Contacts of the helix formed by residues 158 - 177 (chain J) in PDB entry 5JGH
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 158 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J SER 3.6 2.4 + - - -
157J LEU* 1.3 76.9 - - - +
159J GLN* 1.3 66.4 + - - +
160J SER* 4.2 4.5 - - - +
161J ILE* 3.0 36.5 + - + +
162J LYS* 3.1 11.4 + - - +
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Residues in contact with GLN 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LEU 3.4 3.7 + - - -
158J ASP* 1.3 73.4 + - - +
160J SER* 1.3 62.8 + - - +
162J LYS* 3.5 26.5 + - - +
163J ASP* 2.6 49.3 + - - +
166J ILE* 4.5 5.9 - - - +
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Residues in contact with SER 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J ASP* 3.1 3.6 - - - +
159J GLN* 1.3 79.1 - - - +
161J ILE* 1.3 73.0 + - - +
163J ASP* 3.4 17.8 + - - +
164J LYS* 3.5 22.0 + - - +
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Residues in contact with ILE 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J TYR* 5.3 1.8 - - + -
157J LEU* 3.5 31.6 - - + -
158J ASP* 3.0 28.5 + - + +
160J SER* 1.3 84.9 - - - +
162J LYS* 1.3 68.4 + - - +
164J LYS* 3.0 35.6 + - + +
165J TYR* 3.2 19.9 - - + +
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Residues in contact with LYS 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J TRP* 3.0 62.3 - - + +
155J GLN* 3.2 25.3 + - - +
157J LEU* 3.2 23.1 + - + +
158J ASP 3.1 13.2 + - - +
159J GLN* 3.5 29.9 + - - +
161J ILE* 1.3 76.6 - - - +
163J ASP* 1.3 54.1 + - - +
165J TYR* 2.7 27.4 + - - +
166J ILE* 2.9 19.6 + - + +
5K T 4.7 4.3 - - - +
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Residues in contact with ASP 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159J GLN* 2.6 42.9 + - - +
160J SER* 3.6 12.8 - - - +
161J ILE 3.2 0.4 - - - -
162J LYS* 1.3 73.3 - - - +
164J LYS* 1.3 56.8 + - - +
166J ILE* 2.9 15.0 + - - +
167J GLN* 2.6 39.5 + - + +
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Residues in contact with LYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J SER* 3.5 21.3 + - - +
161J ILE* 3.0 25.6 + - + +
163J ASP* 1.3 77.8 - - - +
165J TYR* 1.3 64.1 + - + +
167J GLN* 3.9 5.1 - - - +
168J GLU* 2.9 33.6 + - - +
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Residues in contact with TYR 165 (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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122J PRO* 3.9 18.3 - - + +
125J LYS* 3.9 11.6 - - + +
126J TYR* 3.5 45.9 - + + -
129J GLU* 2.3 41.1 + - - +
154J TRP* 3.9 22.0 - + + -
161J ILE* 3.2 35.6 - - + +
162J LYS 2.7 11.5 + - - +
164J LYS* 1.3 76.5 - - + +
166J ILE* 1.3 59.6 + - - +
168J GLU* 3.1 15.4 + - - +
169J TYR* 2.8 30.8 + - - +
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Residues in contact with ILE 166 (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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122J PRO* 4.0 15.3 - - + -
154J TRP* 5.0 6.1 - - + -
159J GLN* 4.5 3.8 - - - +
162J LYS* 2.9 26.8 + - + +
163J ASP* 3.5 27.1 - - - +
165J TYR* 1.3 76.1 - - - +
167J GLN* 1.3 62.8 + - - +
169J TYR* 3.1 3.8 + - - +
170J LYS* 3.0 51.4 + - + +
5K T 5.2 3.4 - - - +
6K T 3.6 24.0 - - - +
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Residues in contact with GLN 167 (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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163J ASP* 2.6 22.3 + - + +
164J LYS* 3.9 5.4 - - - +
166J ILE* 1.3 74.1 - - - +
168J GLU* 1.3 62.3 + - - +
170J LYS* 3.3 18.5 + - - +
171J LYS* 3.1 64.5 + - - +
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Residues in contact with GLU 168 (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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125J LYS* 4.1 26.0 - - + +
129J GLU* 4.2 13.3 - - - +
