Contacts of the strand formed by residues 315 - 320 (chain B) in PDB entry 1LV5
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 LYS 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA* 3.8 4.7 - - - +
314B ASP* 1.3 89.7 + - - +
316B ALA* 1.3 87.2 + - - +
339B ASN* 3.7 8.8 - - - +
340B GLU* 6.0 0.5 - - - +
367B LYS* 3.3 18.2 - - + +
369B SER* 3.2 24.5 - - - -
391B SER* 4.3 12.8 + - - -
455B TRP* 3.6 28.7 - - + -
458B GLU* 3.2 22.7 + - - -
459B ARG* 5.4 4.6 - - - +
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Residues in contact with ALA 316 (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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313B ALA* 5.0 7.4 - - + +
314B ASP 5.4 0.2 - - - -
315B LYS* 1.3 80.5 - - - +
317B ALA* 1.3 59.2 + - - +
337B VAL* 4.6 6.7 - - + -
338B VAL 4.1 5.4 - - - +
339B ASN* 4.3 7.4 - - + -
360B TRP* 4.3 24.0 - - + -
367B LYS 2.9 8.7 + - - +
368B LYS* 3.1 7.7 - - + -
369B SER* 2.7 33.7 + - - -
455B TRP* 3.4 11.9 - - - -
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Residues in contact with ALA 317 (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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316B ALA* 1.3 73.7 - - - +
318B LEU* 1.3 60.0 + - - +
336B ALA 4.1 0.6 - - - +
337B VAL* 3.7 5.5 - - - +
338B VAL* 3.0 36.8 + - + +
369B SER* 3.4 11.0 - - - +
451B ALA* 3.4 31.4 - - - +
454B ILE* 4.3 6.5 - - + -
455B TRP* 3.5 21.6 - - + +
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Residues in contact with LEU 318 (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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316B ALA 3.9 0.6 - - - -
317B ALA* 1.3 74.1 - - - +
319B VAL* 1.3 71.6 + - - +
320B VAL* 3.9 11.7 - - + -
335B ILE* 4.1 11.7 - - + -
336B ALA 3.6 2.5 - - - +
337B VAL* 3.7 20.2 - - + -
357B PHE* 4.6 0.9 - - + -
360B TRP* 3.4 43.5 - - + -
361B LEU* 4.2 8.7 - - + -
368B LYS* 4.1 18.4 - - + -
369B SER 2.8 11.5 + - - +
370B MET* 3.2 51.4 - - + +
371B PHE 4.9 0.3 + - - -
387B LEU* 4.3 7.4 - - + -
454B ILE* 4.6 1.4 - - - +
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Residues in contact with VAL 319 (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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318B LEU* 1.3 81.0 - - - +
320B VAL* 1.3 63.5 + - - +
321B GLU* 3.8 24.9 - - + +
335B ILE* 3.3 9.0 - - - +
336B ALA* 2.8 44.3 + - + +
370B MET* 4.5 0.9 - - - -
447B LEU* 3.8 32.1 - - + +
450B LYS* 4.5 9.0 - - + +
451B ALA* 3.9 24.2 - - + +
454B ILE* 4.2 12.1 - - + -
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Residues in contact with VAL 320 (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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318B LEU* 3.9 18.4 - - + -
319B VAL* 1.3 78.9 - - - +
321B GLU* 1.3 59.8 + - - +
322B VAL* 3.8 8.3 + - + +
332B ILE* 3.7 37.2 - - + -
334B GLY 4.0 3.1 - - - -
335B ILE* 4.4 12.3 - - + -
352B LEU* 5.5 0.4 - - + -
361B LEU* 4.9 4.5 - - + -
370B MET* 3.8 20.8 - - + +
375B ARG* 5.3 2.8 - - - +
376B ALA* 4.0 23.1 - - + +
380B LEU* 4.3 21.8 - - + -
387B LEU* 5.6 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