Contacts of the helix formed by residues 541 - 552 (chain B) in PDB entry 2V4M
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 MET 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537B GLU* 3.9 14.8 - - - +
538B VAL* 3.2 19.1 + - + +
540B SER* 1.3 81.6 - - - +
542B ASP* 1.3 62.7 + - - +
543B ASP* 3.1 3.4 - - - +
544B GLU* 3.0 48.4 + - + +
545B ILE* 3.0 24.7 + - + +
640B LYS* 6.3 2.9 - - + -
653B ILE* 5.0 7.9 - - + -
654B LYS* 3.5 40.6 - - + +
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Residues in contact with ASP 542 (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 GLN* 5.6 2.4 + - - -
348B PHE* 4.1 24.3 - - + -
539B LEU 3.5 16.3 + - - +
540B SER 3.2 2.7 - - - +
541B MET* 1.3 76.5 - - - +
543B ASP* 1.3 54.2 + - - +
545B ILE* 4.4 8.9 - - - +
546B GLN* 2.8 40.7 + - - +
673B LEU* 4.5 8.1 - - + +
677B HIS* 2.5 38.7 + - - -
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Residues in contact with ASP 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B SER 4.3 6.3 + - - +
541B MET* 4.7 2.2 - - - -
542B ASP* 1.3 81.2 - - - +
544B GLU* 1.3 69.0 + - + +
546B GLN* 3.1 14.5 + - - +
547B LYS* 3.2 36.8 + - - +
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Residues in contact with GLU 544 (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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541B MET* 3.0 45.4 + - + +
543B ASP* 1.3 87.4 - - + +
545B ILE* 1.3 59.0 + - + +
547B LYS* 3.5 33.7 + - - +
548B LEU* 3.1 28.9 + - - +
652B THR 4.6 5.9 - - - +
653B ILE* 5.0 11.1 - - + +
654B LYS* 3.7 24.9 + - - -
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Residues in contact with ILE 545 (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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538B VAL* 4.7 2.2 - - + +
541B MET* 3.0 26.9 + - + +
542B ASP 3.9 3.8 - - - +
544B GLU* 1.3 75.7 - - - +
546B GLN* 1.3 64.4 + - - +
548B LEU* 4.3 4.5 - - - -
549B ALA* 3.2 19.6 + - - +
653B ILE* 4.4 20.4 - - + -
670B PRO* 3.6 25.4 - - + +
673B LEU* 3.3 39.7 - - + -
674B LEU* 3.3 42.1 - - + +
677B HIS* 3.7 5.0 - - + -
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Residues in contact with GLN 546 (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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542B ASP* 2.8 25.4 + - - +
543B ASP* 3.1 8.3 + - - +
545B ILE* 1.3 76.7 - - - +
547B LYS* 1.3 58.0 + - + +
549B ALA* 3.3 20.1 - - - +
550B THR* 3.5 13.3 + - + +
677B HIS* 3.6 34.8 - - + +
681B LEU* 4.2 2.2 - - + +
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Residues in contact with LYS 547 (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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543B ASP* 3.2 32.1 + - - +
544B GLU* 3.5 39.0 + - - +
546B GLN* 1.3 75.6 - - + +
548B LEU* 1.3 65.1 + - - +
549B ALA 3.3 0.7 - - - -
550B THR* 2.8 26.7 + - - +
551B GLU* 3.6 14.9 + - - +
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Residues in contact with LEU 548 (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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544B GLU 3.1 19.2 + - - +
545B ILE 3.9 0.9 - - - +
546B GLN 3.4 0.2 - - - -
547B LYS* 1.3 75.3 - - + +
549B ALA* 1.3 65.5 + - - +
551B GLU* 3.4 23.1 + - - +
552B LEU* 3.3 33.5 + - + +
608B ILE* 5.4 3.6 - - + -
635B VAL* 3.6 25.1 - - + -
651B ARG* 3.8 22.9 - - + +
653B ILE* 3.4 32.3 - - + -
674B LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 549 (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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545B ILE 3.2 6.3 + - - +
546B GLN 3.3 11.9 - - - +
547B LYS 3.3 0.2 - - - -
548B LEU* 1.3 79.4 - - - +
550B THR* 1.3 56.3 + - - +
552B LEU 3.2 1.0 + - - -
553B TYR* 3.0 24.1 + - - -
674B LEU* 3.6 10.2 - - + +
677B HIS* 3.6 23.3 - - + -
678B LEU* 3.1 29.8 - - + +
681B LEU* 3.5 16.0 - - + +
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Residues in contact with THR 550 (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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546B GLN* 3.5 12.5 + - + +
547B LYS* 2.8 25.6 + - - +
549B ALA* 1.3 73.6 - - - +
551B GLU* 1.3 66.2 + - - +
553B TYR* 3.4 18.6 - - - +
554B HIS* 5.1 1.7 + - - -
681B LEU* 3.3 34.8 - - + -
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Residues in contact with GLU 551 (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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547B LYS* 3.6 13.0 + - - +
548B LEU* 3.4 24.9 + - - +
549B ALA 3.3 0.6 - - - -
550B THR* 1.3 80.2 + - - +
552B LEU* 1.3 59.9 + - + +
553B TYR 3.3 3.3 + - - -
554B HIS* 4.7 3.1 + - - +
555B GLN* 4.2 11.1 + - - +
651B ARG* 3.2 43.7 + - - +
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Residues in contact with LEU 552 (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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548B LEU* 3.3 24.7 + - + +
549B ALA 3.2 7.4 + - - +
551B GLU* 1.3 79.6 - - + +
553B TYR* 1.3 63.2 + - - +
554B HIS 3.4 2.0 - - - -
555B GLN* 3.6 26.9 + - + +
558B VAL* 5.1 7.2 - - + -
583B MET* 4.2 7.4 - - + +
606B PRO* 3.9 29.4 - - + -
608B ILE* 4.7 12.1 - - + -
635B VAL* 5.7 3.4 - - + -
651B ARG* 4.4 15.3 - - - +
674B LEU* 4.0 26.5 - - + -
678B LEU* 3.2 20.7 - - + +
682B ARG* 3.8 5.7 + - - -
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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