Contacts of the helix formed by residues 160 - 172 (chain B) in PDB entry 5NJ8
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 THR 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS* 4.1 7.6 - - - +
115A GLY* 5.5 0.2 - - - -
157B SER* 5.0 4.5 - - - +
159B LEU* 1.3 75.6 - - - +
161B ASP* 1.3 69.0 + - - +
162B GLN* 3.3 18.6 + - - +
163B GLU* 3.0 32.3 + - - +
164B LEU* 2.9 23.6 + - - +
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Residues in contact with ASP 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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111A ASN 3.2 19.1 - - - +
112A LEU* 1.9 51.0 - - - +
114A GLU* 4.2 5.4 - - + +
115A GLY* 2.7 28.8 + - - +
116A GLU* 3.7 2.3 - - - +
118A LEU* 5.3 0.2 - - - +
160B THR* 1.3 76.2 - - - +
162B GLN* 1.3 61.2 + - + +
164B LEU 4.6 0.2 - - - +
165B LYS* 2.9 35.6 + - - +
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Residues in contact with GLN 162 (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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87A LEU* 3.8 17.6 - - + +
160B THR* 3.2 11.6 + - - +
161B ASP* 1.3 77.4 - - + +
163B GLU* 1.3 59.9 + - + +
165B LYS* 3.8 19.8 - - - +
166B HIS* 2.9 30.5 + - - +
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Residues in contact with GLU 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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80A LYS* 2.6 42.9 + - - +
83A PHE* 2.9 71.2 - - + +
84A ASP* 4.8 2.4 - - - +
87A LEU* 4.1 5.2 - - + -
159B LEU* 3.3 11.5 - - + +
160B THR* 3.0 34.1 + - - +
162B GLN* 1.3 77.5 - - + +
164B LEU* 1.3 59.2 + - - +
167B LEU* 2.9 26.0 + - - +
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Residues in contact with LEU 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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115A GLY* 3.7 33.0 - - - +
118A LEU* 3.8 14.1 - - + -
119A LEU* 3.8 29.6 - - + -
126A VAL* 5.3 5.4 - - + -
137A TYR* 3.7 28.3 - - + +
157B SER* 6.0 0.9 - - - +
159B LEU* 4.2 27.1 - - + +
160B THR 2.9 14.0 + - - +
161B ASP 4.1 2.5 - - - +
163B GLU* 1.3 73.3 - - - +
165B LYS* 1.3 67.9 - - - +
167B LEU* 2.8 18.1 + - + -
168B ILE* 2.9 19.4 + - + +
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Residues in contact with LYS 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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87A LEU* 5.7 4.6 - - - +
114A GLU* 3.1 29.2 - - - +
118A LEU* 3.5 14.8 - - + +
161B ASP* 2.9 24.3 + - - +
162B GLN* 3.8 24.3 + - - +
164B LEU* 1.3 70.7 - - - +
166B HIS* 1.3 68.2 + - - +
168B ILE* 4.0 1.6 - - - +
169B LEU* 3.0 27.0 + - + +
174B GLY 5.0 0.9 - - - +
190B SER* 4.3 2.5 - - - +
191B ASP* 3.0 40.0 + - - +
192B SER* 3.3 22.1 + - - +
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Residues in contact with HIS 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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82A PHE* 5.5 4.8 - + - -
83A PHE* 4.1 17.5 - + - -
86A ALA* 4.3 21.8 - - + +
87A LEU* 3.4 30.4 - - + +
244A LYS* 4.3 4.8 + - - -
162B GLN 2.9 22.0 + - - +
163B GLU 3.7 3.1 - - - +
165B LYS* 1.3 80.1 - - - +
167B LEU* 1.3 69.4 + - + +
169B LEU* 2.9 18.3 + - + +
170B GLU* 2.9 60.0 + - + +
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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
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82A PHE* 6.1 0.4 - - + -
83A PHE* 4.2 9.9 - - + -
126A VAL* 3.5 31.2 - - + -
128A VAL* 4.1 7.0 - - + -
137A TYR* 3.8 25.6 - - + -
266A PHE* 3.3 41.5 - - + -
159B LEU* 4.2 11.2 - - + -
163B GLU 2.9 17.1 + - - +
164B LEU* 2.8 14.1 + - + +
166B HIS* 1.3 77.5 - - + +
168B ILE* 1.3 63.8 + - + +
170B GLU* 2.8 17.6 + - + +
171B ALA* 2.9 14.3 + - + +
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Residues in contact with ILE 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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118A LEU* 3.8 29.6 - - + +
119A LEU* 6.1 1.1 - - + -
122A LEU* 4.4 7.4 - - + -
126A VAL* 3.3 36.6 - - + -
268A ILE* 3.9 25.1 - - + -
164B LEU* 2.9 26.4 + - + +
165B LYS 4.0 2.0 - - - +
167B LEU* 1.3 73.0 - - + +
169B LEU* 1.3 64.4 + - - +
171B ALA* 4.6 1.8 - - - +
172B ALA* 3.1 22.9 + - + +
173B ASP 3.4 4.3 + - - -
174B GLY* 4.1 22.4 - - - +
340B ILE* 5.0 12.3 - - + -
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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
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165B LYS* 3.0 20.7 + - + +
166B HIS* 2.9 16.9 + - - +
168B ILE* 1.3 76.8 - - - +
170B GLU* 1.3 62.7 + - + +
173B ASP* 3.3 20.3 + - - +
174B GLY 3.9 9.8 + - - +
191B ASP* 5.9 1.6 - - - +
192B SER* 3.5 30.1 - - - +
195B PRO* 3.9 30.7 - - + -
196B VAL* 3.9 27.8 - - + -
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Residues in contact with GLU 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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242A LYS* 3.8 32.3 + - + +
244A LYS* 2.5 41.5 + - + +
266A PHE* 5.6 2.5 - - + -
166B HIS* 2.9 48.9 + - + +
167B LEU* 2.8 15.5 + - + +
169B LEU* 1.3 85.0 - - + +
171B ALA* 1.3 63.2 + - - +
172B ALA 3.3 1.0 + - - -
173B ASP* 4.1 6.2 - - - +
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Residues in contact with ALA 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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126A VAL* 5.7 1.3 - - + -
240A GLN* 3.8 8.2 + - - +
241A GLY* 3.4 20.1 - - - -
242A LYS* 3.8 7.7 + - - +
266A PHE* 3.4 37.5 - - + +
267A ALA* 3.8 16.4 - - - +
268A ILE* 4.3 6.3 - - + +
167B LEU* 2.9 16.6 + - + +
168B ILE* 4.5 1.1 - - - +
170B GLU* 1.3 79.7 - - - +
172B ALA* 1.3 59.8 + - + +
173B ASP* 5.2 0.7 - - - -
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Residues in contact with ALA 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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240A GLN* 3.7 23.7 + - - +
268A ILE* 3.7 30.7 - - + -
168B ILE* 3.1 8.4 + - + +
171B ALA* 1.3 80.4 - - - +
173B ASP* 1.3 75.9 + - - +
174B GLY 4.4 2.2 - - - +
342B ARG* 3.4 24.5 - - + +
343B LEU* 4.2 5.9 + - - +
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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