Contacts of the helix formed by residues 551 - 556 (chain A) in PDB entry 4BSN
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 TYR 551 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ILE* 3.1 41.0 + - + +
502A GLY* 4.6 2.0 - - - -
504A ILE* 3.6 13.0 - - - +
505A SER* 3.3 30.6 + - - -
506A GLY 5.1 0.2 - - - -
508A MET* 6.0 0.7 - - - -
513A GLU* 3.3 40.4 + - + -
516A PHE* 5.6 4.1 - + - -
517A LEU* 3.6 33.0 - - + -
547A ILE 3.5 18.2 - - - +
548A VAL* 3.1 12.6 + - - +
550A GLN* 1.3 83.4 - - + +
552A PRO* 1.3 62.9 - - - +
553A ARG* 3.3 5.2 - - + +
554A PHE* 3.7 4.8 + - + +
555A LEU* 3.2 25.4 + - + +
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Residues in contact with PRO 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A GLY 3.9 12.6 - - - +
550A GLN 3.3 9.2 - - - +
551A TYR* 1.3 86.8 - - - +
553A ARG* 1.3 68.4 + - + +
554A PHE 3.2 1.1 - - - -
555A LEU* 3.3 5.0 + - + +
556A ARG* 3.1 49.0 + - - +
590A LYS 5.4 3.4 - - - +
591A ILE* 6.2 0.9 - - - -
594A LYS* 3.6 26.0 - - + -
595A CYS* 4.3 10.5 - - - -
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Residues in contact with ARG 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A GLY* 4.8 16.2 + - - +
508A MET 2.7 30.1 + - - -
509A HIS* 3.4 2.0 - - - +
510A GLU* 3.3 31.7 - - - +
513A GLU* 2.6 31.7 + - - +
551A TYR* 5.1 3.8 - - + -
552A PRO* 1.3 84.2 - - + +
554A PHE* 1.3 62.6 + - + +
556A ARG* 3.9 22.2 - - - +
557A ALA* 3.9 15.8 + - - +
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Residues in contact with PHE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A GLU* 4.7 9.2 - - + +
514A LYS* 3.6 35.4 - - + -
517A LEU* 3.7 33.4 - - + -
518A VAL* 4.3 15.9 - - + -
521A ILE* 5.1 1.6 - - + -
551A TYR* 3.7 9.3 + - + +
552A PRO 3.2 0.4 - - - -
553A ARG* 1.3 81.5 - - - +
555A LEU* 1.3 74.9 + - + +
556A ARG 3.3 0.4 - - - -
557A ALA* 3.3 14.9 + - + +
558A HIS* 3.5 44.5 + + - -
561A PHE* 3.6 40.6 - + - -
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ILE* 6.5 0.9 - - + -
548A VAL* 4.0 31.6 - - + +
551A TYR* 3.2 18.8 - - + +
552A PRO* 3.3 6.8 + - + +
554A PHE* 1.3 93.3 - - + +
556A ARG* 1.3 58.1 + - - +
557A ALA 3.1 5.4 - - - -
558A HIS* 2.8 25.3 - - - +
559A TRP* 4.7 0.5 - - - -
561A PHE* 4.6 7.4 - - + -
562A LEU* 3.7 44.0 - - + +
565A VAL* 4.5 19.7 - - + -
591A ILE* 4.6 12.3 - - + -
595A CYS* 4.1 6.7 - - - -
598A HIS* 5.1 0.5 + - - -
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Residues in contact with ARG 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A PRO* 3.1 29.4 + - - +
553A ARG* 3.9 22.8 - - - +
554A PHE 3.3 0.2 - - - -
555A LEU* 1.3 75.7 - - - +
557A ALA* 1.3 58.5 + - - +
558A HIS 3.5 0.2 - - - -
594A LYS* 3.3 48.3 + - - +
595A CYS* 3.6 20.6 - - + +
597A ARG* 5.9 4.3 - - - -
598A HIS* 2.5 48.9 + - + -
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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