Contacts of the helix formed by residues 158 - 180 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D SER 3.5 4.7 + - - +
157D LEU* 1.3 78.1 - - - +
159D GLN* 1.3 70.2 + - - +
160D SER* 4.5 5.2 - - - +
161D ILE* 3.2 24.2 + - + +
162D LYS* 3.0 15.9 + - - +
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU 3.6 1.8 + - - -
158D ASP* 1.3 70.0 - - - +
160D SER* 1.3 57.6 + - - +
162D LYS* 2.6 58.3 + - - +
163D ASP* 2.7 37.1 + - - +
166D ILE* 5.2 4.2 - - - +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D ASP* 4.5 4.1 - - - +
159D GLN* 1.3 77.9 - - - +
161D ILE* 1.3 69.0 + - - +
163D ASP* 3.4 11.5 + - - +
164D LYS* 3.3 26.7 + - - +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 5.9 0.7 - - + -
157D LEU* 3.7 30.5 - - + -
158D ASP* 3.2 29.3 + - + +
159D GLN 2.8 4.6 + - - -
160D SER* 1.3 76.2 - - - +
162D LYS* 1.3 66.5 + - - +
164D LYS* 3.1 39.6 + - + +
165D TYR* 3.4 16.6 - - + -
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D TRP* 3.1 61.9 + - + +
155D GLN* 3.3 24.2 + - - +
157D LEU* 3.3 27.8 - - + +
158D ASP 3.0 14.1 + - - +
159D GLN* 2.6 39.3 + - - +
161D ILE* 1.3 71.5 - - - +
163D ASP* 1.3 53.2 + - - +
165D TYR* 2.7 28.6 + - - +
166D ILE* 2.9 19.8 + - + +
5E T 4.6 7.0 + - - +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D GLN* 2.7 54.9 + - - +
160D SER* 3.4 11.0 + - - +
162D LYS* 1.3 71.7 - - - +
164D LYS* 1.3 55.5 + - + +
166D ILE* 4.1 14.1 - - - +
167D GLN* 2.5 43.1 + - + +
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Residues in contact with LYS 164 (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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160D SER* 3.3 17.7 + - - +
161D ILE* 3.2 29.2 - - + +
162D LYS 3.0 0.4 + - - -
163D ASP* 1.3 77.5 - - - +
165D TYR* 1.3 63.1 + - + +
167D GLN* 3.2 22.5 + - - +
168D GLU* 2.9 30.0 + - - +
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PRO* 3.7 20.5 - - + +
125D LYS* 4.2 11.2 - - + -
126D TYR* 3.6 54.5 - + + -
129D GLU* 2.1 41.9 + - - +
130D VAL* 5.4 1.2 - - - +
154D TRP* 3.9 15.0 - + + -
157D LEU* 4.7 0.7 - - + -
161D ILE* 3.4 28.7 - - + -
162D LYS 2.7 12.8 + - - +
164D LYS* 1.3 75.4 - - + +
166D ILE* 1.3 59.3 + - - +
168D GLU* 3.2 9.2 + - + +
169D TYR* 2.8 30.0 + - - +
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Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PRO* 3.8 21.3 - - + -
154D TRP* 4.6 7.9 - - + -
159D GLN* 5.2 4.3 - - - +
162D LYS* 2.9 28.3 + - + +
163D ASP* 3.6 14.1 - - - +
165D TYR* 1.3 75.1 - - - +
167D GLN* 1.3 62.3 + - - +
169D TYR* 3.1 6.0 + - + +
170D LYS* 3.0 37.5 + - + +
5E T 4.9 4.3 - - - +
6E T 3.2 23.6 - - - +
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Residues in contact with GLN 167 (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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163D ASP* 2.5 26.7 + - + +
164D LYS* 3.2 33.1 + - - +
166D ILE* 1.3 72.8 - - - +
168D GLU* 1.3 66.8 + - + +
170D LYS* 3.0 21.3 + - - +
171D LYS* 3.2 24.6 + - - +
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PRO* 6.0 0.3 - - - +
125D LYS* 3.5 34.4 - - - +
164D LYS 2.9 21.7 + - - +
165D TYR* 3.2 11.9 + - + +
167D GLN* 1.3 76.9 - - + +
169D TYR* 1.3 65.0 + - - +
171D LYS* 3.4 23.7 + - - +
172D ALA* 3.1 23.7 + - - +
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Residues in contact with TYR 169 (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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118D LYS* 5.5 1.4 - - - +
119D PRO* 3.7 21.9 + - + +
120D ALA 3.2 27.6 - - - +
121D GLY* 4.1 7.0 - - - -
122D PRO* 3.7 17.5 - - + -
165D TYR 2.8 12.9 + - - +
166D ILE 3.1 8.3 + - - +
168D GLU* 1.3 78.7 + - - +
170D LYS* 1.3 73.7 + - + +
172D ALA* 2.8 24.4 + - + +
173D ILE* 2.9 39.7 + - + +
6E T 3.3 31.4 + - - -
7E A 2.7 32.2 + - - -
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ILE* 3.0 32.3 + - + +
167D GLN* 3.0 15.7 + - - +
169D TYR* 1.3 91.5 - - + +
