Contacts of the helix formed by residues 546 - 555 (chain B) in PDB entry 6WG4
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 PHE 546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542B CYS* 4.2 10.5 - - + -
543B GLU* 2.9 40.6 + - + +
545B ALA* 1.3 82.3 - - + +
547B TYR* 1.3 65.7 + - - +
548B THR 3.2 3.4 + - - -
549B CYS* 3.3 9.5 + - - -
550B VAL* 3.0 31.2 + - + +
607B ILE* 5.5 2.5 - - + -
612B LYS* 3.6 50.9 - - + -
632B ILE* 4.2 17.0 - - + -
653B LEU* 3.5 30.7 - - + -
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Residues in contact with TYR 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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540B PHE* 6.2 0.7 - + - -
541B GLU* 5.5 2.4 + - - -
542B CYS* 3.8 36.6 + - - -
544B PRO* 3.2 45.1 + - + +
546B PHE* 1.3 75.9 - - - +
548B THR* 1.3 64.6 + - - +
550B VAL* 3.8 3.0 - - + +
551B GLU* 3.0 45.6 + - + +
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Residues in contact with THR 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 PRO 4.8 0.5 + - - -
545B ALA 4.6 3.3 + - - -
546B PHE 3.3 0.8 - - - -
547B TYR* 1.3 80.5 - - - +
549B CYS* 1.3 59.4 + - - +
551B GLU* 3.4 4.2 + - - +
552B VAL* 3.0 44.8 + - + +
653B LEU 3.9 13.5 + - - -
654B GLU* 4.2 20.9 - - - +
655B GLY* 5.3 0.2 - - - -
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Residues in contact with CYS 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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546B PHE* 3.3 15.0 - - - -
548B THR* 1.3 79.3 - - - +
550B VAL* 1.3 55.9 + - - +
552B VAL* 4.5 0.9 - - - -
553B THR* 2.7 37.1 + - - -
609B MET* 4.4 1.3 - - - -
632B ILE* 3.6 32.8 - - - -
651B ILE* 3.5 17.6 - - + +
652B THR 3.2 26.2 - - - +
653B LEU* 3.7 24.9 + - - -
655B GLY* 4.9 1.6 - - - -
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B PHE* 3.8 31.9 - - + -
542B CYS* 4.2 7.0 - - - -
546B PHE* 3.0 30.0 + - + +
547B TYR* 3.8 4.7 - - + +
549B CYS* 1.3 76.3 - - - +
551B GLU* 1.3 63.6 + - + +
553B THR* 3.4 1.4 + - - -
554B ALA* 2.9 28.8 + - - +
558B LEU* 5.1 3.1 - - + -
609B MET* 3.9 21.1 - - + -
612B LYS* 6.2 0.4 - - + -
613B LEU* 3.8 21.8 - - + -
627B PHE* 3.9 15.6 - - + -
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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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537B MET* 6.1 1.9 - - - +
547B TYR* 3.0 34.7 + - - +
548B THR* 4.1 3.6 - - - +
550B VAL* 1.3 77.4 - - + +
552B VAL* 1.3 58.4 + - + +
554B ALA* 4.2 0.2 - - - +
555B GLY* 3.0 30.3 + - - +
558B LEU* 4.2 28.7 - - + +
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Residues in contact with VAL 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 THR* 3.0 30.2 + - + +
549B CYS* 4.5 0.4 - - - -
551B GLU* 1.3 79.1 - - + +
553B THR* 1.3 62.9 + - - +
555B GLY* 3.8 6.1 + - - -
651B ILE* 3.7 18.6 - - + -
655B GLY* 3.8 18.4 - - - +
657B GLN* 3.3 29.3 + - - +
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Residues in contact with THR 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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549B CYS 2.7 23.8 + - - -
550B VAL 3.9 1.8 - - - -
552B VAL* 1.3 79.6 - - - +
554B ALA* 1.3 63.5 + - - +
555B GLY* 4.7 0.2 - - - -
557B ARG* 3.5 16.7 + - - +
609B MET* 3.5 33.6 - - + +
626B VAL 4.7 6.7 - - - +
627B PHE* 4.5 4.9 - - + -
630B THR* 3.5 19.0 - - + +
651B ILE* 3.3 20.7 - - - +
657B GLN* 5.4 3.8 - - - +
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Residues in contact with ALA 554 (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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550B VAL 2.9 17.9 + - - +
551B GLU 4.2 1.8 - - - +
553B THR* 1.3 76.9 - - - +
555B GLY* 1.3 66.2 + - - +
556B ASN 3.4 0.2 + - - -
557B ARG* 3.2 31.1 + - - +
558B LEU* 3.9 28.3 - - + +
626B VAL* 4.2 9.4 - - + -
627B PHE* 3.6 25.8 - - + -
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Residues in contact with GLY 555 (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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551B GLU 3.0 16.0 + - - +
552B VAL 3.8 5.1 + - - -
553B THR 3.4 2.2 - - - -
554B ALA* 1.3 75.3 - - - +
556B ASN* 1.3 65.2 + - - -
557B ARG* 3.3 1.1 + - - -
558B LEU* 3.4 19.6 + - - +
559B PHE* 4.1 4.7 - - - -
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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