Contacts of the helix formed by residues 542 - 553 (chain B) in PDB entry 3IW4
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 ASP 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A VAL* 5.0 2.0 - - - -
540B GLY 4.0 2.2 - - - -
541B GLU* 1.3 82.1 - - + +
543B GLU* 1.3 66.0 + - - +
544B ASP* 3.0 18.6 + - - +
545B GLU* 2.8 37.2 + - - +
546B LEU* 2.8 23.2 + - - +
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Residues in contact with GLU 543 (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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498B PHE* 4.2 11.8 - - - -
502B PRO* 3.6 24.0 - - + +
542B ASP* 1.3 75.3 - - - +
544B ASP* 1.3 65.3 + - - +
546B LEU* 3.0 11.5 + - - +
547B PHE* 2.8 66.1 + - + -
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Residues in contact with ASP 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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542B ASP* 3.0 17.8 + - - +
543B GLU* 1.3 80.4 + - - +
545B GLU* 1.3 57.8 + - - +
547B PHE* 3.1 8.5 + - - +
548B GLN* 2.9 32.8 + - - +
609C GLU* 5.5 7.4 - - - +
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Residues in contact with GLU 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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539B ASP 4.6 0.7 - - - +
540B GLY* 3.2 8.5 - - - -
541B GLU* 3.1 44.6 - - - +
542B ASP* 2.8 25.7 + - - +
544B ASP* 1.3 72.9 - - - +
546B LEU* 1.3 57.5 + - - +
548B GLN* 3.5 7.8 + - - +
549B SER* 2.9 27.5 + - - -
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Residues in contact with LEU 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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502B PRO* 3.7 17.7 - - + +
503B ASP* 3.5 55.6 - - - +
538B PHE* 4.0 9.2 - - + -
539B ASP* 3.8 34.8 - - - +
540B GLY* 4.0 3.1 - - - +
542B ASP 2.8 18.3 + - - +
543B GLU* 3.2 9.9 - - - +
545B GLU* 1.3 74.0 - - - +
547B PHE* 1.3 60.8 + - + +
549B SER* 3.0 6.4 - - - -
550B ILE* 2.9 32.4 + - + +
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Residues in contact with PHE 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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498B PHE* 3.7 31.0 - + - -
502B PRO* 4.0 25.6 - - + -
505B ILE* 4.3 9.4 - - + -
510B ILE* 3.5 42.3 - - + +
543B GLU* 2.8 55.0 + - + +
544B ASP* 3.7 9.2 - - - +
546B LEU* 1.3 72.6 - - + +
548B GLN* 1.3 65.9 + - - +
550B ILE* 3.1 18.8 + - + +
551B MET* 3.1 21.6 + - + +
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Residues in contact with GLN 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 ASP 2.9 18.3 + - - +
545B GLU* 3.5 8.2 - - - +
547B PHE* 1.3 78.2 - - - +
549B SER* 1.3 62.1 + - - +
551B MET* 3.3 5.8 + - - -
552B GLU* 3.2 62.2 + - - +
607C ASN* 4.2 35.5 + - - +
609C GLU* 5.6 3.8 - - - +
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Residues in contact with SER 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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538B PHE* 3.5 10.9 - - - -
539B ASP* 3.1 41.1 + - - -
545B GLU 2.9 9.2 + - - -
546B LEU 3.0 14.1 - - - -
548B GLN* 1.3 78.2 + - - +
550B ILE* 1.3 54.0 + - - +
553B HIS* 2.7 50.2 + - - +
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Residues in contact with ILE 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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502B PRO 3.8 22.2 - - - +
503B ASP 4.4 7.4 - - - +
505B ILE 3.8 22.2 - - - +
507B PRO* 4.1 21.2 - - + +
510B ILE* 4.0 15.5 - - + -
522B TRP* 4.2 6.8 - - + +
538B PHE* 3.7 31.3 - - + -
546B LEU* 2.9 33.9 + - + +
547B PHE* 3.1 16.5 + - + +
549B SER* 1.3 77.3 - - - +
551B MET* 1.3 58.1 + - - +
575B LYS* 3.0 20.1 + - - +
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Residues in contact with MET 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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507B PRO* 3.9 35.7 - - + +
510B ILE* 3.2 32.3 - - + -
511B ALA* 4.5 4.9 - - - +
547B PHE* 3.1 19.2 + - + +
548B GLN* 3.3 6.0 + - - +
550B ILE* 1.3 75.1 - - - +
552B GLU* 1.3 65.4 + - + +
575B LYS* 2.8 23.4 + - + +
664C VAL* 4.8 0.7 - - - +
665C HIS 4.9 1.7 - - - +
666C PRO 5.5 0.2 - - - +
667C ILE* 3.0 45.7 - - + +
668C LEU* 4.4 12.1 - - + +
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Residues in contact with GLU 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 GLN* 3.2 49.0 + - - +
551B MET* 1.3 88.8 - - + +
553B HIS* 1.3 61.8 + - - +
554B ASN* 3.7 3.7 + - - -
575B LYS* 3.4 3.4 - - - -
607C ASN 5.6 0.5 - - - +
608C ARG* 6.0 1.6 - - - -
662C GLN* 3.5 12.1 + - - -
664C VAL* 3.5 41.4 - - + +
665C HIS 5.0 1.1 + - - +
667C ILE* 3.5 24.6 - - + +
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Residues in contact with HIS 553 (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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537B PRO 3.7 23.1 + - - -
538B PHE* 3.7 15.6 - - + -
539B ASP* 5.7 6.6 + - - -
549B SER* 2.7 35.1 + - - +
552B GLU* 1.3 79.3 - - - +
554B ASN* 1.3 78.1 + - - +
555B VAL* 3.7 6.8 + - - +
556B SER* 4.2 13.7 + - - -
575B LYS* 2.9 22.9 + - - +
662C GLN* 3.4 29.0 + - + +
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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