Contacts of the helix formed by residues 183 - 188 (chain A) in PDB entry 3NJ4
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN 4.4 4.9 + - - -
180A VAL* 3.2 20.1 + - - -
181A ASN 3.0 1.4 + - - -
182A ASP* 1.3 78.6 - - - +
184A VAL* 1.3 54.9 + - - +
185A THR* 3.4 2.4 + - - -
186A LYS* 2.6 28.4 + - - -
187A SER* 3.2 10.2 + - - -
364A ASN* 3.3 19.2 + - - -
385A PHE* 5.7 3.4 - - - -
386A LEU* 5.3 13.3 - - - +
391A ASP* 3.0 26.3 + - - -
431B ARG* 5.5 0.4 - - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP 3.6 2.6 + - - -
183A SER* 1.3 68.4 - - - +
185A THR* 1.3 53.3 + - - +
186A LYS 2.7 11.4 + - - -
187A SER* 4.4 2.9 - - - -
188A LYS* 3.2 32.9 + - + -
189A PHE* 3.2 6.8 - - + -
388A LYS* 4.3 5.8 - - - +
391A ASP* 3.1 20.8 + - - +
432A TYR* 3.5 41.1 - - + -
247B ILE* 3.6 31.9 - - + -
431B ARG* 3.6 27.1 - - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.4 0.3 + - - -
184A VAL* 1.3 69.6 - - - +
186A LYS* 1.3 56.5 + - - +
189A PHE* 3.6 18.2 - - + +
190A ASP 4.8 0.2 + - - -
360A ASN* 3.1 32.4 + - - +
364A ASN* 2.8 29.3 + - - -
391A ASP* 2.6 52.4 + - - +
394A VAL* 3.4 11.6 - - + +
395A ALA* 3.5 26.9 - - + +
247B ILE* 4.4 6.3 - - + -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.0 38.5 + - - +
180A VAL* 3.4 23.6 - - + +
181A ASN* 3.2 16.4 - - - +
183A SER 2.6 18.2 + - - +
184A VAL 2.7 0.6 + - - -
185A THR* 1.3 72.6 + - - +
187A SER* 1.3 61.3 + - - +
188A LYS 3.2 1.1 - - - -
189A PHE 3.1 0.3 + - - -
190A ASP* 2.6 43.5 + - + +
191A ASN* 3.0 19.5 - - - +
361A SER* 3.6 26.9 - - - +
364A ASN* 4.1 7.4 - - - +
601A AFX 2.8 28.1 + - - -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASN* 3.1 26.2 + - - -
182A ASP* 4.2 9.3 + - - -
183A SER 3.2 12.5 + - - -
184A VAL* 4.1 2.8 + - - -
186A LYS* 1.3 79.0 - - - +
188A LYS* 1.3 66.3 + - - +
189A PHE 3.2 2.0 + - - -
191A ASN* 3.4 34.0 + - - +
192A LEU* 3.9 1.9 + - - +
223A ASP* 3.6 24.8 - - - +
431B ARG* 4.4 5.9 + - - +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.2 25.5 + - + +
187A SER* 1.3 87.1 + - - +
189A PHE* 1.3 75.6 + - + +
192A LEU* 4.2 20.7 - - + +
193A TYR* 3.6 15.8 + - - -
223A ASP* 4.4 7.9 - - - +
431A ARG 3.1 28.2 + - - +
432A TYR* 3.7 7.9 + - + +
188B LYS* 3.2 22.0 - - - +
251B GLN* 4.6 14.3 + - - +
431B ARG* 3.8 14.6 - - + -
432B TYR* 2.9 28.4 + - - +
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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