Contacts of the strand formed by residues 381 - 388 (chain L) in PDB entry 2HPC
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 LYS 381 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196L LYS* 4.2 14.5 - - - +
197L ARG 2.9 17.5 - - - +
198L LEU* 3.4 31.7 - - + +
249L GLU 3.1 5.9 - - - +
250L LEU* 3.3 2.3 - - - -
251L GLU* 2.6 75.4 + - + +
379L MET* 3.4 1.3 - - - +
380L LYS* 1.3 93.4 - - + +
382L THR* 1.3 64.1 + - - +
383L THR* 5.0 5.6 - - + -
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Residues in contact with THR 382 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L GLN* 2.8 20.9 + - - +
196L LYS* 2.9 4.3 - - - -
197L ARG* 2.8 39.2 + - + +
249L GLU 3.5 3.8 - - - -
250L LEU* 4.2 4.9 - - + -
344L LEU* 3.5 25.1 - - + +
367L ILE* 3.4 31.6 - - + -
379L MET* 4.0 12.6 - - + +
381L LYS* 1.3 78.9 - - - +
383L THR* 1.3 62.8 + - - +
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Residues in contact with THR 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L GLU* 5.3 2.1 + - - -
193L VAL* 5.2 6.2 - - - +
195L GLN 3.1 8.3 - - - -
196L LYS* 3.4 39.0 - - + +
248L VAL* 3.7 2.0 - - - +
249L GLU* 3.2 48.9 + - + +
381L LYS* 4.8 4.9 - - + -
382L THR* 1.3 82.4 - - - +
384L MET* 1.3 62.5 + - - +
385L LYS* 3.5 16.3 + - - +
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Residues in contact with MET 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L VAL* 4.2 0.2 - - - -
194L PHE* 2.5 73.0 + - + -
195L GLN* 2.9 26.7 + - + +
227L TRP* 3.2 37.0 - - + -
246L LEU* 5.0 5.2 - - + -
247L ARG 3.2 11.7 - - - +
248L VAL* 4.1 11.7 - - + +
290L PHE* 5.8 2.5 - - - -
334L TRP* 4.3 17.0 - - - -
335L TRP* 4.8 7.0 - - + -
344L LEU* 4.0 31.2 - - + -
383L THR* 1.3 71.7 - - - +
385L LYS* 1.3 55.0 + - - +
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Residues in contact with LYS 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L GLU* 2.6 41.0 + - - +
191L TRP* 3.1 49.1 - - + +
192L THR 3.5 13.9 - - - +
193L VAL* 3.8 16.2 - - + +
247L ARG* 3.3 37.7 + - + +
249L GLU* 3.7 32.3 + - - -
383L THR* 4.3 12.8 - - - +
384L MET* 1.3 74.4 - - - +
386L ILE* 1.3 60.8 + - - +
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Residues in contact with ILE 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L TRP* 2.7 23.6 - - - -
192L THR* 3.1 33.1 + - + +
194L PHE* 4.5 12.3 - - + -
233L ILE* 5.2 4.3 - - + -
236L ILE* 3.1 39.3 - - + +
237L SER* 4.3 11.2 - - - +
244L TYR* 4.1 13.0 - - + -
245L ALA 3.3 10.5 - - - +
246L LEU* 3.4 30.7 - - + +
265L PHE* 3.5 18.8 - - + -
384L MET 4.3 0.2 + - - -
385L LYS* 1.3 72.4 - - - +
387L ILE* 1.3 60.1 + - - +
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Residues in contact with ILE 387 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L GLN* 3.9 20.4 - - - +
189L ASN* 4.3 9.4 - - + +
190L GLY 4.3 5.4 - - - +
191L TRP* 3.1 58.3 - - + +
192L THR* 4.6 2.7 - - - -
244L TYR* 3.1 8.1 - - - -
245L ALA* 2.8 39.6 + - + +
386L ILE* 1.3 81.9 - - - +
388L PRO* 1.3 87.6 - - + +
389L PHE* 2.9 3.7 + - - +
391L ARG* 4.7 12.6 - - + +
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Residues in contact with PRO 388 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ASP* 3.1 28.9 - - - +
154L GLN* 3.5 20.9 - - + -
190L GLY 5.0 0.2 - - - +
242L ILE* 4.2 16.4 - - + -
243L PRO 3.1 8.1 - - - +
244L TYR* 3.3 17.9 - - + +
387L ILE* 1.3 95.9 - - + +
389L PHE* 1.3 72.4 - - - +
390L ASN* 4.0 9.8 - - - +
391L ARG* 3.5 10.3 + - - +
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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