Contacts of the strand formed by residues 382 - 386 (chain A) in PDB entry 3LGP
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 SER 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LEU* 4.0 3.4 - - - +
321A PHE* 4.3 15.9 - - - -
322A SER* 2.7 32.2 + - - -
325A ILE* 5.5 1.6 - - - -
329A ALA* 6.2 0.9 - - - -
335A ALA* 3.3 13.2 - - - -
351A ALA* 3.6 0.3 - - - -
352A TYR* 3.2 31.4 + - - -
379A TYR 3.9 5.2 + - - -
380A LEU 3.2 3.4 + - - -
381A ASN* 1.3 76.8 - - - +
383A GLY* 1.3 58.3 + - - +
410A ASN* 3.0 20.5 + - - +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LEU* 3.7 7.4 - - - +
321A PHE* 4.0 3.1 - - - -
335A ALA 3.2 6.1 + - - +
336A HIS* 3.4 17.9 + - - -
337A LEU* 2.9 23.0 + - - +
350A LEU 3.3 12.6 - - - -
351A ALA* 3.8 8.3 - - - -
382A SER* 1.3 77.9 - - - +
384A LEU* 1.3 62.1 + - - +
410A ASN* 4.5 0.9 - - - -
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A VAL* 4.0 15.3 - - + +
317A LEU* 3.9 19.7 - - + -
318A LEU* 3.8 40.4 - - + +
321A PHE* 5.6 0.4 - - + -
336A HIS* 3.3 8.5 - - - -
337A LEU* 3.2 26.9 - - + +
339A THR* 4.7 1.8 - - + -
343A PHE* 3.8 32.3 - - + -
349A GLY* 3.3 8.4 - - - -
350A LEU 2.8 38.5 + - - +
383A GLY* 1.3 73.8 - - - +
385A THR* 1.3 61.8 + - - +
406A GLU* 3.5 8.8 - - - +
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 5.7 0.2 - - + -
336A HIS* 2.8 23.4 + - - -
337A LEU 2.9 5.7 + - - +
338A PHE* 3.4 20.0 - - + +
339A THR* 2.9 29.7 + - - +
348A LEU 3.8 3.6 - - - -
384A LEU* 1.3 73.4 + - - +
386A SER* 1.4 69.6 + - - +
387A THR* 4.2 10.7 - - + +
399A ALA* 4.6 3.4 - - - +
402A VAL* 3.7 21.8 - - + +
403A THR* 2.9 29.9 + - - +
406A GLU* 4.5 0.5 - - - +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A THR* 3.3 11.9 - - - -
341A GLN 2.6 40.6 + - - -
343A PHE* 3.5 24.4 - - - -
348A LEU* 2.8 24.8 + - - +
385A THR* 1.4 76.7 - - - +
387A THR* 1.3 61.4 + - - +
388A LYS 3.3 10.4 + - - -
394A ILE* 3.9 11.4 - - - +
402A VAL* 4.7 0.2 - - - +
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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