171D LYS* 1.3 57.5 + - + +
173D ILE* 3.6 9.4 - - + +
174D GLN* 2.8 43.7 + - - +
6E T 4.9 3.0 + - - -
7E A 6.2 0.2 - - - -
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLN* 3.2 16.8 + - - +
168D GLU* 3.6 28.9 - - - +
169D TYR 3.3 0.2 - - - -
170D LYS* 1.3 77.5 - - + +
172D ALA* 1.3 58.2 + - - +
174D GLN* 3.5 11.8 - - - +
175D GLU* 2.9 31.5 + - - +
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Residues in contact with ALA 172 (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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119D PRO* 3.8 25.3 - - + +
120D ALA 5.4 0.7 - - - +
168D GLU* 3.1 19.0 + - - +
169D TYR* 2.8 17.8 + - + +
171D LYS* 1.3 77.7 - - - +
173D ILE* 1.3 55.3 - - - +
175D GLU* 3.5 5.0 + - - +
176D TYR* 2.9 26.2 + - - +
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Residues in contact with ILE 173 (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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118D LYS* 4.6 13.0 - - + -
119D PRO* 4.0 6.2 - - + +
169D TYR* 2.9 51.4 + - + +
170D LYS* 3.6 15.9 - - + +
172D ALA* 1.3 74.1 - - - +
174D GLN* 1.3 59.0 + - - +
176D TYR* 3.7 14.8 - - + -
177D ASN* 2.5 62.8 + - - +
7E A 3.3 25.6 - - - +
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Residues in contact with GLN 174 (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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170D LYS* 2.8 30.9 + - - +
171D LYS* 3.5 12.8 - - - +
172D ALA 3.2 0.2 - - - -
173D ILE* 1.3 78.9 - - - +
175D GLU* 1.3 58.3 + - - +
177D ASN* 3.7 5.5 - - - +
178D ALA* 2.8 32.2 + - + +
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Residues in contact with GLU 175 (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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171D LYS 2.9 20.1 + - - +
172D ALA* 3.8 4.3 - - - +
174D GLN* 1.3 72.5 - - - +
176D TYR* 1.3 54.9 + - - +
178D ALA* 4.1 5.1 - - + +
179D ARG* 2.7 59.7 + - + +
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Residues in contact with TYR 176 (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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31D ARG* 3.7 20.0 + - - -
116D PRO* 3.1 23.6 + - + +
117D LYS 3.5 20.0 + - - -
118D LYS* 3.7 29.4 - - + +
119D PRO* 3.7 21.1 - - + -
172D ALA 2.9 19.2 + - - +
173D ILE* 3.1 13.2 + - + +
175D GLU* 1.3 78.1 + - - +
177D ASN* 1.3 70.5 + - - +
179D ARG* 4.5 1.1 - - - +
180D TYR* 2.9 70.2 + + + +
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Residues in contact with ASN 177 (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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118D LYS* 5.7 1.4 - - - -
173D ILE* 2.5 44.9 + - - +
174D GLN* 3.9 5.4 - - - +
176D TYR* 1.3 86.9 - - - +
178D ALA* 1.3 59.5 + - - +
180D TYR 3.0 6.9 - - - +
181D PRO* 3.0 33.6 - - + +
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Residues in contact with ALA 178 (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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174D GLN* 2.8 18.1 + - + +
175D GLU* 4.1 4.9 - - + +
177D ASN* 1.3 78.9 - - - +
179D ARG* 1.3 63.8 + - - +
181D PRO* 3.6 13.5 - - - +
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Residues in contact with ARG 179 (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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175D GLU* 2.7 43.6 + - + +
176D TYR* 4.5 0.7 - - - +
178D ALA* 1.3 73.2 - - - +
180D TYR* 1.3 100.6 + - + +
181D PRO* 3.3 8.3 - - - +
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Residues in contact with TYR 180 (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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116D PRO* 3.4 38.5 - - + +
176D TYR* 2.9 52.1 + + + +
177D ASN* 3.0 14.1 - - - +
179D ARG* 1.3 122.0 + - + +
181D PRO* 1.3 67.6 - - - +
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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