Contacts of the helix formed by residues 185 - 196 (chain V) in PDB entry 5LN3
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 ASN 185 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358N ASP 3.5 18.0 + - - +
359N ALA* 3.5 10.0 - - - +
360N VAL 3.5 6.3 - - - -
361N ARG* 4.0 5.0 - - - -
720N LYS* 3.7 9.4 + - - -
184V LEU* 1.4 82.5 + - - +
186V LYS* 1.4 62.4 + - - +
187V PRO* 3.8 7.0 - - + -
188V SER* 3.6 30.9 + - - +
189V ILE* 3.6 8.0 + - - +
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Residues in contact with LYS 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357N LYS 4.6 9.9 - - - +
358N ASP 4.6 3.6 + - - +
360N VAL* 3.2 18.2 + - + +
361N ARG* 4.5 1.8 - - - +
362N ASN 3.4 22.9 - - - +
363N SER* 4.2 9.4 - - - -
366N HIS* 3.3 39.0 - - + -
395N ARG* 3.4 50.1 - - - +
185V ASN* 1.4 71.0 - - - +
187V PRO* 1.4 67.2 - - + +
188V SER 3.2 0.9 - - - -
189V ILE* 3.5 16.8 - - - +
190V GLN* 3.3 29.3 - - - +
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Residues in contact with PRO 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358N ASP 5.9 0.9 - - - +
395N ARG* 3.5 36.1 - - + +
185V ASN* 4.1 6.3 - - + -
186V LYS* 1.4 92.2 - - + +
188V SER* 1.3 65.2 + - - +
189V ILE 3.3 0.4 + - - -
190V GLN* 4.2 10.6 + - - +
191V ALA* 3.9 18.5 + - - +
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Residues in contact with SER 188 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V LEU 5.4 3.4 - - - -
185V ASN* 3.6 28.9 + - - +
186V LYS 3.2 1.2 - - - -
187V PRO* 1.3 82.5 - - - +
189V ILE* 1.4 62.6 + - - +
191V ALA* 4.0 3.4 + - - +
192V LEU* 3.4 24.8 + - - +
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Residues in contact with ILE 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361N ARG* 3.8 43.1 - - + +
362N ASN* 3.9 33.2 - - - +
363N SER 5.1 0.4 - - - +
168V MET 5.7 1.6 - - - +
169V VAL* 5.6 5.4 - - - +
184V LEU 5.5 2.0 - - - +
185V ASN 3.6 4.0 + - - +
186V LYS 3.5 17.0 - - - +
188V SER* 1.4 79.0 - - - +
190V GLN* 1.4 69.5 + - + +
192V LEU* 3.3 14.6 + - + +
193V ILE* 3.1 37.1 + - + +
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Residues in contact with GLN 190 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363N SER* 3.6 21.3 + - - +
395N ARG* 3.0 30.0 + - - +
396N ALA* 4.8 3.8 - - - -
397N THR* 4.9 5.5 - - - -
169V VAL* 4.1 17.9 - - + +
186V LYS* 3.3 35.2 + - - +
187V PRO* 4.2 9.9 + - - +
188V SER 3.6 0.6 - - - -
189V ILE* 1.4 82.7 - - + +
191V ALA* 1.3 54.0 + - - +
193V ILE* 3.5 3.3 + - - +
194V HIS* 3.0 49.6 + - + +
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Residues in contact with ALA 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187V PRO 3.9 16.1 + - - +
188V SER* 4.1 3.6 - - - +
190V GLN* 1.3 77.1 - - + +
192V LEU* 1.3 59.1 + - - +
194V HIS* 3.6 10.4 - - - +
195V GLY* 2.9 29.1 + - - -
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Residues in contact with LEU 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V SER* 3.4 16.5 + - - +
189V ILE* 3.3 20.9 + - + +
191V ALA* 1.3 79.3 - - - +
193V ILE* 1.4 70.0 + - + +
194V HIS 3.3 0.2 + - - -
195V GLY* 3.3 7.6 + - - -
196V LEU* 3.3 35.4 + - + +
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Residues in contact with ILE 193 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163V ILE* 4.5 20.5 - - + +
165V ALA* 3.9 15.4 - - + +
168V MET* 3.8 42.2 - - + +
169V VAL* 3.4 29.4 - - + -
189V ILE* 3.1 26.8 + - + +
190V GLN 3.7 1.6 - - - +
191V ALA 3.3 0.2 - - - -
192V LEU* 1.4 80.9 - - + +
194V HIS* 1.3 55.8 + - - +
196V LEU 2.8 20.6 - - - +
197V ASN* 4.0 6.4 + - - -
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Residues in contact with HIS 194 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165V ALA* 4.2 14.2 - - + +
169V VAL* 3.3 32.5 - - + +
190V GLN* 3.0 28.4 + - + +
191V ALA* 3.2 11.0 + - - +
193V ILE* 1.3 77.3 - - - +
195V GLY* 1.4 64.7 - - - +
196V LEU 3.3 0.4 + - - -
197V ASN* 3.6 17.1 + - - +
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Residues in contact with GLY 195 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191V ALA 2.9 17.8 + - - -
192V LEU* 3.3 1.5 + - - -
194V HIS* 1.4 75.4 - - - +
196V LEU* 1.3 68.4 + - - +
197V ASN* 4.1 5.2 + - - +
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Residues in contact with LEU 196 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163V ILE* 4.1 6.5 - - - +
192V LEU* 3.3 31.8 + - + +
193V ILE* 2.8 22.3 - - - +
195V GLY* 1.3 84.9 - - - +
197V ASN* 1.4 60.5 + - - +
199V HIS* 6.3 2.9 - - + -
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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