Contacts of the helix formed by residues 160 - 174 (chain B) in PDB entry 1R9J
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 GLU 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.6 11.7 - - - +
407A VAL* 3.1 30.6 - - + +
409A GLU* 2.6 27.6 + - - +
410A HIS 5.6 0.2 + - - -
438A TYR* 3.6 19.2 - - - -
116B LEU* 3.7 18.2 - - + +
117B GLY* 4.4 0.4 - - - -
156B GLY 3.7 11.4 - - - +
157B CYS 3.1 10.2 + - - +
159B MET* 1.3 79.2 - - - +
161B GLY* 1.3 65.2 + - - +
162B VAL* 4.1 16.9 + - + -
163B CYS* 3.1 12.1 + - - +
164B GLN* 3.1 13.1 + - - +
2671B TPP 3.2 10.9 - - - +
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY* 3.6 23.3 - - - -
165A GLU* 2.8 31.7 + - - +
160B GLU* 1.3 72.6 + - - +
162B VAL* 1.3 56.8 + - - +
164B GLN* 3.1 7.4 + - - +
165B GLU* 2.8 35.5 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 4.7 0.2 + - - -
438A TYR* 4.5 2.9 - - + -
116B LEU 3.9 7.6 - - - +
117B GLY* 3.6 28.9 - - - +
118B GLN* 4.1 5.6 - - - +
121B ALA* 4.4 5.3 - - + +
160B GLU* 4.1 6.7 + - + +
161B GLY* 1.3 75.7 - - - +
163B CYS* 1.3 63.7 + - - +
165B GLU* 3.6 10.1 + - - +
166B ALA* 3.2 22.3 + - - +
410B HIS* 3.5 60.6 + - + +
411B ALA* 3.8 4.1 - - - +
414B ALA* 4.3 12.6 - - + -
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Residues in contact with CYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY* 4.1 17.7 - - - +
120B ILE* 3.9 24.2 - - - -
157B CYS 3.0 35.7 - - - +
158B LEU* 3.8 11.7 - - - -
160B GLU 3.1 3.3 + - - +
161B GLY 3.1 0.4 - - - -
162B VAL* 1.3 79.7 - - - +
164B GLN* 1.3 60.7 + - - +
166B ALA* 3.1 3.0 + - - +
167B LEU* 2.9 55.1 + - - +
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 4.3 33.5 - - + +
165A GLU* 6.2 0.2 - - + -
204A LYS* 5.2 2.0 + - - +
158B LEU* 2.8 32.9 + - - +
159B MET 5.1 2.0 - - - +
160B GLU 3.1 7.5 + - - +
161B GLY* 3.1 8.8 + - - +
163B CYS* 1.3 77.7 - - - +
165B GLU* 1.3 62.6 + - - +
167B LEU* 3.5 7.3 + - - +
168B SER* 3.0 24.8 + - - -
204B LYS* 2.9 31.8 + - - +
205B TYR* 3.0 24.5 + - - -
208B MET* 3.7 15.2 - - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MET 3.5 19.7 - - - +
160A GLU* 3.5 9.2 - - - +
161A GLY* 2.8 26.8 + - - +
164A GLN* 5.9 1.1 - - + +
161B GLY 2.8 19.9 + - - +
162B VAL* 3.7 1.1 - - - +
164B GLN* 1.3 76.9 - - - +
166B ALA* 1.3 62.0 + - - +
168B SER* 3.2 7.8 + - - -
169B LEU* 3.0 18.0 + - - +
408B ARG* 3.4 36.6 - - + +
410B HIS* 3.6 13.4 + - - +
411B ALA* 2.9 38.5 + - + +
438B TYR* 5.8 0.5 - - - -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ILE* 4.5 2.7 - - + -
121B ALA* 3.6 33.9 - - + +
124B VAL* 3.8 15.7 - - + +
162B VAL 3.2 14.4 + - - +
163B CYS 3.1 4.6 + - - +
165B GLU* 1.3 76.6 - - - +
167B LEU* 1.3 60.2 + - - +
169B LEU* 3.2 6.4 + - - +
170B ALA* 2.8 29.6 + - - +
411B ALA* 3.6 8.9 - - + +
415B ILE* 4.7 3.6 - - + -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 3.7 22.9 - - + -
124B VAL* 5.4 2.2 - - + -
158B LEU* 3.8 11.2 - - + -
163B CYS* 2.9 41.9 + - - +
