Contacts of the helix formed by residues 19 - 35 (chain 1) 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 GLY 19 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171 ARG 3.2 7.3 + - - -
181 TYR* 1.3 79.7 - - - +
201 LEU* 1.3 65.4 + - - -
211 LYS 3.7 0.9 - - - -
221 ILE 3.8 0.6 + - - -
231 ARG* 3.0 30.6 + - - +
1771A U 3.4 18.4 + - - -
1885A A 3.6 13.5 + - - -
1886A A 3.8 6.7 - - - -
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Residues in contact with LEU 20 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 GLY* 1.3 72.4 - - - +
211 LYS* 1.3 66.3 + - + +
231 ARG* 3.7 3.4 - - - +
241 VAL* 2.8 39.3 + - + +
1771A U 3.5 33.0 + - - +
1772A C 3.4 30.5 - - - +
1886A A 3.0 25.8 + - - +
1887A U 4.0 22.0 - - - +
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Residues in contact with LYS 21 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 GLY 3.7 0.2 - - - -
201 LEU* 1.3 77.0 - - + +
221 ILE* 1.3 66.8 + - + +
241 VAL* 4.5 4.9 - - - -
251 ARG* 3.0 59.8 + - - +
1886A A 3.8 14.0 + - - +
1887A U 3.0 40.0 + - - +
1888A C 5.2 5.0 + - - -
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Residues in contact with ILE 22 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 TYR* 3.6 24.4 + - + +
191 GLY 3.8 0.8 + - - -
201 LEU 3.2 0.8 + - - -
211 LYS* 1.3 82.3 - - + +
231 ARG* 1.3 61.2 + - + +
251 ARG 3.6 0.2 + - - -
261 VAL* 3.1 27.4 + - + +
1829A A 6.2 0.2 - - - +
1847A A 3.2 31.0 - - + +
1848A G 4.2 11.9 - - - +
1885A A 3.4 26.0 - - - +
1886A A 5.4 4.6 - - - -
168C PRO* 3.8 21.2 - - + +
170C VAL* 3.3 41.3 - - + +
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Residues in contact with ARG 23 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 THR* 2.6 56.4 + - + +
141 PHE* 3.9 12.8 - - + -
151 GLY 3.4 16.6 + - - -
161 PRO 3.5 11.9 + - - -
171 ARG 2.9 28.1 + - - +
191 GLY* 3.0 24.9 + - - +
201 LEU* 3.2 4.9 + - - +
221 ILE* 1.3 78.2 - - + +
241 VAL* 1.3 68.8 + - + +
251 ARG 3.1 1.8 - - - -
261 VAL* 4.2 3.6 - - - -
271 ALA* 3.1 12.3 + - - +
1771A U 2.7 50.7 + - - +
1772A C 3.4 11.7 + - - -
1773A G 3.2 12.6 + - - -
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Residues in contact with VAL 24 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 THR* 5.7 0.4 - - - -
201 LEU* 2.8 35.9 + - + +
211 LYS* 3.9 4.9 - - - +
231 ARG* 1.3 79.2 - - + +
251 ARG* 1.3 63.2 + - + +
271 ALA* 3.5 4.8 + - - +
281 ASP* 2.9 43.1 + - - +
1772A C 5.6 2.9 - - - +
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Residues in contact with ARG 25 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 LYS* 3.0 50.0 + - - +
221 ILE* 3.8 4.0 - - - +
241 VAL* 1.3 81.9 - - + +
261 VAL* 1.3 59.5 + - - +
281 ASP* 4.2 7.6 - - + +
291 VAL* 2.9 39.9 + - + +
1849A G 4.9 9.9 + - - -
166C ASP 4.9 10.4 + - - +
168C PRO* 4.3 20.6 - - + +
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Residues in contact with VAL 26 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 THR* 3.7 14.6 - - - +
131 ARG* 3.9 11.4 - - - +
141 PHE* 4.0 15.3 - - + -
221 ILE 3.1 17.8 + - - +
231 ARG 3.3 0.6 + - - -
251 ARG* 1.3 77.3 - - - +
271 ALA* 1.3 59.0 + - - +
291 VAL* 5.0 0.2 - - - -
301 GLU* 2.9 62.6 + - - +
167C LYS* 4.0 18.6 - - - +
168C PRO* 4.2 7.2 - - + -
170C VAL* 3.7 26.2 - - + -
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Residues in contact with ALA 27 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 ARG* 4.1 39.3 - - + +
