Contacts of the helix formed by residues 149 - 163 (chain J) in PDB entry 5ANC
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 SER 149 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107J MET* 6.0 1.8 - - - -
147J ASN 4.0 0.2 + - - -
148J LYS* 1.3 74.4 - - - +
150J THR* 1.3 66.8 + - - +
151J LYS 3.4 1.1 - - - -
152J GLN* 3.7 2.5 + - - +
153J GLN* 3.0 25.4 + - - +
2525N A 3.7 30.0 + - - -
2526N U 3.2 22.6 + - - -
2572N C 4.2 3.8 + - - +
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Residues in contact with THR 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J MET* 4.4 19.1 - - + +
110J ASP* 3.3 49.6 - - + +
111J ILE* 3.9 5.5 - - - +
114J ILE* 4.2 5.7 - - - +
149J SER* 1.3 73.3 - - - +
151J LYS* 1.3 82.5 + - - +
153J GLN* 3.2 9.6 + - - +
154J ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ILE* 3.7 34.1 - - + -
149J SER* 3.4 0.6 - - - -
150J THR* 1.3 88.2 + - - +
152J GLN* 1.3 62.4 + - - +
154J ALA* 3.2 9.2 + - - +
155J LEU* 3.1 18.2 + - - +
240J LYS* 4.1 10.7 - - - +
1113K GLN* 3.7 24.2 - - - +
2523N C 5.9 1.0 - - - -
2524N U 3.7 48.9 + - + +
2525N A 3.2 32.5 + - - +
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Residues in contact with GLN 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J LYS* 4.4 13.0 - - + -
149J SER 3.7 10.2 + - - +
150J THR 3.2 0.2 - - - -
151J LYS* 1.3 78.3 - - - +
153J GLN* 1.3 63.5 + - - +
155J LEU* 3.1 29.2 + - - +
156J GLU* 3.1 40.0 + - - +
2525N A 2.9 49.6 + - - +
2526N U 3.3 44.4 + - + +
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Residues in contact with GLN 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J MET* 4.9 5.2 - - - +
111J ILE* 3.4 22.6 - - + +
142J TYR* 3.6 17.9 + - + +
143J SER 4.0 3.6 + - - -
144J VAL* 3.6 12.9 - - - +
145J LYS* 2.7 50.9 + - - +
148J LYS* 3.0 30.8 - - + +
149J SER 3.0 11.2 + - - +
150J THR* 3.2 5.4 + - - +
152J GLN* 1.3 72.7 - - - +
154J ALA* 1.3 59.4 + - - +
156J GLU* 3.2 11.9 + - - +
157J VAL* 2.9 36.1 + - - +
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J ILE* 4.3 3.3 - - - +
114J ILE* 3.5 33.0 - - + -
115J VAL* 4.0 11.4 - - + -
118J LYS* 4.3 9.9 - - - +
150J THR 2.9 10.0 + - - +
151J LYS 3.2 10.3 + - - +
153J GLN* 1.3 76.1 - - - +
155J LEU* 1.3 61.5 + - - +
157J VAL* 3.0 27.5 + - - +
158J ILE* 3.2 13.7 + - - +
2524N U 5.1 1.3 - - - +
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LYS* 4.9 0.7 - - - +
151J LYS 3.1 7.6 + - - +
152J GLN* 3.2 31.2 - - - +
154J ALA* 1.3 75.5 - - - +
156J GLU* 1.3 65.1 + - + +
158J ILE* 3.0 27.4 - - + +
159J LYS* 3.6 14.4 - - + +
216J CYS* 4.7 13.2 - - + +
217J PHE* 4.7 22.9 - - + -
2524N U 3.7 19.6 + - - +
2525N A 3.7 28.3 - - + +
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Residues in contact with GLU 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J TYR* 2.7 33.5 + - + +
143J SER 5.4 0.5 - - - +
145J LYS* 5.7 3.3 - - - +
148J LYS* 3.7 21.1 - - - +
152J GLN* 3.1 39.4 + - - +
153J GLN* 3.2 11.7 + - - +
155J LEU* 1.3 81.7 - - + +
