Contacts of the helix formed by residues 158 - 180 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A SER 3.4 3.8 + - - +
157A LEU* 1.3 82.3 - - - +
159A GLN* 1.3 60.8 + - - +
160A SER* 4.3 4.3 - - - +
161A ILE* 3.1 25.2 + - + +
162A LYS* 2.8 26.5 + - - +
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 3.6 2.0 + - - -
158A ASP* 1.3 73.5 - - - +
160A SER* 1.3 58.8 + - - +
162A LYS* 3.8 27.6 + - - +
163A ASP* 2.7 67.0 + - - +
166A ILE* 5.0 4.9 - - - +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 3.3 3.9 - - - +
159A GLN* 1.3 78.8 - - - +
161A ILE* 1.3 67.8 + - - +
163A ASP* 3.7 9.2 + - - +
164A LYS* 3.4 27.7 + - - +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 5.6 0.9 - - + -
157A LEU* 3.9 22.2 - - + -
158A ASP* 3.1 30.0 + - + +
160A SER* 1.3 81.9 - - - +
162A LYS* 1.3 65.3 + - - +
164A LYS* 2.9 41.9 + - + +
165A TYR* 3.3 30.3 - - + +
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Residues in contact with LYS 162 (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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154A TRP* 3.5 54.1 + - + +
155A GLN* 3.7 19.2 + - - +
157A LEU* 3.2 35.8 + - + -
158A ASP 2.8 14.3 + - - +
159A GLN* 3.7 30.6 + - - +
161A ILE* 1.3 72.7 - - - +
163A ASP* 1.3 63.3 + - - +
165A TYR* 3.5 3.0 + - - +
166A ILE* 3.0 32.2 + - + +
5B T 4.7 4.2 + - - +
141J LYS* 4.7 14.3 - - - +
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Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 2.7 52.3 + - - +
160A SER* 3.8 9.6 - - - +
161A ILE 3.1 0.2 - - - -
162A LYS* 1.3 77.1 - - - +
164A LYS* 1.3 54.1 + - - +
166A ILE* 3.1 11.2 + - - +
167A GLN* 2.5 40.0 + - + +
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A SER* 3.4 19.2 + - - +
161A ILE* 2.9 31.9 + - + +
163A ASP* 1.3 77.2 - - - +
165A TYR* 1.3 64.2 + - + +
167A GLN* 3.5 8.4 + - - +
168A GLU* 2.9 30.7 + - - +
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Residues in contact with TYR 165 (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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122A PRO* 4.0 13.5 - - + +
125A LYS* 4.1 6.0 - - + +
126A TYR* 3.5 50.0 - + - -
129A GLU* 2.4 36.0 + - - +
154A TRP* 4.0 27.8 - + + -
157A LEU* 4.5 0.4 - - + -
161A ILE* 3.3 35.6 - - + +
162A LYS 4.1 0.2 - - - +
163A ASP 3.3 0.4 - - - -
164A LYS* 1.3 79.8 - - + +
166A ILE* 1.3 52.8 + - - +
168A GLU* 3.0 20.8 + - - +
169A TYR* 2.7 36.0 + - - +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 4.1 23.6 - - + -
154A TRP* 4.5 11.9 - - + -
159A GLN* 5.0 3.4 - - - +
162A LYS* 3.0 33.2 + - + +
163A ASP* 3.6 14.4 - - - +
165A TYR* 1.3 74.8 - - - +
167A GLN* 1.3 63.6 + - - +
169A TYR* 3.3 2.9 + - - +
170A LYS* 3.1 54.8 + - - +
5B T 4.6 7.6 - - - +
6B T 3.8 16.4 - - - +
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Residues in contact with GLN 167 (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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163A ASP* 2.5 23.0 + - + +
164A LYS* 3.9 6.6 - - - +
166A ILE* 1.3 73.3 - - - +
168A GLU* 1.3 62.1 + - - +
170A LYS* 3.3 12.2 + - + +
171A LYS* 3.3 24.3 + - - +
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Residues in contact with GLU 168 (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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125A LYS* 3.3 34.8 + - - +
129A GLU* 5.1 5.0 - - - +
164A LYS 2.9 17.7 + - - +
165A TYR* 3.3 26.9 - - - +
167A GLN* 1.3 79.9 + - - +
169A TYR* 1.3 61.8 + - - +
171A LYS* 3.5 7.5 + - - +
172A ALA* 3.4 17.7 + - - +
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Residues in contact with TYR 169 (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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118A LYS* 3.5 18.8 - - - -
119A PRO* 3.6 13.0 - - + -
120A ALA 2.9 31.0 - - - +
121A GLY* 3.9 9.9 - - - -
122A PRO* 3.7 17.5 - - + -
125A LYS* 4.6 7.4 - - + +
165A TYR 2.7 19.0 + - - +
166A ILE 3.3 4.0 + - - +
168A GLU* 1.3 71.5 - - - +
170A LYS* 1.3 76.8 + - + +
172A ALA* 2.9 16.3 + - - +
173A ILE* 3.0 48.5 + - + +
5B T 6.1 0.2 - - - -
6B T 3.4 52.3 + - - -
7B A 3.8 2.6 - - - -
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Residues in contact with LYS 170 (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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166A ILE* 3.1 38.7 + - + +
