Contacts of the helix formed by residues 160 - 175 (chain B) in PDB entry 5J2N
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 PHE 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ALA* 3.5 38.4 - - + -
115B TYR* 4.0 19.5 - + + -
117B SER* 3.7 13.0 - - - -
118B VAL* 3.6 23.1 - - + -
149B LEU* 4.4 3.7 - - + +
156B SER 3.2 20.5 + - - +
157B PRO* 3.6 2.9 - - + +
159B ILE* 1.3 73.7 - - - +
161B GLN* 1.3 58.4 + - - +
162B SER 3.2 2.7 - - - -
163B SER* 3.3 23.3 + - - +
164B MET* 2.8 65.8 + - + +
167B ILE* 4.6 13.7 - - + -
182B GLN* 5.1 0.7 - - - -
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Residues in contact with GLN 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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94B ILE* 3.7 38.6 - - + +
157B PRO 2.9 13.6 + - - +
158B ALA* 3.2 19.3 + - - +
160B PHE* 1.3 78.2 - - - +
162B SER* 1.3 65.1 + - - +
164B MET* 3.3 5.6 + - - +
165B THR* 3.2 46.8 + - + +
182B GLN* 3.8 16.5 - - - +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA 4.6 1.4 + - - -
159B ILE 4.2 8.2 + - - -
160B PHE 3.2 0.6 - - - -
161B GLN* 1.3 79.0 - - - +
163B SER* 1.3 60.5 + - - +
165B THR* 3.0 22.3 + - - -
166B LYS* 3.2 25.1 - - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.3 3.8 - - - +
159B ILE 5.0 1.6 + - - -
160B PHE* 3.3 35.8 + - - -
162B SER* 1.3 76.9 - - - +
164B MET* 1.3 63.9 + - - +
166B LYS* 3.5 23.0 + - - +
167B ILE* 3.3 26.4 + - - +
212B TRP* 5.7 0.3 - - - -
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Residues in contact with MET 164 (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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111B VAL* 4.6 16.4 - - + -
114B ALA* 5.2 4.3 - - + -
115B TYR* 5.1 1.6 - - + -
160B PHE* 2.8 46.3 + - + +
161B GLN* 3.7 9.0 - - - +
162B SER 3.3 0.4 - - - -
163B SER* 1.3 75.2 - - - +
165B THR* 1.3 67.7 + - + +
167B ILE* 3.2 16.3 + - + +
168B LEU* 3.2 44.7 + - + +
172B ARG* 5.7 1.6 - - - +
182B GLN* 3.3 42.6 - - + +
187B LEU* 4.3 7.4 - - + -
209B LEU* 5.6 3.4 - - - -
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Residues in contact with THR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLN* 3.2 36.0 + - + +
162B SER* 3.0 16.7 + - - -
164B MET* 1.3 78.3 - - + +
166B LYS* 1.3 63.7 + - - +
168B LEU 4.7 0.2 - - - +
169B GLU* 3.1 28.1 + - - +
172B ARG* 4.4 22.6 + - - +
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Residues in contact with LYS 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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162B SER* 3.2 30.4 - - - +
163B SER* 3.7 22.4 + - - +
164B MET 3.2 0.6 - - - -
165B THR* 1.3 81.2 + - - +
167B ILE* 1.3 60.9 + - - +
169B GLU* 4.2 3.4 - - - +
170B PRO* 3.8 13.5 - - - +
212B TRP* 4.3 20.6 - - + -
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Residues in contact with ILE 167 (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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114B ALA* 6.0 2.2 - - + -
160B PHE* 4.6 20.9 - - + -
163B SER* 3.3 17.0 - - - +
164B MET* 3.2 11.5 + - + +
166B LYS* 1.3 77.7 - - - +
168B LEU* 1.3 63.3 + - + +
169B GLU 3.5 0.7 + - - -
170B PRO* 3.5 11.3 - - - +
208B HIS* 3.7 20.4 + - + +
209B LEU* 3.8 28.9 - - + -
212B TRP* 3.6 62.5 - - + -
213B GLY 6.0 1.1 - - - +
