Contacts of the helix formed by residues 549 - 559 (chain B) in PDB entry 4A8W
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 549 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B PHE* 3.5 39.3 - - + +
547B PRO 3.2 0.8 - - - -
548B GLY* 1.4 70.6 - - - +
550B ALA* 1.3 58.4 + - - +
551B TRP 3.1 2.9 - - - -
552B ALA* 3.0 27.0 + - + +
553B SER* 3.7 5.0 + - - -
591B LEU* 4.0 9.2 - - + -
594B ASP* 3.9 6.1 - - + +
595B THR* 3.6 39.7 - - - +
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Residues in contact with ALA 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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525B GLN* 5.3 8.5 - - + +
546B PHE 4.5 0.8 + - - -
547B PRO 3.5 14.1 + - - +
548B GLY 3.4 1.2 - - - -
549B LEU* 1.3 75.8 - - - +
551B TRP* 1.4 56.4 + - - +
552B ALA 3.3 0.2 - - - -
553B SER* 3.2 11.7 + - - +
554B MET* 3.1 27.9 + - - +
587B ARG* 4.7 5.2 - - - +
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Residues in contact with TRP 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLN* 3.7 13.2 - - - -
548B GLY 3.4 15.2 + - - +
549B LEU 3.1 1.0 - - - -
550B ALA* 1.4 76.6 - - - +
552B ALA* 1.3 61.8 + - - +
554B MET* 3.4 57.4 - - + +
555B LYS* 4.7 1.4 + - - +
568B LEU* 4.1 12.3 - - + -
583B TYR* 3.6 37.2 - + - -
584B ARG* 4.0 26.7 - - + +
587B ARG* 3.4 42.1 - - + +
588B GLU* 4.1 19.6 + - + +
591B LEU* 4.1 18.6 - - + -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B LEU* 3.0 12.9 + - + +
551B TRP* 1.3 79.4 - - - +
553B SER* 1.3 56.9 + - - +
554B MET 3.5 0.2 - - - -
555B LYS* 5.1 3.7 + - - +
556B ASP* 5.4 1.7 + - - +
591B LEU* 3.7 28.3 - - + +
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B LEU 3.7 3.3 + - - -
550B ALA* 3.2 20.6 + - - +
552B ALA* 1.3 77.0 - - - +
554B MET* 1.3 64.8 + - - +
555B LYS 3.5 1.6 - - - -
556B ASP* 3.2 11.4 + - - +
557B THR* 2.9 34.8 + - - -
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Residues in contact with MET 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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521B MET* 3.9 20.4 - - - +
525B GLN* 3.5 22.4 - - - +
550B ALA 3.1 13.2 + - - +
551B TRP* 3.4 56.7 + - + +
553B SER* 1.3 74.7 - - - +
555B LYS* 1.3 56.6 + - + +
557B THR* 3.0 2.9 + - - -
558B TYR* 2.7 44.7 + - + -
564B TYR* 3.3 21.5 - - + +
568B LEU* 3.9 20.9 - - + -
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Residues in contact with LYS 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 TRP 4.7 1.6 + - - +
552B ALA 5.1 4.0 + - - +
553B SER 3.5 0.4 - - - -
554B MET* 1.3 78.7 - - + +
556B ASP* 1.3 59.2 + - - +
559B GLY* 2.8 32.8 + - - -
560B ALA 4.7 0.2 + - - -
564B TYR* 3.4 39.4 + - + +
565B SER* 5.9 1.0 + - - -
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Residues in contact with ASP 556 (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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307B ARG* 4.8 12.8 + - - -
552B ALA 5.4 1.5 + - - +
553B SER* 3.2 14.9 + - - +
555B LYS* 1.3 80.7 - - - +
557B THR* 1.3 64.8 + - - +
559B GLY 4.5 1.0 + - - -
560B ALA* 5.4 2.1 + - - +
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Residues in contact with THR 557 (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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307B ARG* 4.8 7.3 - - - +
499B ASP* 5.0 3.5 - - - +
516B GLY* 3.7 19.7 + - - -
553B SER* 2.9 25.8 + - - -
554B MET 3.7 2.0 - - - -
556B ASP* 1.3 80.6 + - - +
558B TYR* 1.4 91.7 + - + +
560B ALA* 5.3 1.3 + - - +
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Residues in contact with TYR 558 (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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516B GLY* 4.8 3.8 - - - -
517B ASN 3.2 39.9 - - - -
518B ILE* 4.1 5.2 - - + -
520B SER* 3.8 7.7 - - - -
521B MET* 3.6 50.2 + - + -
524B ASN* 3.7 17.2 + - - +
525B GLN* 5.7 0.2 - - - -
554B MET* 2.7 29.2 + - + +
557B THR* 1.4 100.3 - - + +
559B GLY* 1.3 56.5 - - - +
560B ALA* 3.2 3.6 - - - -
561B CYS* 3.0 26.1 + - + +
564B TYR* 3.4 23.4 - - + -
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Residues in contact with GLY 559 (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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555B LYS* 2.8 34.6 + - - -
556B ASP 4.5 0.2 + - - -
557B THR 3.8 0.4 - - - -
558B TYR* 1.3 70.0 - - - +
560B ALA* 1.3 58.4 + - - +
561B CYS 3.3 6.9 + - - +
564B TYR* 3.8 27.4 - - - +
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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