111 THR* 4.0 8.5 + - - +
231 ARG 3.1 16.7 + - - +
241 VAL* 3.7 5.8 - - - +
261 VAL* 1.3 76.7 - - - +
281 ASP* 1.3 59.2 + - - +
301 GLU* 4.6 2.5 - - - -
311 ILE* 2.7 39.8 + - - +
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Residues in contact with ASP 28 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241 VAL* 2.9 37.1 + - - +
251 ARG* 3.8 8.7 - - - +
271 ALA* 1.3 76.5 - - - +
291 VAL* 1.3 64.8 + - + +
311 ILE* 2.9 25.4 - - - +
321 LYS* 3.2 10.2 + - - +
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Residues in contact with VAL 29 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 ARG* 2.9 29.9 + - + +
261 VAL* 4.1 3.8 - - - +
281 ASP* 1.3 78.0 - - + +
301 GLU* 1.3 61.2 + - + +
321 LYS* 3.5 5.3 + - - +
331 HIS* 2.8 28.0 + - + +
691 TYR* 3.5 43.3 - - + +
166C ASP* 4.9 11.4 - - + +
167C LYS* 4.5 26.9 - - + +
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Residues in contact with GLU 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 ARG* 4.7 9.0 - - - -
131 ARG* 2.9 32.4 + - - -
261 VAL* 2.9 32.6 + - - +
271 ALA* 4.0 2.7 - - - +
291 VAL* 1.3 76.4 - - + +
311 ILE* 1.3 60.1 + - - +
331 HIS* 3.2 15.5 - - + -
341 LYS* 2.9 63.7 + - - +
1651A C 4.1 9.3 + - - -
167C LYS* 2.6 35.1 + - - +
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Residues in contact with ILE 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 ARG* 6.5 0.7 - - + -
271 ALA 2.7 20.6 + - - +
281 ASP* 2.9 23.3 - - - +
301 GLU* 1.3 69.0 - - - +
321 LYS* 1.3 82.5 + - + +
341 LYS* 3.0 8.3 + - - +
351 LYS* 3.0 36.4 + - + +
798A G 5.1 12.1 - - - +
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Residues in contact with LYS 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281 ASP 3.2 8.2 + - - +
291 VAL* 3.7 8.7 - - - +
311 ILE* 1.3 83.0 - - + +
331 HIS* 1.3 62.8 + - - +
351 LYS* 3.0 44.1 + - - +
371 HIS* 3.1 25.0 - - - -
691 TYR 4.5 2.2 - - - +
701 GLN* 2.7 50.1 + - + +
711 PRO* 6.0 0.4 - - - +
721 GLU 5.1 1.4 + - - -
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Residues in contact with HIS 33 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 VAL 2.8 20.4 + - - +
301 GLU* 3.1 29.8 - - + +
321 LYS* 1.3 77.0 - - - +
341 LYS* 1.3 61.6 + - + -
371 HIS* 3.2 16.9 + - - -
491 ARG* 3.0 64.6 + - + +
551 TRP* 3.7 9.5 - + - -
691 TYR* 3.1 42.8 + + + +
1651A C 4.2 11.7 + - - -
1652A C 5.2 0.2 + - - -
167C LYS* 5.5 1.1 + - - -
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Residues in contact with LYS 34 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 ARG* 4.3 10.3 + - - +
131 ARG* 6.1 0.2 - - - +
301 GLU* 2.9 51.6 + - - +
311 ILE* 3.0 5.8 + - - +
331 HIS* 1.3 84.1 - - + +
351 LYS* 1.3 67.7 + - - +
361 LYS* 3.8 1.0 + - - +
481 LYS* 5.6 6.4 - - - -
797A A 3.2 30.6 + - + +
798A G 5.1 15.0 - - - +
1650A C 5.2 13.5 - - - +
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Residues in contact with LYS 35 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311 ILE* 3.0 26.7 + - + +
321 LYS* 3.0 48.1 + - + +
331 HIS 3.4 0.2 - - - -
341 LYS* 1.3 81.7 - - - +
361 LYS* 1.3 65.1 + - - +
371 HIS* 2.9 29.3 + - + +
471 LEU 4.3 2.3 - - - +
481 LYS* 6.0 0.7 - - - +
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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
------------------------------------------------------------
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