Contacts of the helix formed by residues 170 - 185 (chain D) in PDB entry 1NJI
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 SER 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D GLY* 1.3 76.4 - - - -
171D VAL* 1.3 61.9 + - - +
172D SER* 3.4 7.3 + - - -
173D ASP* 2.7 50.2 + - - +
174D ARG* 3.0 29.2 + - - +
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Residues in contact with VAL 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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132D HIS* 3.1 34.8 - - + +
137D LEU* 5.1 15.5 - - + +
140D LEU* 4.0 5.0 - - + +
170D SER* 1.3 74.0 - - - +
172D SER* 1.3 62.8 + - - +
174D ARG* 3.6 32.3 - - - +
175D LEU* 2.8 37.6 + - - +
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Residues in contact with SER 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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129D ARG* 5.0 1.2 + - - +
132D HIS* 2.8 31.7 + - - -
170D SER* 3.2 7.0 + - - -
171D VAL* 1.3 81.3 - - - +
173D ASP* 1.3 58.8 + - - +
175D LEU* 3.5 6.5 - - - +
176D ASP* 2.6 37.7 + - - +
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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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36D PRO* 4.2 10.4 - - + +
169D GLY* 5.3 0.4 - - - -
170D SER* 2.7 39.5 + - - +
172D SER* 1.3 77.0 - - - +
174D ARG* 1.3 57.9 + - - +
176D ASP* 3.4 10.3 + - - +
177D HIS* 2.9 24.4 + - - +
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Residues in contact with ARG 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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32D ASP* 3.8 26.7 + - - +
36D PRO* 3.5 29.8 - - + +
139D ASP* 5.1 7.1 - - - +
140D LEU* 4.2 17.0 - - + +
165D ARG* 3.9 8.7 - - - +
166D VAL* 3.1 33.6 + - + +
167D GLY 3.8 0.2 - - - -
168D GLY* 2.7 40.5 + - - +
169D GLY 3.4 9.1 + - - -
170D SER 3.0 21.2 + - - +
171D VAL* 3.6 29.5 - - - +
173D ASP* 1.3 73.2 - - - +
175D LEU* 1.3 63.7 + - - +
177D HIS* 3.5 1.9 - - - +
178D ALA* 2.8 28.6 + - - +
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Residues in contact with LEU 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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84D LEU* 5.8 4.3 - - + -
125D GLU* 5.4 0.7 - - + -
128D ILE* 3.9 28.7 - - + -
129D ARG* 3.8 29.6 - - + +
132D HIS* 4.8 14.1 - - + -
137D LEU* 4.3 14.6 - - + -
140D LEU* 3.5 19.3 - - + -
171D VAL 2.8 20.0 + - - +
172D SER* 3.5 5.8 - - - +
174D ARG* 1.3 76.3 - - - +
176D ASP* 1.3 65.8 + - - +
178D ALA* 3.0 7.4 + - - +
179D LEU* 3.0 46.7 + - + +
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Residues in contact with ASP 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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129D ARG* 2.5 31.6 + - - -
172D SER* 2.6 22.3 + - - +
173D ASP* 3.5 10.1 - - - +
175D LEU* 1.3 81.7 - - - +
177D HIS* 1.3 63.7 + - - +
178D ALA 3.1 0.3 + - - -
179D LEU* 3.1 7.8 + - - +
180D ASP* 2.9 34.2 + - - +
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Residues in contact with HIS 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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36D PRO* 3.3 46.6 + - + -
37D GLY* 3.6 11.2 - - - -
166D VAL* 4.4 8.1 - - + -
173D ASP 2.9 15.7 + - - +
174D ARG 3.3 6.9 + - - +
176D ASP* 1.3 75.1 - - - +
178D ALA* 1.3 61.6 + - - +
180D ASP* 3.6 10.7 + - - +
181D ILE* 3.1 58.3 + - + +
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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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84D LEU* 3.6 31.2 - - + -
140D LEU* 5.3 1.8 - - + -