164B GLN* 4.0 7.6 - - - +
166B ALA* 1.3 71.5 - - - +
168B SER* 1.3 56.6 + - - +
170B ALA* 3.3 2.9 + - + -
171B GLY* 2.9 25.8 + - - -
178B LEU* 5.4 0.7 - - + -
180B VAL* 4.3 13.0 - - + -
205B TYR* 3.8 29.4 - - + -
208B MET* 4.7 4.8 - - - +
210B PHE* 3.0 42.7 - - + -
241B MET* 4.1 5.2 - - + -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MET* 6.0 0.3 - - - -
197A PHE* 4.4 1.4 - - - -
199A GLU* 2.8 32.9 + - - +
204A LYS* 5.5 0.9 - - - -
164B GLN 3.0 14.6 + - - -
165B GLU* 3.3 11.0 - - - -
167B LEU* 1.3 78.6 - - - +
169B LEU* 1.3 61.4 + - - +
171B GLY* 3.4 1.0 + - - -
172B HIS* 3.0 22.5 + - - +
208B MET* 4.6 10.9 - - - +
408B ARG* 2.9 24.8 + - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER 4.3 6.5 - - - +
124B VAL* 5.4 1.6 - - + -
128B ILE* 5.4 0.9 - - + -
165B GLU 3.0 12.7 + - - +
166B ALA* 3.7 7.9 - - - +
168B SER* 1.3 73.6 + - - +
170B ALA* 1.3 60.1 + - - +
172B HIS* 3.2 10.8 + - + +
173B LEU* 2.8 58.9 + - + +
403B ILE* 4.9 3.1 - - + -
404B ARG 3.8 15.7 - - - +
405B PHE* 3.8 39.0 - - + +
408B ARG* 3.7 25.7 - - + +
411B ALA* 5.9 0.7 - - + -
415B ILE* 3.9 18.2 - - + -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.9 10.7 - - + +
166B ALA 2.8 18.1 + - - +
167B LEU* 3.5 5.4 - - - +
169B LEU* 1.3 75.0 - - - +
171B GLY* 1.3 63.1 + - - +
173B LEU 3.3 0.9 + - - -
174B ALA 2.9 17.7 + - - -
175B LEU* 3.3 18.2 + - + -
178B LEU* 3.9 28.7 - - + -
210B PHE* 4.1 8.7 - - + -
239B PRO* 3.3 11.6 - - + +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LEU 2.9 13.4 + - - -
168B SER 3.8 0.2 - - - -
170B ALA* 1.3 77.0 - - - +
172B HIS* 1.3 62.4 + - - +
174B ALA* 3.0 14.9 + - - +
208B MET 3.3 25.6 - - - -
209B GLY* 4.3 8.5 - - - +
210B PHE* 3.9 3.5 - - - -
239B PRO* 3.9 14.4 - - - -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A SER 3.0 26.0 + - - -
195A LEU 3.2 19.4 + - - -
196A SER* 3.4 31.6 - - - +
197A PHE 4.0 1.4 + - - -
198A THR* 3.0 39.7 + - + +
168B SER 3.0 14.4 + - - +
169B LEU* 3.5 13.0 - - + +
171B GLY* 1.3 75.9 - - - +
173B LEU* 1.3 75.4 + - + +
174B ALA* 3.5 2.4 + - - +
208B MET 4.4 0.8 + - - -
394B SER* 6.1 3.0 - - - -
395B SER* 4.7 5.5 + - - -
408B ARG* 5.5 0.2 - - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU 6.0 0.2 - - - +
128B ILE* 3.8 30.5 - - + -
169B LEU* 2.8 44.7 + - + +
171B GLY 3.2 0.4 - - - -
172B HIS* 1.3 85.5 - - + +
174B ALA* 1.3 71.3 + - - +
175B LEU* 3.4 21.5 + - + +
393B PHE* 3.9 40.0 - - + +
394B SER* 4.1 9.5 - - - -
395B SER* 3.2 19.9 + - - +
403B ILE* 5.2 6.5 - - + -
404B ARG 6.1 0.2 - - - +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ALA 2.9 5.9 + - - -
171B GLY 3.0 13.0 + - - +
172B HIS 3.2 1.5 - - - +
173B LEU* 1.3 81.4 - - - +
175B LEU* 1.3 60.4 + - - +
176B GLU* 2.8 16.8 + - - +
237B GLY* 3.2 27.9 - - - +
239B PRO* 4.3 7.0 - - - -
395B SER* 3.7 17.9 - - - +
398B LYS* 6.1 0.3 - - - -
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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