167A GLN* 3.7 10.5 - - + +
168A GLU 3.3 0.4 - - - -
169A TYR* 1.3 83.3 - - + +
171A LYS* 1.3 57.9 + - - +
173A ILE* 3.3 14.5 - - + +
174A GLN* 2.9 34.0 + - - +
6B T 4.3 8.7 - - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 3.3 13.0 + - - +
168A GLU* 3.8 10.1 - - - +
169A TYR 3.2 0.8 - - - -
170A LYS* 1.3 77.9 - - - +
172A ALA* 1.3 55.9 + - - +
174A GLN* 3.9 21.0 + - - +
175A GLU* 3.1 50.9 + - - +
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Residues in contact with ALA 172 (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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119A PRO* 3.8 22.6 - - + +
125A LYS* 4.1 13.0 - - - +
168A GLU 3.4 10.6 + - - +
169A TYR 2.9 11.6 + - - +
171A LYS* 1.3 77.0 - - - +
173A ILE* 1.3 54.2 + - - +
175A GLU* 3.2 11.2 + - - +
176A TYR* 2.6 35.2 + - - +
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Residues in contact with ILE 173 (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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118A LYS* 5.0 3.6 - - + -
119A PRO* 3.9 16.4 - - + +
169A TYR* 3.0 52.5 + - + +
170A LYS* 3.3 20.9 - - + +
172A ALA* 1.3 74.2 - - - +
174A GLN* 1.3 71.3 + - + +
176A TYR* 3.3 9.5 - - + +
177A ASN* 2.7 51.4 + - - +
7B A 3.5 25.6 - - - +
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Residues in contact with GLN 174 (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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170A LYS 2.9 19.8 + - - +
171A LYS* 4.1 23.7 - - - +
173A ILE* 1.3 83.9 - - + +
175A GLU* 1.3 62.4 + - - +
177A ASN* 3.6 7.9 + - + +
178A ALA* 3.3 19.9 + - - +
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Residues in contact with GLU 175 (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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171A LYS* 3.1 39.7 + - - +
172A ALA* 3.5 8.1 - - - +
174A GLN* 1.3 75.4 - - - +
176A TYR* 1.3 63.1 + - - +
178A ALA* 3.1 8.6 + - + +
179A ARG* 2.5 57.2 + - - +
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Residues in contact with TYR 176 (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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31A ARG* 3.5 37.5 + - - +
32A THR* 5.4 4.0 + - - +
35A ARG* 5.7 0.9 - - - -
116A PRO* 3.5 36.5 + - + -
117A LYS 3.7 10.5 - - - -
118A LYS* 4.0 16.1 + - + +
119A PRO* 3.5 29.2 - - + -
172A ALA 2.6 21.4 + - - +
173A ILE* 3.1 7.4 + - + +
175A GLU* 1.3 72.9 - - - +
177A ASN* 1.3 81.2 + - - +
179A ARG* 3.2 5.8 + - - +
180A TYR* 2.8 50.8 + + + +
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Residues in contact with ASN 177 (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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31A ARG* 3.6 22.1 + - - +
173A ILE* 2.7 34.8 + - - +
174A GLN* 3.9 8.1 - - - +
176A TYR* 1.3 93.4 - - - +
178A ALA* 1.3 61.9 + - - +
180A TYR 4.1 6.3 - - - -
181A PRO* 3.3 27.1 - - + +
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Residues in contact with ALA 178 (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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174A GLN 3.3 11.9 + - - +
175A GLU* 3.1 13.2 + - + +
177A ASN* 1.3 80.1 - - - +
179A ARG* 1.3 61.7 + - + +
181A PRO* 3.7 11.0 - - - +
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Residues in contact with ARG 179 (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 PRO* 5.9 6.5 - - + -
175A GLU* 2.5 52.8 + - + +
176A TYR* 4.0 4.0 - - - +
178A ALA* 1.3 78.1 - - + +
180A TYR* 1.3 60.7 + - + +
181A PRO* 3.4 7.5 - - - +
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Residues in contact with TYR 180 (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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31A ARG* 3.2 63.2 + - + -
34A LEU* 3.3 29.7 - - + +
35A ARG* 4.8 2.0 - - + -
115A PRO* 3.6 34.0 - - + +
116A PRO* 4.3 20.2 - - + -
176A TYR* 2.8 42.6 + + + +
177A ASN* 3.4 7.7 - - - +
179A ARG* 1.3 78.4 - - + +
181A PRO* 1.3 73.5 - - + +
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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
------------------------------------------------------------
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