Contacts of the strand formed by residues 289 - 294 (chain J) 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 ILE 289 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184J LYS 4.3 1.0 - - - +
235J PHE* 4.6 7.6 - - + -
238J ALA* 4.3 22.2 - - + +
239J ARG* 3.3 45.8 - - - +
242J ALA* 4.6 0.9 - - + -
244J SER* 3.8 10.5 - - - +
246J ILE* 3.5 33.4 - - + -
273J MET* 5.6 0.2 - - - -
277J LEU* 4.5 23.5 - - + +
287J LYS* 3.2 27.3 - - + +
288J ASN* 1.4 95.0 - - - +
290J LYS* 1.3 64.6 + - - +
291J VAL* 5.5 0.7 - - + -
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Residues in contact with LYS 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J VAL* 5.2 3.6 + - - +
165J ILE* 4.6 26.0 + - + +
168J PRO* 5.5 1.7 - - - +
169J VAL* 5.0 17.3 - - + -
183J PRO* 2.7 49.7 + - - +
184J LYS 3.7 11.2 + - - +
185J GLY* 4.0 4.8 - - - +
186J VAL* 4.4 18.3 - - + +
244J SER 3.7 5.8 + - - +
245J ILE* 4.2 16.8 - - + -
246J ILE* 3.1 31.8 + - - +
287J LYS* 5.7 0.9 - - - -
288J ASN 5.6 0.4 - - - -
289J ILE* 1.3 76.7 - - - +
291J VAL* 1.4 75.6 + - - +
292J ILE* 4.5 10.1 - - + -
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Residues in contact with VAL 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J LYS 3.5 9.4 + - - +
185J GLY* 3.4 5.2 - - - -
186J VAL* 3.0 26.9 + - - +
246J ILE* 3.4 15.0 - - + +
248J MET* 5.6 3.1 - - + +
270J GLN* 5.2 9.4 - - + -
273J MET* 4.3 19.5 - - + -
274J LEU* 5.2 8.7 - - + -
277J LEU* 3.5 31.6 - - + -
289J ILE* 5.5 0.7 - - + -
290J LYS* 1.4 79.7 - - - +
292J ILE* 1.4 70.8 + - - +
293J MET* 3.8 22.9 - - + -
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Residues in contact with ILE 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J ILE* 5.2 8.5 - - + -
186J VAL* 3.7 17.0 - - + -
188J LEU* 6.3 1.1 - - + -
200J ALA* 4.1 29.8 - - + +
203J VAL* 5.2 0.9 - - + -
245J ILE* 3.8 37.2 - - + -
246J ILE 2.9 13.4 + - - +
247J PHE* 3.4 23.2 - - + -
248J MET* 3.0 28.1 + - - +
290J LYS* 4.5 9.2 - - + -
291J VAL* 1.4 80.6 - - - +
293J MET* 1.4 72.8 + - - +
294J ALA* 5.5 1.6 - - + -
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Residues in contact with MET 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J GLY* 4.4 6.5 - - - +
186J VAL 3.0 32.9 + - - +
187J LEU* 3.6 28.4 - - + +
188J LEU* 3.4 19.8 + - - +
247J PHE* 4.9 0.2 - - - -
248J MET* 5.0 2.9 - - + -
251J ILE* 5.7 0.4 - - + -
270J GLN* 3.4 40.6 - - + +
274J LEU* 5.1 13.2 - - + -
291J VAL* 3.8 28.7 - - + +
292J ILE* 1.4 83.6 - - - +
294J ALA* 1.4 59.7 + - - +
295J THR* 5.6 2.0 - - + -
310J ARG 5.9 2.5 - - - +
313J ARG 6.0 0.2 - - - +
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Residues in contact with ALA 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J LEU* 3.7 12.8 - - + +
196J LYS* 5.1 7.9 - - + -
197J THR* 5.7 5.2 - - - +
247J PHE* 3.8 24.7 - - + -
251J ILE* 3.1 30.8 - - - +
252J ASP* 3.8 19.7 - - + +
292J ILE* 5.5 2.0 - - + -
293J MET* 1.4 73.7 - - - +
295J THR* 1.4 66.6 + - - +
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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