142D LEU* 4.1 10.3 - - + +
166D VAL* 5.0 10.1 - - + -
174D ARG 2.8 13.2 + - - +
175D LEU* 3.1 13.0 - - - +
177D HIS* 1.3 75.5 - - - +
179D LEU* 1.3 67.9 + - - +
181D ILE* 3.1 19.2 + - - +
182D VAL* 3.1 17.9 + - - +
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Residues in contact with LEU 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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84D LEU* 4.5 12.6 - - + -
100D VAL* 3.9 39.0 - - + -
125D GLU* 3.5 22.7 - - + +
128D ILE* 6.0 0.4 - - + -
129D ARG* 3.3 30.7 - - - +
175D LEU* 3.0 26.6 + - + +
176D ASP* 3.6 8.3 - - - +
178D ALA* 1.3 79.7 - - + +
180D ASP* 1.3 65.2 + - - +
182D VAL* 3.2 4.8 + - + +
183D GLU* 2.8 38.3 + - + +
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Residues in contact with ASP 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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176D ASP* 2.9 31.7 + - - +
177D HIS* 3.7 11.9 + - - +
178D ALA 3.2 0.2 - - - -
179D LEU* 1.3 78.3 - - - +
181D ILE* 1.3 58.4 + - + +
183D GLU* 3.5 6.9 + - - +
184D ASP* 2.6 34.1 + - - +
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Residues in contact with ILE 181 (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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38D VAL* 4.0 22.7 - - + -
81D ALA* 4.2 12.1 - - + -
142D LEU* 4.4 7.9 - - + -
166D VAL* 6.0 0.7 - - + -
177D HIS* 3.1 47.6 - - + +
178D ALA* 3.1 6.2 + - - +
180D ASP* 1.3 78.2 - - + +
182D VAL* 1.3 67.4 + - - +
184D ASP* 3.3 14.4 + - - +
186D GLY* 3.1 37.0 + - - +
187D GLU 5.4 1.3 - - - +
188D HIS* 5.1 11.4 - - + +
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Residues in contact with VAL 182 (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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81D ALA* 3.9 14.8 - - + +
82D VAL 4.2 0.9 - - - +
83D ALA* 3.7 23.8 - - - +
84D LEU* 3.9 5.6 - - + +
100D VAL* 3.8 22.2 - - + +
101D TRP 4.4 1.1 - - - -
102D THR* 2.9 34.4 - - + +
142D LEU* 3.7 24.0 - - + -
178D ALA 3.1 12.6 + - - +
179D LEU* 3.6 8.1 - - - +
181D ILE* 1.3 77.6 - - - +
183D GLU* 1.3 72.9 + - - +
184D ASP 3.0 1.2 + - - -
185D GLY 3.2 8.5 + - - -
186D GLY 3.4 2.6 + - - -
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Residues in contact with GLU 183 (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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100D VAL* 4.3 13.1 - - - +
101D TRP 4.3 10.2 - - - +
102D THR* 3.9 11.6 - - - +
104D GLU* 4.8 1.7 - - - +
121D PRO* 5.2 7.2 - - - +
125D GLU* 4.7 9.9 - - - +
179D LEU* 2.8 39.5 + - + +
180D ASP* 3.9 5.8 - - - +
182D VAL* 1.3 80.3 - - - +
184D ASP* 1.3 69.7 + - - +
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Residues in contact with ASP 184 (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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104D GLU* 3.2 23.7 - - - +
180D ASP* 2.6 23.7 - - - +
181D ILE* 3.3 11.6 - - - +
182D VAL 3.0 0.8 + - - -
183D GLU* 1.3 81.9 - - - +
185D GLY* 1.3 59.0 + - - +
186D GLY 4.2 1.1 - - - +
187D GLU 5.6 1.1 - - - +
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Residues in contact with GLY 185 (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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80D ARG* 4.0 18.5 - - - +
81D ALA 4.1 3.8 - - - +
82D VAL* 5.1 3.3 - - - +
102D THR* 5.1 5.6 + - - -
104D GLU* 4.7 23.4 - - - +
182D VAL 3.2 6.2 + - - -
183D GLU 4.3 0.7 - - - -
184D ASP* 1.3 77.8 - - - +
186D GLY* 1.3 61.4 + - - +
187D GLU* 3.0 13.0 + - - +
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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