Contacts of the strand formed by residues 392 - 394 (chain B) in PDB entry 3LPI
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 THR 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ILE* 4.0 21.0 - - + +
281B TYR* 2.7 21.3 + - - -
285B LYS* 2.7 9.8 + - - +
286B SER* 3.3 18.0 - - - +
287B ILE* 3.0 26.3 + - - +
295B LEU* 4.4 2.5 - - + -
296B ARG 3.2 11.7 - - - +
297B LEU* 4.1 14.5 - - + +
298B PRO* 3.1 16.2 - - - +
346B LEU* 6.1 0.2 - - + -
390B THR 5.2 0.2 - - - +
391B GLY* 1.3 72.6 - - - -
393B VAL* 1.3 73.0 + - - +
394B MET* 4.3 11.0 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 3.8 14.4 - - + -
289B ASP* 3.7 30.1 - - + +
292B THR* 3.8 25.6 - - + +
295B LEU* 3.3 4.2 - - - +
296B ARG* 2.8 63.5 + - + +
388B SER* 4.7 1.1 - - - +
390B THR* 5.1 6.3 - - - +
391B GLY 4.0 9.6 - - - +
392B THR* 1.3 77.6 - - - +
394B MET* 1.3 61.6 + - - +
395B GLY 3.1 8.2 + - - +
456B Z74 5.4 3.8 - - - -
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Residues in contact with MET 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 4.4 21.3 - - - -
264B ILE* 4.7 8.7 - - - -
286B SER* 5.8 0.4 - - - -
287B ILE 2.8 20.8 + - - +
288B VAL* 3.8 12.9 - - + -
289B ASP 3.0 22.6 + - - +
295B LEU* 4.2 12.3 - - + -
346B LEU* 4.2 13.5 - - + -
348B LEU* 4.8 7.0 - - + -
359B ILE* 3.7 29.8 - - + -
392B THR* 4.3 13.7 - - + -
393B VAL* 1.3 69.4 - - - +
395B GLY* 1.3 65.8 + - - +
398B ILE* 4.0 17.3 - - + -
399B MET* 4.1 6.3 - - + +
415B PHE* 4.1 19.7 - - + -
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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
------------------------------------------------------------
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