Contacts of the helix formed by residues 404 - 412 (chain B) in PDB entry 4L6V
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 ASN 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR* 5.9 0.4 - - - -
315B ALA* 3.6 14.1 - - + -
316B GLY 3.3 17.5 - - - +
318B THR* 3.6 13.8 + - - +
320B LEU* 3.2 31.2 - - - +
401B ASN* 2.7 42.6 + - - +
402B LYS 2.9 3.9 + - - +
403B ASP* 1.3 79.7 - - - +
405B VAL* 1.3 64.7 + - - +
406B LEU* 3.1 4.9 + - - +
407B ALA 2.8 16.3 + - - -
408B ARG* 3.0 21.1 + - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 3.8 34.3 - - + +
316B GLY* 2.8 28.4 + - - +
317B HIS* 3.5 31.6 - - + +
320B LEU* 3.9 12.8 - - + -
404B ASN* 1.3 71.2 - - - +
406B LEU* 1.3 61.7 + - + +
408B ARG* 4.1 5.5 - - - +
409B MET* 3.1 30.1 + - - +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 3.9 23.8 - - + -
323B THR* 4.0 7.9 - - + -
330B PHE* 4.0 12.8 - - + -
391B PHE* 3.7 28.3 - - + -
392B PHE* 3.3 36.5 - - + -
396B TYR* 4.5 3.6 - - + -
401B ASN* 4.1 9.2 - - + +
404B ASN* 3.0 13.9 + - - +
405B VAL* 1.3 81.6 - - + +
407B ALA* 1.3 65.7 + - - +
409B MET* 3.3 22.2 + - + +
410B LEU* 4.0 3.8 + - - +
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Residues in contact with ALA 407 (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 TYR* 3.0 27.3 - - + +
398B PRO 5.5 0.2 - - - +
401B ASN 3.0 25.8 - - - +
402B LYS* 4.7 1.1 - - - -
403B ASP* 4.1 9.9 - - - +
404B ASN* 2.8 11.0 + - - +
406B LEU* 1.3 69.0 - - - +
408B ARG* 1.3 58.2 + - + +
409B MET 3.0 5.2 - - - -
410B LEU* 3.0 24.7 + - - +
411B GLU* 3.2 8.6 + - - +
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Residues in contact with ARG 408 (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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311B PRO 5.4 1.4 + - - -
312B LEU 3.7 15.5 + - - -
313B THR* 4.8 7.2 - - - +
314B GLY* 3.3 37.9 - - - +
403B ASP* 3.1 42.0 + - - +
404B ASN 3.0 17.0 + - - +
405B VAL* 4.3 5.2 - - - +
406B LEU 3.3 0.2 - - - -
407B ALA* 1.3 72.9 - - - +
409B MET* 1.3 64.0 + - + +
411B GLU* 3.2 21.3 + - + +
412B HIS* 2.9 28.5 - - + -
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Residues in contact with MET 409 (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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392B PHE* 5.6 2.2 - - + -
405B VAL 3.1 20.6 + - - +
406B LEU* 3.3 15.0 - - + +
407B ALA 3.0 0.2 - - - -
408B ARG* 1.3 80.2 - - + +
410B LEU* 1.3 62.0 + - + +
411B GLU 3.3 0.2 + - - -
412B HIS* 3.3 40.1 + - + +
413B LYS* 3.2 21.0 + - - -
416B LEU* 3.8 24.5 - - + +
536B LEU* 4.5 11.2 - - + -
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Residues in contact with LEU 410 (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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392B PHE* 3.9 33.0 - - + -
396B TYR* 3.6 46.7 - - + +
406B LEU 4.4 4.7 - - - +
407B ALA* 3.0 9.9 + - - +
409B MET* 1.3 76.2 - - - +
411B GLU* 1.3 62.4 + - - +
412B HIS 3.3 0.5 + - - -
413B LYS* 3.4 28.4 + - + +
414B GLU* 4.5 0.5 - - - +
536B LEU* 3.8 29.6 - - + +
539B ARG* 4.3 11.9 - - + -
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Residues in contact with GLU 411 (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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407B ALA 3.2 4.6 + - - +
408B ARG* 3.2 25.5 + - + +
409B MET 3.1 0.6 - - - -
410B LEU* 1.3 80.2 - - - +
412B HIS* 1.3 63.4 + - + +
413B LYS 3.6 0.4 - - - -
414B GLU* 3.5 10.9 - - - +
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Residues in contact with HIS 412 (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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702A TRP* 6.0 2.2 - - + -
408B ARG* 2.9 26.4 + - + +
409B MET* 3.3 25.7 + - + +
410B LEU 3.2 0.2 - - - -
411B GLU* 1.3 85.5 - - + +
413B LYS* 1.3 58.3 + - - +
414B GLU* 3.1 7.2 - - - -
415B ALA* 2.9 34.6 + - + +
416B LEU* 3.2 36.7 + - + +
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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