Contacts of the helix formed by residues 189 - 194 (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 ALA 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.8 11.6 - - - -
76D THR 5.7 1.1 - - - +
78D PRO* 4.5 17.5 - - + -
188D HIS* 1.3 75.4 - - - +
190D MET* 1.3 68.6 + - - +
191D ASN* 3.1 16.8 - - + +
192D ASP* 2.9 30.8 + - - +
193D ILE* 3.7 7.6 + - - +
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Residues in contact with MET 190 (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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41D PHE* 3.1 55.9 - - + -
76D THR* 3.7 20.5 + - - +
189D ALA* 1.3 74.9 - - - +
191D ASN* 1.3 57.5 + - - +
193D ILE* 3.2 3.0 + - - +
194D PHE* 2.9 67.4 + - + +
269D LEU* 5.8 1.1 - - - -
272D ILE* 3.8 27.4 - - + -
295D THR* 3.3 29.8 - - - +
311D PHE* 4.2 13.7 - - + -
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Residues in contact with ASN 191 (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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189D ALA* 4.5 12.1 - - + +
190D MET* 1.3 78.5 - - - +
192D ASP* 1.3 67.3 + - - +
193D ILE 3.1 1.2 + - - -
194D PHE 3.1 18.8 + - - +
272D ILE* 3.9 23.4 - - - +
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Residues in contact with ASP 192 (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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187D GLU 5.0 0.2 - - - +
188D HIS* 3.6 14.3 - - + +
189D ALA* 2.9 33.6 + - - +
191D ASN* 1.3 80.3 - - - +
193D ILE* 1.3 65.5 + - + +
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Residues in contact with ILE 193 (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* 3.3 40.4 - - + +
40D GLY 3.1 32.1 - - - +
41D PHE* 4.0 19.1 - - + -
188D HIS* 4.1 11.4 - - + -
189D ALA 4.3 4.3 - - - +
190D MET 3.2 3.2 + - - +
191D ASN 3.1 0.6 - - - -
192D ASP* 1.3 86.7 - - + +
194D PHE* 1.3 90.8 + - + +
198D GLU* 4.1 5.5 - - - +
313D PRO* 4.8 8.1 - - + +
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Residues in contact with PHE 194 (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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40D GLY* 4.4 0.2 - - - -
41D PHE* 4.1 7.9 - - + -
190D MET* 2.9 49.1 + - + +
191D ASN* 3.1 19.3 - - - +
193D ILE* 1.3 94.3 - - + +
195D ARG* 1.3 60.9 + - - +
198D GLU* 3.3 11.7 - - + -
199D TYR 5.2 0.7 - - - -
200D ALA* 3.8 12.3 - - + -
269D LEU* 3.4 31.0 - - + -
272D ILE* 3.5 14.1 - - + +
311D PHE* 3.8 7.2 - - + -
312D ARG* 3.7 32.5 - - - -
313D PRO* 3.6 30.5 - - + -
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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