Contacts of the helix formed by residues 160 - 173 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B ASP* 5.7 5.6 - - - -
87C LEU* 6.4 0.9 - - - -
157D SER* 5.2 2.2 - - - -
159D LEU* 1.3 75.5 - - - +
161D ASP* 1.3 56.3 + - - +
162D GLN* 3.4 4.5 - - - -
163D GLU* 2.9 18.6 + - - +
164D LEU* 2.4 37.4 + - - +
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Residues in contact with ASP 161 (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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326B ASP* 2.3 43.2 + - - +
111C ASN 4.6 10.3 - - - +
112C LEU* 2.6 24.8 - - - +
114C GLU* 4.7 8.6 - - + +
115C GLY* 3.8 23.6 - - - +
116C GLU* 3.9 7.3 - - - +
157D SER* 5.4 2.1 + - - -
159D LEU 4.8 2.6 - - - +
160D THR* 1.3 71.6 - - - +
162D GLN* 1.3 52.8 + - - +
164D LEU* 3.2 6.4 + - - +
165D LYS* 2.7 36.5 + - - +
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Residues in contact with GLN 162 (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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87C LEU* 5.0 19.4 - - + +
114C GLU* 5.6 1.1 + - - -
160D THR* 3.4 3.7 - - - -
161D ASP* 1.3 77.5 - - - +
163D GLU* 1.3 57.0 + - - +
165D LYS* 3.5 8.1 - - - +
166D HIS* 2.9 27.9 + - - +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.2 41.3 - - + -
87C LEU* 4.8 7.9 - - + +
159D LEU* 3.9 6.3 - - + -
160D THR* 2.9 31.5 + - - +
162D GLN* 1.3 75.4 - - - +
164D LEU* 1.3 61.9 + - - +
166D HIS* 2.8 19.8 + - - +
167D LEU* 2.9 12.0 + - - +
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Residues in contact with LEU 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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115C GLY* 4.7 17.0 - - - +
118C LEU* 5.0 5.6 - - + +
119C LEU* 5.6 8.7 - - + -
137C TYR* 5.8 1.8 - - - +
159D LEU* 4.5 17.8 - - + +
160D THR 2.4 30.9 + - - +
161D ASP* 3.9 6.3 - - - +
163D GLU* 1.3 67.0 - - - +
165D LYS* 1.3 49.3 + - - +
167D LEU* 4.5 2.9 - - - +
168D ILE* 2.6 38.4 + - - +
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Residues in contact with LYS 165 (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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114C GLU* 3.8 22.2 - - + +
118C LEU* 5.7 3.1 - - - +
161D ASP 2.7 22.3 + - - +
162D GLN* 3.5 9.4 - - - +
163D GLU 3.0 0.2 - - - -
164D LEU* 1.3 71.7 - - - +
166D HIS* 1.3 59.3 + - - +
168D ILE* 3.6 5.1 - - - +
169D LEU* 2.9 32.9 + - - +
176D LEU* 5.9 4.7 - - + -
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Residues in contact with HIS 166 (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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82C PHE* 6.1 0.2 - + - -
83C PHE* 4.6 10.5 - + + -
86C ALA* 3.4 48.5 + - + +
87C LEU* 4.2 13.9 - - + +
162D GLN 2.9 13.7 + - - +
163D GLU* 2.8 11.4 + - - +
165D LYS* 1.3 72.4 - - - +
167D LEU* 1.3 64.6 + - - +
169D LEU* 5.4 0.7 - - - -
170D GLU* 2.8 53.4 + - + +
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Residues in contact with LEU 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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83C PHE* 4.0 18.7 - - + -
126C VAL* 5.3 13.8 - - + +
128C VAL* 5.9 2.7 - - + -
137C TYR* 6.3 2.5 - - + -
266C PHE* 5.2 14.6 - - + -
159D LEU* 4.9 4.9 - - + -
163D GLU 2.9 12.1 + - - +
164D LEU* 4.5 4.7 - - - +
166D HIS* 1.3 78.3 - - - +
168D ILE* 1.3 64.3 + - - +
170D GLU* 4.6 3.1 - - - -
171D ALA* 2.9 30.8 + - + +
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Residues in contact with ILE 168 (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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118C LEU* 4.4 24.9 - - + -
126C VAL* 5.8 7.6 - - - -
164D LEU 2.6 25.8 + - - +
165D LYS* 3.6 8.1 - - - +
166D HIS 3.2 0.2 - - - -
167D LEU* 1.3 75.7 - - - +
169D LEU* 1.3 58.0 + - - +
171D ALA* 4.0 0.7 - - - +
172D ALA* 2.9 32.2 + - - +
176D LEU* 6.3 1.8 - - + -
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Residues in contact with LEU 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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165D LYS 2.9 19.6 + - - +
166D HIS* 5.4 0.2 - - - -
168D ILE* 1.3 69.9 - - - +
170D GLU* 1.3 56.9 + - - +
171D ALA 3.0 1.6 - - - -
172D ALA* 2.5 8.4 + - - -
173D ASP* 2.1 53.7 + - - +
175D PHE 4.9 6.1 - - - +
176D LEU* 5.8 2.0 - - + -
192D SER* 4.2 24.7 - - - +
195D PRO* 6.1 3.6 - - + -
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Residues in contact with GLU 170 (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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242C LYS* 5.1 12.2 - - - +
243C LEU 5.7 0.2 - - - +
244C LYS* 3.6 25.8 - - - +
266C PHE* 5.1 9.5 - - - +
166D HIS* 2.8 46.6 + - + +
167D LEU* 4.4 2.5 - - - +
169D LEU* 1.3 73.2 - - - +
171D ALA* 1.3 59.7 + - - +
173D ASP* 3.8 13.4 - - - +
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Residues in contact with ALA 171 (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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126C VAL* 5.7 7.6 - - + -
240C GLN 5.5 0.2 - - - +
241C GLY* 4.8 3.8 - - - -
242C LYS* 4.5 19.5 + - - +
266C PHE* 3.6 34.2 - - + +
267C ALA 5.5 0.7 - - - -
268C ILE* 5.1 12.7 - - + +
167D LEU* 2.9 23.6 + - + +
168D ILE 4.0 1.3 - - - +
169D LEU 2.8 3.2 + - - -
170D GLU* 1.3 78.6 - - - +
172D ALA* 1.3 57.9 + - + +
173D ASP* 3.9 3.6 + - - +
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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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268C ILE* 5.0 13.5 - - + -
168D ILE 2.9 14.9 + - - +
169D LEU 2.5 7.0 + - - -
171D ALA* 1.3 74.2 - - + +
173D ASP* 1.3 73.1 + - - +
342D ARG* 4.1 28.8 - - + +
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Residues in contact with ASP 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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169D LEU* 2.1 37.0 + - - -
170D GLU* 3.8 14.9 - - - +
171D ALA 4.8 3.5 - - - +
172D ALA* 1.3 77.2 - - - +
175D PHE* 3.8 25.5 + - - +
192D SER 6.0 0.4 - - - -
196D VAL* 4.0 27.5 - - + +
341D GLY 4.3 6.6 - - - +
342D ARG 4.6 4.3 - - - -
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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