Contacts of the strand formed by residues 323 - 327 (chain B) in PDB entry 1LPB
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 GLN 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B HIS 2.9 10.2 + - - +
224B LEU* 3.6 10.1 - - - +
225B ASP 2.8 27.6 + - - -
314B TYR* 4.7 5.2 + - - -
316B GLY 3.7 12.0 + - - +
317B LYS 3.2 20.8 + - - -
319B ASN* 4.6 3.3 - - - +
320B ASP* 2.6 51.9 + - + +
321B VAL 4.5 0.4 - - - +
322B GLY* 1.3 76.0 - - - +
324B LYS* 1.3 60.2 + - - +
325B PHE* 3.1 29.0 - - + -
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL* 3.7 20.4 - - + +
225B ASP 3.4 2.7 - - - -
227B PHE* 3.3 27.1 - - + -
284B PRO* 3.5 20.1 - - - +
285B CYS 3.7 9.7 + - - +
286B ALA 4.5 14.1 + - - -
322B GLY 3.2 6.6 + - - +
323B GLN* 1.3 69.8 - - - +
325B PHE* 1.3 64.6 + - - +
326B TYR* 3.5 28.1 + - + +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU* 3.3 33.9 - - + -
225B ASP 3.0 8.0 + - - -
226B PHE* 3.5 24.8 - + + -
227B PHE* 2.9 26.5 + - - -
282B GLY 3.9 7.2 - - - -
283B PHE 3.4 4.5 - - - +
284B PRO* 3.7 33.2 - - + -
305B PRO* 3.3 35.7 - - + -
314B TYR* 4.3 10.5 - + - -
323B GLN* 3.1 41.5 - - + -
324B LYS* 1.3 73.7 - - - +
326B TYR* 1.3 69.0 + - - +
327B LEU* 4.6 1.1 - - - -
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Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B PHE* 3.5 43.2 - + + -
230B GLY 5.0 1.3 - - - -
283B PHE* 2.7 44.9 + - - +
285B CYS* 3.3 40.6 - - + -
287B SER* 3.7 16.4 - - - -
288B TYR* 3.7 35.4 + + + -
291B PHE* 4.0 22.4 - - + -
324B LYS* 3.5 34.1 + - + +
325B PHE* 1.3 74.1 - - - +
327B LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PHE* 3.9 11.4 - - + -
227B PHE 4.1 2.0 + - - -
228B PRO* 3.1 10.6 - - + +
229B ASN 2.7 30.7 + - - -
230B GLY 4.7 0.2 + - - -
280B PHE* 3.5 45.8 - - + +
281B ALA 3.4 14.8 - - - +
282B GLY* 3.8 11.4 - - - -
283B PHE* 4.9 1.1 - - + -
288B TYR* 4.7 1.0 - - - -
291B PHE* 4.0 12.0 - - - -
307B MET* 3.0 37.0 - - + -
325B PHE 4.4 1.1 - - - +
326B TYR* 1.3 85.6 - - - +
328B ASP* 1.3 62.7 + - - +
329B THR* 4.5 6.1 - - + -
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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