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Residues in contact with LEU 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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164B MET* 3.2 39.8 + - + +
165B THR 4.0 0.7 - - - +
167B ILE* 1.3 77.9 - - + +
169B GLU* 1.3 57.9 + - - +
170B PRO* 3.5 0.9 - - - -
171B PHE* 3.3 6.9 + - - +
172B ARG* 2.8 60.2 + - + +
180B ILE* 3.8 28.5 - - + -
182B GLN* 6.1 0.2 - - + -
187B LEU* 4.1 13.0 - - + -
205B LEU* 4.0 17.9 - - + -
209B LEU* 3.7 29.4 - - + -
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Residues in contact with GLU 169 (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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165B THR 3.1 19.9 + - - +
166B LYS* 4.2 4.9 - - - +
168B LEU* 1.3 75.9 - - - +
170B PRO* 1.3 87.6 - - + +
172B ARG* 3.2 10.2 + - - +
173B LYS* 3.0 34.3 + - - +
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Residues in contact with PRO 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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166B LYS 3.8 8.3 - - - +
167B ILE 3.5 14.6 - - - +
169B GLU* 1.3 105.9 - - + +
171B PHE* 1.3 56.9 + - - +
173B LYS* 3.9 10.9 + - + +
174B GLN* 3.0 29.5 + - - +
208B HIS* 4.3 15.7 - - + +
212B TRP* 6.5 0.7 - - + -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.3 8.6 + - - +
169B GLU 3.3 0.8 - - - -
170B PRO* 1.3 76.9 - - - +
172B ARG* 1.3 64.6 + - - +
174B GLN* 4.6 2.2 - - + -
175B ASN* 3.1 42.3 + - + +
178B ILE* 4.5 14.4 - - + -
180B ILE* 3.7 29.6 - - + -
189B VAL* 5.2 2.0 - - + -
201B LYS* 3.7 35.0 - - + -
204B GLU* 4.1 26.0 - - + -
205B LEU* 3.9 30.3 - - + -
208B HIS* 4.2 22.9 + + + -
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Residues in contact with ARG 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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164B MET* 5.7 1.8 - - - +
165B THR* 4.4 28.5 + - - +
168B LEU* 2.8 50.4 + - + +
169B GLU* 3.2 7.4 + - - +
171B PHE* 1.3 78.2 - - - +
173B LYS* 1.3 60.3 + - - +
175B ASN 3.0 24.1 - - - +
176B PRO* 3.5 7.3 - - - +
178B ILE 5.3 6.0 - - - +
180B ILE* 3.2 44.8 + - + +
182B GLN* 5.8 3.4 - - - +
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Residues in contact with LYS 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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169B GLU* 3.0 28.7 + - - +
170B PRO* 3.9 9.8 + - + +
172B ARG* 1.3 77.6 - - - +
174B GLN* 1.3 95.6 + - - +
175B ASN 3.3 0.7 + - - -
176B PRO* 3.5 12.7 - - - +
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Residues in contact with GLN 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 PRO 3.0 18.6 + - - +
171B PHE* 4.2 2.5 - - + +
173B LYS* 1.3 97.8 + - - +
175B ASN* 1.3 75.3 + - - +
176B PRO* 3.5 6.3 - - - +
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Residues in contact with ASN 175 (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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171B PHE* 3.1 41.3 + - + +
172B ARG* 3.0 12.9 - - - +
173B LYS 3.1 0.2 - - - -
174B GLN* 1.3 93.0 - - - +
176B PRO* 1.3 65.6 - - - +
177B ASP 3.3 2.5 - - - +
178B ILE* 3.4 37.3 + - + +
201B LYS* 3.5 33.0 + - - +
204B GLU* 5.6 1.0 + - - -
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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