Contacts of the strand formed by residues 415 - 424 (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 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B LEU* 4.1 13.5 - - + -
347B SER 3.5 10.1 - - - +
349B LYS 3.9 11.9 - - - +
351B VAL* 3.7 24.2 - - + -
376B LEU* 4.8 10.8 - - + +
400B PHE* 3.7 15.1 - - + -
402B TRP* 3.3 37.5 + - + +
413B PRO* 5.3 0.9 - - + -
414B ARG* 1.3 78.5 - - - +
416B GLY* 1.3 69.5 + - - +
437B THR* 4.0 0.9 - - - -
438B VAL* 3.0 34.1 + - - +
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Residues in contact with GLY 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.5 14.6 - - - +
347B SER* 2.7 43.2 + - - +
400B PHE* 4.1 7.9 - - - -
415B VAL* 1.3 75.6 - - - +
417B ALA* 1.3 60.7 + - - +
436B GLU 3.9 13.2 - - - -
437B THR* 3.8 3.4 - - - +
444B LEU* 4.6 2.5 - - - -
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 3.9 13.9 - - + -
345B THR 3.3 6.3 - - - -
347B SER* 3.5 1.3 + - - -
400B PHE* 3.7 32.5 - - + -
416B GLY* 1.3 73.0 - - - +
418B SER* 1.3 64.4 + - - +
419B LYS 3.2 0.7 - - - +
420B ILE* 4.0 5.4 - - + -
434B SER* 3.4 14.5 - - - +
436B GLU 4.6 0.6 + - - +
444B LEU* 3.9 6.0 - - + +
446B LEU* 3.3 27.3 - - + +
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR* 3.0 27.5 + - - +
346B LEU 4.0 4.7 + - - -
347B SER* 4.0 16.6 + - - -
379B ASP* 5.0 3.1 + - - -
417B ALA* 1.3 73.0 - - - +
419B LYS* 1.3 63.4 + - - +
433B CYS* 3.2 10.0 - - - +
434B SER 3.1 33.9 + - - +
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Residues in contact with LYS 419 (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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343B SER 3.6 1.8 - - - +
344B VAL* 3.6 1.2 - - - -
345B THR* 2.8 39.0 + - - +
417B ALA 3.2 1.0 - - - -
418B SER* 1.3 87.6 + - - +
420B ILE* 1.3 69.6 - - - +
421B ILE* 4.2 20.3 - - + +
431B ASN* 3.6 33.7 - - - +
432B PHE 3.1 16.8 - - - +
433B CYS* 4.6 10.3 - - - -
446B LEU* 4.5 0.7 - - - -
449B CYS* 5.2 0.4 - - - -
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Residues in contact with ILE 420 (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* 3.2 31.2 - - + -
343B SER 3.2 4.0 - - - -
344B VAL* 4.0 18.2 - - + -
357B VAL* 4.1 13.5 - - + -
398B VAL* 3.6 34.5 - - + -
400B PHE* 4.2 4.0 - - + -
417B ALA* 4.0 9.6 - - + -
419B LYS* 1.3 79.3 - - - +
421B ILE* 1.3 64.4 + - - +
422B VAL* 4.3 5.6 - - + -
431B ASN* 3.6 1.7 - - - -
432B PHE* 2.8 40.2 + - + -
446B LEU* 3.7 26.7 - - + -
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Residues in contact with ILE 421 (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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341B LYS 3.5 1.4 - - - +
342B VAL* 3.1 6.3 - - - -
343B SER* 2.9 46.5 + - - +
419B LYS* 4.2 27.8 - - + +
420B ILE* 1.3 78.8 - - - +
422B VAL* 1.3 67.2 + - - +
423B GLU* 4.0 2.1 + - + +
429B GLN* 4.0 24.7 - - + +
430B PHE 3.4 13.9 - - - +
431B ASN* 3.5 21.5 - - - +
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Residues in contact with VAL 422 (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* 4.0 22.7 - - + -
341B LYS 3.3 8.1 - - - +
342B VAL* 4.4 4.7 - - + -
359B LEU* 4.3 12.8 - - + -
395B LEU* 3.6 39.9 - - + -
398B VAL* 3.7 21.5 - - + -
420B ILE* 4.3 7.9 - - + -
421B ILE* 1.3 74.6 - - - +
423B GLU* 1.3 62.6 + - - +
424B THR* 4.2 0.7 - - + -
428B LYS 3.6 1.0 - - - +
429B GLN* 3.2 4.3 - - - +
430B PHE* 2.9 35.5 + - + +
432B PHE* 4.0 7.4 - - + -
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Residues in contact with GLU 423 (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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297B PHE* 3.4 18.3 - - - +
298B PRO* 4.1 21.2 - - - +
340B TYR* 3.7 2.1 - - - -
341B LYS* 2.8 59.6 + - + +
421B ILE* 5.4 2.7 - - + +
422B VAL* 1.3 77.1 - - - +
424B THR* 1.3 70.1 + - - +
427B GLY* 4.2 7.9 - - - +
428B LYS 3.2 4.3 - - - +
429B GLN* 3.3 36.7 - - + +
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Residues in contact with THR 424 (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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297B PHE* 3.5 8.1 - - - -
340B TYR* 3.7 31.2 - - + -
393B GLY 5.0 3.8 - - - +
395B LEU* 4.1 6.7 - - + -
422B VAL* 5.0 0.4 - - + -
423B GLU* 1.3 78.2 - - - +
425B ASN* 1.3 64.9 + - - +
426B VAL* 3.8 8.3 - - - +
427B GLY* 2.8 20.6 + - - -
428B LYS* 2.8 40.0 + - + +
430B PHE* 4.0 20.0 - - + -
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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