Contacts of the helix formed by residues 394 - 402 (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 LEU 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B MET 2.6 15.1 + - - +
371B PHE* 3.4 19.3 - - + -
392B PHE* 3.6 28.3 - - + -
393B ASP* 1.3 72.2 - - - +
395B LEU* 1.3 54.8 + - - +
397B ALA* 2.9 2.3 + - - +
398B ALA* 2.7 36.6 + - - +
410B VAL* 4.3 11.4 - - + -
413B ALA* 3.8 23.1 - - + -
454B ILE* 4.2 24.5 - - + -
457B LEU* 4.3 20.0 - - + -
461B PHE* 4.1 29.6 - - + -
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE* 3.2 28.0 - - + -
372B ASP* 3.5 41.1 - - + +
393B ASP* 3.2 12.1 + - - +
394B LEU* 1.3 77.7 - - - +
396B LEU* 1.3 61.2 + - + +
398B ALA* 4.6 0.9 - - - -
399B TYR* 3.1 22.7 + - + +
407B VAL* 3.8 24.2 - - + +
408B ASP* 5.6 0.4 - - - -
609B ALA* 3.3 29.2 - - + -
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP* 2.8 22.7 + - + +
395B LEU* 1.3 82.6 - - + +
397B ALA* 1.3 62.1 + - - +
399B TYR* 3.8 6.6 - - + +
400B LEU* 2.9 35.7 + - - +
474B LEU* 3.5 12.1 - - + -
478B GLU* 3.4 42.2 - - + +
479B GLN* 3.7 15.5 - - + +
482B SER* 4.3 7.2 - - - +
608B GLN* 3.6 44.4 - - + +
609B ALA* 4.8 4.5 - - + -
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 3.6 26.5 - - + -
393B ASP 3.0 7.5 + - - +
394B LEU* 2.9 7.4 + - - +
396B LEU* 1.3 75.1 - - - +
398B ALA* 1.3 59.6 + - - +
400B LEU* 3.2 3.6 + - - +
401B LEU* 2.9 32.4 + - - +
461B PHE* 3.4 22.4 - - + -
465B LEU* 4.0 15.8 - - + +
474B LEU* 3.7 9.1 - - + +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU 2.7 18.4 + - - +
395B LEU 4.1 1.6 - - - +
397B ALA* 1.3 68.7 - - - +
399B TYR* 1.3 68.2 + - - +
401B LEU* 2.8 15.0 + - - +
402B ASP 3.1 13.9 + - - +
407B VAL* 3.9 24.7 - - + -
413B ALA* 3.8 25.8 - - + -
416B MET* 3.9 7.8 - - - +
461B PHE* 3.6 14.7 - - + -
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Residues in contact with TYR 399 (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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395B LEU* 3.1 20.1 + - + +
396B LEU* 3.8 9.9 - - + +
398B ALA* 1.3 78.4 - - - +
400B LEU* 1.3 74.0 + - + +
402B ASP 4.6 4.3 - - - -
403B PRO* 3.1 40.8 - - + +
407B VAL* 5.0 4.9 - - - +
478B GLU* 4.6 5.6 - - - -
608B GLN 3.4 19.7 + - - -
609B ALA* 3.2 25.8 - - + -
610B LEU* 3.2 20.6 - - - -
611B THR* 2.8 31.3 + - - -
614B GLY* 3.3 22.3 + - - -
615B ARG 4.0 1.9 + - - -
769B ARG* 4.2 19.7 - - + -
805B LYS* 4.9 0.6 + - - -
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Residues in contact with LEU 400 (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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396B LEU* 2.9 25.4 + - - +
397B ALA 3.6 3.6 - - - +
399B TYR* 1.3 85.5 - - + +
401B LEU* 1.3 65.7 + - - +
402B ASP 3.4 0.3 + - - -
403B PRO* 4.1 6.2 - - - +
465B LEU* 4.3 10.3 - - + -
470B GLN* 3.7 24.2 + - + +
473B LEU* 3.4 42.0 - - + -
474B LEU* 3.9 33.0 - - + +
478B GLU* 4.0 13.5 - - + -
769B ARG* 3.5 23.1 - - + +
770B ARG* 4.8 5.0 + - - +
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Residues in contact with LEU 401 (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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397B ALA 2.9 13.9 + - - +
398B ALA 2.8 13.0 + - - +
400B LEU* 1.3 73.1 - - - +
402B ASP* 1.3 60.2 + - + +
403B PRO* 4.4 0.7 - - - +
416B MET* 4.0 12.8 - - + -
417B LYS* 4.3 16.6 - - - -
461B PHE* 3.3 42.0 - - + -
464B GLU* 3.9 26.0 - - + +
465B LEU* 3.2 32.5 - - + +
468B ASN* 4.4 7.1 + - - +
470B GLN* 4.2 8.9 - - - +
770B ARG* 4.9 2.8 - - - +
772B TYR* 3.6 21.0 + - - -
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Residues in contact with ASP 402 (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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398B ALA 3.1 10.3 + - - +
399B TYR* 3.5 3.8 - - - -
401B LEU* 1.3 80.2 - - + +
403B PRO* 1.3 69.1 - - - +
404B ALA* 2.8 30.2 + - - +
405B GLN* 3.3 37.9 + - + +
406B GLY 4.7 0.3 + - - -
407B VAL* 5.3 1.4 + - - +
416B MET* 4.3 8.3 - - + +
772B TYR* 4.2 22.7 + - + +
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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