157J VAL* 1.3 62.0 + - - +
159J LYS* 3.2 22.0 + - - +
160J GLN* 3.4 14.0 + - - +
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Residues in contact with VAL 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J ILE* 4.3 9.4 - - + +
115J VAL* 3.6 26.2 - - + -
137J MET* 4.2 27.1 - - + +
142J TYR* 3.5 39.0 - - + -
153J GLN 2.9 19.3 + - - +
154J ALA* 3.0 22.2 - - - +
156J GLU* 1.3 75.5 - - - +
158J ILE* 1.3 61.6 + - + +
160J GLN* 3.2 9.6 + - - +
161J LEU* 2.9 27.0 + - - +
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Residues in contact with ILE 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J VAL* 4.6 14.1 - - + -
118J LYS* 4.0 42.6 - - + +
154J ALA 3.2 12.5 + - - +
155J LEU* 3.0 29.6 - - + +
157J VAL* 1.3 78.3 - - + +
159J LYS* 1.3 83.0 + - - +
161J LEU* 3.2 18.1 + - + +
162J LYS* 3.1 19.9 + - - +
168J GLU* 4.4 19.7 - - + +
169J ARG 4.7 7.2 - - - +
170J ALA* 5.4 1.8 - - + -
216J CYS* 4.7 12.6 - - + -
217J PHE* 5.7 1.1 - - + -
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Residues in contact with LYS 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J LEU* 3.6 18.7 + - + +
156J GLU* 3.2 11.1 + - - +
158J ILE* 1.3 99.6 - - - +
160J GLN* 1.3 57.6 + - + +
162J LYS* 3.1 31.2 - - + +
163J GLU* 3.8 10.1 + - - +
168J GLU* 3.4 28.3 + - - +
217J PHE* 4.1 25.6 - - - -
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Residues in contact with GLN 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ILE* 3.5 39.4 + - + +
141J HIS 4.5 6.3 + - - -
142J TYR* 3.3 39.9 - - - +
156J GLU* 3.4 11.0 + - - +
157J VAL* 3.2 9.9 + - - +
159J LYS* 1.3 75.1 - - + +
161J LEU* 1.3 58.4 + - - +
162J LYS 3.1 1.8 - - - -
163J GLU* 2.8 40.1 + - + +
164J LYS* 2.9 11.8 + - - -
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Residues in contact with LEU 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J VAL* 5.3 4.5 - - + -
118J LYS 4.6 9.4 - - - +
120J VAL* 3.7 34.3 - - + -
136J ALA* 5.6 0.9 - - + -
137J MET* 6.0 5.6 - - + -
157J VAL 2.9 13.7 + - - +
158J ILE* 3.2 23.3 + - + +
160J GLN* 1.3 74.9 - - - +
162J LYS* 1.3 60.9 + - - +
164J LYS* 3.2 43.7 - - + +
166J LYS* 3.1 30.2 + - + -
167J ILE 3.8 13.3 + - - +
168J GLU* 5.4 2.0 - - - -
169J ARG* 4.0 13.9 - - + +
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Residues in contact with LYS 162 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158J ILE 3.1 9.7 + - - +
159J LYS* 3.1 23.6 - - + +
160J GLN 3.1 0.4 - - - -
161J LEU* 1.3 76.2 - - - +
163J GLU* 1.3 57.7 + - + +
165J MET* 3.2 25.1 - - - +
166J LYS 3.9 1.4 + - - -
167J ILE* 4.1 21.3 + - + +
168J GLU* 4.4 32.1 + - + +
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Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ILE* 4.9 10.2 - - + +
159J LYS* 4.1 5.2 - - - +
160J GLN* 2.8 39.8 + - + +
162J LYS* 1.3 73.3 - - + +
164J LYS* 1.3 62.3 + - - +
165J MET* 3.6 15.5 - - + +
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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