164J LYS* 2.9 23.1 + - - +
165J TYR* 3.1 25.7 + - - +
167J GLN* 1.3 78.2 - - - +
169J TYR* 1.3 59.7 + - - +
171J LYS* 3.8 7.7 + - - +
172J ALA* 3.3 22.3 + - - +
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Residues in contact with TYR 169 (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* 5.4 4.2 - - - +
119J PRO* 3.5 28.8 + - + +
120J ALA 3.1 26.9 - - - +
121J GLY* 3.6 11.0 - - - -
122J PRO* 3.6 16.6 - - + -
125J LYS* 6.4 2.0 - - + -
165J TYR 2.8 15.7 + - - +
166J ILE 3.1 4.5 + - - +
168J GLU* 1.3 76.5 - - - +
170J LYS* 1.3 62.6 + - + +
172J ALA* 3.0 5.4 + - + +
173J ILE* 2.7 68.8 + - + +
6K T 3.4 46.7 + - - -
7K A 3.8 6.4 - - - -
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Residues in contact with LYS 170 (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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166J ILE* 3.0 42.0 + - + +
167J GLN* 3.8 19.3 + - - +
169J TYR* 1.3 81.8 - - + +
171J LYS* 1.3 58.3 + - - +
173J ILE* 3.4 11.1 - - + +
174J GLN* 2.9 34.2 + - - +
6K T 5.0 5.2 - - - +
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Residues in contact with LYS 171 (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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167J GLN* 3.1 49.7 + - - +
168J GLU* 4.1 7.2 - - - +
170J LYS* 1.3 75.0 - - - +
172J ALA* 1.3 63.5 + - - +
174J GLN* 3.5 10.4 + - - +
175J GLU* 3.1 24.8 + - - +
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Residues in contact with ALA 172 (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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119J PRO* 4.2 20.2 - - + +
168J GLU 3.3 13.1 + - - +
169J TYR* 3.0 11.0 + - + +
171J LYS* 1.3 79.8 - - - +
173J ILE* 1.3 57.8 + - - +
175J GLU* 3.2 14.8 + - - +
176J TYR* 2.8 26.9 + - - +
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Residues in contact with ILE 173 (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* 4.5 16.2 - - + +
119J PRO* 4.0 11.0 - - + +
169J TYR* 2.7 51.2 + - + +
170J LYS* 3.4 18.6 - - + +
172J ALA* 1.3 71.4 - - - +
174J GLN* 1.3 65.2 + - + +
176J TYR* 3.0 7.7 + - + -
177J ASN* 2.8 42.1 + - - +
7K A 3.1 39.0 - - - +
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Residues in contact with GLN 174 (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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170J LYS 2.9 19.7 + - - +
171J LYS* 3.9 10.3 - - - +
173J ILE* 1.3 79.3 - - + +
175J GLU* 1.3 62.6 + - - +
177J ASN* 3.5 11.7 + - + +
178J ALA* 3.3 17.7 + - - +
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Residues in contact with GLU 175 (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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171J LYS 3.1 15.9 + - - +
172J ALA* 3.5 14.5 - - - +
174J GLN* 1.3 76.3 - - - +
176J TYR* 1.3 65.7 + - - +
178J ALA* 3.0 22.4 + - + +
179J ARG* 2.3 46.9 + - - +
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Residues in contact with TYR 176 (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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31J ARG* 2.8 42.5 + - - -
116J PRO* 3.1 31.2 + - + -
117J LYS 3.6 10.5 - - - -
118J LYS* 3.2 37.7 - - + -
119J PRO* 3.7 25.4 - - + -
172J ALA 2.8 14.5 + - - +
173J ILE* 3.0 10.3 + - + +
175J GLU* 1.3 76.9 - - - +
177J ASN* 1.3 66.6 + - - +
178J ALA 3.1 1.2 + - - -
179J ARG* 3.2 20.3 + - + +
180J TYR* 3.2 34.6 - + - +
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Residues in contact with ASN 177 (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* 3.8 6.1 + - - -
173J ILE* 2.8 36.8 + - - +
174J GLN* 3.8 9.6 - - - +
175J GLU 3.2 0.2 - - - -
176J TYR* 1.3 79.3 - - - +
178J ALA* 1.3 61.4 + - - +
180J TYR* 3.3 33.8 - - + +
181J PRO 3.1 21.6 - - - +
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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