Contacts of the strand formed by residues 351 - 361 (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 VAL 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B LYS* 3.4 7.8 + - - +
350B LYS* 1.3 78.8 - - - +
352B THR* 1.3 68.8 + - - +
375B THR* 3.6 5.7 - - - +
376B LEU* 2.7 54.2 + - + -
402B TRP* 3.9 27.4 - - + -
404B ASN* 6.0 0.2 - - - +
409B ASN* 5.4 5.4 - - + -
413B PRO* 4.3 20.4 - - + -
415B VAL* 3.7 26.2 - - + -
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Residues in contact with THR 352 (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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351B VAL* 1.3 90.0 + - - +
353B GLY* 1.3 60.0 + - - +
374B GLY* 3.5 17.5 - - - +
375B THR* 4.5 9.2 + - - +
402B TRP* 4.7 0.5 - - - -
404B ASN* 2.8 40.6 + - - +
407B VAL* 5.9 1.1 - - + -
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Residues in contact with GLY 353 (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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352B THR* 1.3 77.0 - - - +
354B HIS* 1.3 65.2 + - - -
373B LYS* 3.4 0.3 - - - -
374B GLY 3.0 31.8 + - - +
376B LEU* 3.3 23.6 - - - +
402B TRP* 4.9 1.3 - - - -
403B TYR 3.2 12.6 - - - -
404B ASN* 3.9 6.7 - - - -
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Residues in contact with HIS 354 (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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353B GLY* 1.3 79.0 - - - -
355B ILE* 1.3 62.1 + - - +
356B LEU* 3.6 4.0 - - + +
370B GLU* 2.8 26.9 + - - +
372B PHE 3.4 5.4 - - - -
373B LYS* 3.5 29.8 - - + +
402B TRP* 3.1 24.8 - - - +
403B TYR* 2.9 57.6 + + + -
404B ASN* 4.5 10.1 + - - -
406B ASN* 4.9 5.1 + - - -
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Residues in contact with ILE 355 (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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344B VAL* 4.4 21.8 - - + -
346B LEU* 4.2 18.4 - - + -
354B HIS* 1.3 74.8 - - - +
356B LEU* 1.3 57.4 + - - +
357B VAL* 6.3 0.4 - - + -
370B GLU* 3.6 3.6 - - - +
371B ILE* 2.7 41.4 + - + -
372B PHE* 2.8 46.6 + - + +
376B LEU* 3.4 31.0 - - + -
382B HIS* 4.8 7.0 - - + -
400B PHE* 3.8 28.3 - - + -
401B ILE 3.5 2.2 - - - -
402B TRP* 3.9 2.2 - - + -
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Residues in contact with LEU 356 (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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65A ARG* 4.5 12.8 - - - +
354B HIS* 3.6 6.7 - - + +
355B ILE* 1.3 79.4 - - - +
357B VAL* 1.3 69.8 + - - +
368B GLN* 4.1 29.8 - - + +
369B TYR 3.3 8.3 - - - +
370B GLU* 4.3 20.2 - - + +
371B ILE* 4.5 0.4 - - - +
400B PHE* 3.5 1.7 - - - -
401B ILE* 2.7 61.4 + - + +
403B TYR* 3.6 33.2 - - + +
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Residues in contact with VAL 357 (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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342B VAL* 4.2 15.0 - - + -
344B VAL* 4.1 20.0 - - + -
355B ILE* 5.8 0.7 - - + -
356B LEU* 1.3 81.2 - - - +
358B SER* 1.3 62.7 + - - +
359B LEU* 3.7 18.3 - - + +
367B LYS 3.7 0.9 - - - +
368B GLN* 3.2 3.9 - - - -
369B TYR* 2.8 32.7 + - - +
371B ILE* 4.1 14.1 - - + -
386B PHE* 5.2 2.2 - - + -
398B VAL* 3.6 20.0 - - + -
399B LYS 3.4 8.3 - - - +
400B PHE* 4.4 5.8 - - + -
420B ILE* 4.1 23.3 - - + -
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Residues in contact with SER 358 (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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45A GLU* 5.3 0.9 + - - -
357B VAL* 1.3 74.5 - - - +
359B LEU* 1.3 65.2 + - - +
360B PHE* 3.6 20.3 - - - -
366B SER* 3.8 12.1 - - - -
367B LYS 3.5 18.4 - - - -
368B GLN* 4.0 17.0 + - - +
398B VAL* 3.4 9.4 - - - +
399B LYS* 3.2 37.4 + - - +
443B LEU* 4.9 2.9 - - - +
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Residues in contact with LEU 359 (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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340B TYR* 3.7 47.1 - - + -
342B VAL* 4.4 7.6 - - + -
357B VAL* 3.7 20.6 - - + -
358B SER* 1.3 80.2 - - - +
360B PHE* 1.3 64.5 + - - +
365B ASN* 3.0 26.2 - - - +
366B SER* 3.0 20.2 + - - +
386B PHE* 4.0 20.4 - - + -
388B SER* 5.5 1.1 - - - +
392B VAL* 4.0 11.7 - - + +
395B LEU* 3.9 15.9 - - + -
397B MET 3.9 3.1 - - - -
398B VAL* 4.5 2.5 - - + -
422B VAL* 4.3 14.4 - - + -
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Residues in contact with PHE 360 (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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45A GLU* 3.5 38.6 - - + -
46A ASN* 4.0 7.4 - - - -
358B SER* 3.6 31.4 - - - -
359B LEU* 1.3 77.1 - - - +
361B GLY* 1.3 58.2 + - - +
364B GLY 3.8 2.7 - - - -
365B ASN* 3.2 36.8 - - + -
366B SER 5.3 0.2 - - - -
392B VAL* 4.6 2.2 - - - -
395B LEU* 3.5 5.0 - - - +
396B GLN* 2.8 28.1 + - - +
397B MET* 2.8 46.1 + - + +
399B LYS* 3.7 22.2 - - + -
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Residues in contact with GLY 361 (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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360B PHE* 1.3 74.4 - - - +
362B ASN* 1.3 67.5 + - - +
363B LYS 3.2 0.2 - - - -
364B GLY* 2.9 21.5 + - - +
392B VAL* 3.2 16.5 - - - +
394B ASP 3.0 17.5 - - - -
395B LEU* 4.1 0.9 - - - -
396B GLN* 3.8 11.9 - - - +
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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