5 28.0 - - - -
116D MET* 3.9 23.8 - - + -
126D VAL* 4.0 24.9 - - + -
128D ILE* 4.5 7.0 - - + -
141D ARG 3.0 20.1 + - - +
142D ILE* 3.8 3.1 - - - +
143D GLN 3.4 0.2 - - - -
144D GLY* 1.3 75.1 - - - +
146D LYS* 1.3 66.5 + - - +
148D ALA* 3.5 1.7 + - - +
149D ILE* 3.3 33.3 + - + +
154D ILE* 5.7 0.2 - - + -
156D ILE* 3.9 31.0 - - + -
187D PHE* 3.6 46.7 - + + -
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ILE* 2.8 41.0 + - + +
143D GLN* 3.5 18.7 + - - +
145D PHE* 1.3 74.7 - - + +
147D ASP* 1.3 56.3 + - - +
149D ILE* 3.2 10.5 - - - +
150D LYS* 2.8 36.0 + - + +
156D ILE* 3.5 24.9 - - + -
159D ILE* 4.3 21.0 - - - +
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Residues in contact with ASP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR* 2.6 34.3 + - - +
110D TYR* 4.0 10.6 + - + -
143D GLN* 2.9 42.3 + - - +
144D GLY 3.9 1.8 - - - +
146D LYS* 1.3 73.7 - - - +
148D ALA* 1.3 66.6 + - - +
150D LYS* 3.3 38.2 + - - +
151D ASP* 4.4 2.4 + - - +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D TYR* 3.5 53.1 + - + +
113D GLY* 4.0 1.6 - - - -
114D LEU* 3.7 21.6 - - + +
117D LYS* 4.4 7.3 + - - +
144D GLY 3.1 14.6 + - - +
145D PHE 3.7 5.2 - - - +
147D ASP* 1.3 79.4 - - - +
149D ILE* 1.3 58.9 + - - +
151D ASP* 4.2 13.7 + - - +
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLY* 3.8 25.6 - - - +
116D MET* 5.1 0.4 - - + -
117D LYS* 4.6 11.0 - - + +
145D PHE* 3.3 28.0 + - + +
146D LYS* 3.2 14.3 + - - +
148D ALA* 1.3 73.9 - - - +
150D LYS* 1.3 59.0 + - - +
151D ASP* 2.8 13.5 + - - -
152D SER* 2.9 32.0 + - - +
154D ILE* 3.4 46.2 - - + +
156D ILE* 3.7 30.1 - - + -
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 2.8 16.7 + - - +
147D ASP* 3.3 33.0 + - - +
149D ILE* 1.3 78.2 - - - +
151D ASP* 1.3 59.8 + - - +
152D SER 3.7 4.1 + - - +
154D ILE 5.8 0.4 - - - -
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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