Contacts of the strand formed by residues 362 - 372 (chain A) in PDB entry 5LG1
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A GLU* 3.9 1.7 - - - +
360A LYS* 3.7 17.0 - - - +
361A ASN* 1.3 87.9 - - + +
363A VAL* 1.3 64.2 + - - +
390A ASN* 5.1 7.2 + - - +
411A THR* 3.8 25.3 - - + +
412A VAL 3.3 12.1 - - - +
413A ASP* 3.3 28.3 + - - +
370B LYS* 3.9 15.0 + - - +
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Residues in contact with VAL 363 (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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353A PRO* 3.7 24.7 - - + -
357A GLU* 3.5 26.9 - - - +
358A MET* 4.0 25.4 - - - -
360A LYS 5.1 0.2 - - - +
362A GLN* 1.3 75.9 - - - +
364A SER* 1.3 62.9 + - - +
365A LEU* 4.7 1.1 - - + -
410A LEU 3.8 0.7 - - - +
411A THR* 3.7 5.9 - - - +
412A VAL* 3.1 47.2 + - + +
414A LYS* 4.4 16.4 - - + +
417A TRP* 4.0 16.4 - - + -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO 4.2 0.5 - - - +
353A PRO* 3.3 26.3 - - - +
357A GLU* 2.6 34.1 + - - -
363A VAL* 1.3 72.7 + - - +
365A LEU* 1.3 60.7 + - - +
366A THR* 4.0 6.5 + - - -
409A ARG* 3.1 31.5 + - - +
410A LEU 3.7 3.8 - - - -
411A THR* 5.0 0.6 - - - +
351B LEU* 6.1 0.2 - - - +
368B LEU* 3.7 21.5 - - - +
370B LYS* 3.7 4.9 + - - -
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Residues in contact with LEU 365 (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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351A LEU 4.2 2.7 - - - -
353A PRO* 3.6 31.6 - - + -
363A VAL* 4.7 4.0 - - + -
364A SER* 1.3 72.3 - - - +
366A THR* 1.3 60.0 + - - +
381A TRP* 3.6 11.3 - - + -
408A SER 3.5 1.7 - - - +
409A ARG* 3.3 4.0 - - - -
410A LEU* 2.8 57.0 + - + +
412A VAL* 4.1 11.4 - - + -
417A TRP* 3.8 12.6 - - + -
423A PHE* 3.6 46.4 - - + -
441A LEU* 3.8 21.8 - - + -
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Residues in contact with THR 366 (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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350A THR* 3.5 4.7 - - - -
351A LEU* 2.7 59.9 + - + +
364A SER* 4.5 8.3 + - - -
365A LEU* 1.3 74.2 - - - +
367A CYS* 1.3 63.9 + - - +
381A TRP* 4.1 2.7 - - - -
407A TYR* 3.5 33.2 - - + -
408A SER 3.6 3.6 - - - +
441A LEU* 4.8 0.7 - - - +
351B LEU* 3.7 13.8 - - + +
368B LEU* 4.9 0.3 - - - +
407B TYR* 2.9 29.8 + - + +
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Residues in contact with CYS 367 (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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348A VAL* 3.7 21.3 - - - -
349A TYR 3.5 4.9 - - - -
350A THR* 4.5 3.1 - - + +
366A THR* 1.3 75.5 - - - +
368A LEU* 1.3 62.8 + - - +
369A VAL* 3.8 12.0 + - - +
381A TRP* 3.4 17.5 - - + -
407A TYR* 3.5 4.3 - - - -
408A SER* 2.9 34.5 + - - +
425A CYS* 2.0 50.5 - - + -
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Residues in contact with LEU 368 (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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347A GLN 3.4 2.9 - - - +
348A VAL* 3.4 2.3 - - - +
349A TYR* 2.7 62.8 + - + +
351A LEU* 4.8 10.7 - - + +
366A THR* 4.1 1.2 - - - +
367A CYS* 1.3 71.9 - - - +
369A VAL* 1.3 69.4 + - - +
370A LYS* 4.5 8.3 - - + -
405A PHE* 4.2 11.2 - - + -
406A LEU 3.5 11.4 - - - +
407A TYR* 3.5 44.8 - - + +
357B GLU* 5.1 1.6 - - - +
364B SER* 4.0 26.0 - - - +
366B THR* 4.5 2.7 - - - +
409B ARG* 4.1 5.8 - - - -
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Residues in contact with VAL 369 (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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346A PRO* 3.8 20.4 - - + -
347A GLN 3.3 5.4 - - - +
348A VAL* 4.3 4.3 - - + -
367A CYS* 4.0 14.6 - - - +
368A LEU* 1.3 77.4 - - - +
370A LYS* 1.3 61.3 + - - +
372A PHE* 3.4 4.9 - - + -
377A ILE* 3.8 27.1 - - + -
379A VAL* 4.5 5.2 - - + -
405A PHE* 3.1 3.5 - - - +
406A LEU* 2.8 55.0 + - + -
427A VAL* 3.8 28.0 - - + -
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Residues in contact with LYS 370 (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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346A PRO* 3.6 0.2 - - - +
347A GLN* 2.8 61.5 + - - +
349A TYR* 3.6 21.3 + - + -
368A LEU* 4.5 10.1 - - + -
369A VAL* 1.3 74.8 - - - +
371A GLY* 1.3 63.0 + - - +
372A PHE* 3.6 3.4 - - - -
399A ASP* 5.5 0.7 - - - +
404A PHE 3.6 0.9 - - - -
405A PHE* 3.6 18.4 - - + -
357B GLU* 2.7 32.8 + - - +
360B LYS* 5.3 4.0 - - - +
362B GLN* 4.3 9.9 + - - +
363B VAL 5.4 0.2 - - - -
364B SER* 3.7 5.2 + - - +
409B ARG* 3.9 23.6 - - - +
411B THR* 6.3 0.6 - - - +
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Residues in contact with GLY 371 (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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344A ARG* 3.4 14.7 - - - +
345A GLU 3.2 16.5 - - - +
347A GLN* 4.6 10.2 + - - -
370A LYS* 1.3 77.6 - - - +
372A PHE* 1.3 56.5 + - - -
399A ASP* 5.7 1.4 + - - -
401A ASP* 5.2 2.5 - - - -
403A SER* 3.3 23.9 + - - -
404A PHE 2.8 11.3 + - - -
405A PHE* 4.5 0.4 - - - +
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Residues in contact with PHE 372 (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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344A ARG* 3.3 9.9 - - - +
346A PRO* 3.5 22.0 - - + -
369A VAL* 3.4 36.8 - - + -
370A LYS 4.2 2.0 - - - -
371A GLY* 1.3 78.6 - - - +
373A TYR* 1.3 61.9 + - - +
374A PRO 3.3 13.5 - - - -
375A SER* 3.8 22.0 - - - -
377A ILE* 3.9 20.2 - - + -
396A PRO* 4.5 2.7 - - + -
403A SER* 3.7 1.2 - - - -
404A PHE* 2.9 62.2 + - + -
405A PHE* 3.8 3.4 - - - -
406A LEU* 4.2 18.2 - - + -
429A HIS* 3.9 14.4 - + + +
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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