Contacts of the strand formed by residues 546 - 552 (chain C) in PDB entry 4AY6
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 546 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539C LEU* 4.3 11.3 - - + +
544C GLY 4.0 1.0 + - - -
545C ARG* 1.3 72.3 - - - +
547C ARG* 1.3 59.4 + - - +
548C VAL* 3.5 9.0 + - + -
575C LYS 2.9 14.3 + - - +
576C PHE* 3.3 31.7 - - + +
577C GLU 2.9 21.0 + - - -
624C HIS* 3.4 35.0 - - + -
625C ILE* 4.0 13.0 - - + -
1010C TYR* 3.9 25.8 - - + +
1011C LEU* 4.3 13.0 - - + -
1014C TRP* 4.2 24.0 - - + -
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Residues in contact with ARG 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C LEU* 3.7 12.5 + - - +
542C SER* 3.2 37.1 - - - +
545C ARG 4.2 0.4 - - - +
546C LEU* 1.3 71.7 - - - +
548C VAL* 1.3 60.6 + - - +
577C GLU* 2.9 36.9 + - + +
579C PHE* 3.9 17.7 - - + -
621C ASP 2.8 27.3 + - - -
622C GLY* 3.2 24.2 + - - +
623C ILE* 3.4 7.8 - - - +
624C HIS* 2.9 42.4 + - + +
625C ILE 3.2 7.8 + - - -
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Residues in contact with VAL 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 4.1 17.0 - - + +
547C ARG* 1.3 75.4 - - - +
549C GLY* 1.3 63.3 + - - +
550C TYR* 4.0 16.4 - - + -
571C HIS* 5.3 3.1 - - + +
576C PHE* 4.2 13.2 - - + -
577C GLU 3.1 6.7 + - - +
578C VAL* 3.6 6.2 - - + +
579C PHE* 2.7 27.7 + - - +
623C ILE* 4.4 1.6 - - - -
625C ILE* 3.3 17.0 - - + +
627C VAL* 3.7 22.7 - - + -
1010C TYR* 4.0 34.5 - - + -
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Residues in contact with GLY 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C VAL* 1.3 77.0 - - - +
550C TYR* 1.3 65.1 + - - -
579C PHE* 3.1 14.4 - - - -
581C TYR* 4.1 10.1 - - - -
623C ILE* 3.9 4.1 - - - +
625C ILE 2.8 12.8 + - - -
626C LEU* 3.5 13.0 - - - +
627C VAL* 2.8 29.3 + - - +
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Residues in contact with TYR 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C VAL* 4.0 11.9 - - + -
549C GLY* 1.3 73.5 - - - -
551C VAL* 1.3 62.7 + - - +
552C SER 4.1 0.4 - - - -
555C PHE* 4.2 12.7 - - + -
564C MET* 5.6 3.4 - - + -
567C ILE* 4.4 4.6 - - + +
568C PRO* 5.3 6.7 - - + -
571C HIS* 2.9 27.7 + + - -
578C VAL* 3.7 31.9 - - + -
579C PHE 2.7 12.8 + - - +
580C CYS* 3.6 7.8 - - - -
581C TYR* 2.8 28.1 + - - +
627C VAL* 3.8 17.0 - - + -
629C MET* 4.0 13.5 - - - -
652C TRP* 3.6 33.4 - + - -
1006C LEU* 3.7 5.8 - - + +
1010C TYR* 2.9 32.8 + - - -
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Residues in contact with VAL 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C TYR* 1.3 81.1 - - - +
552C SER* 1.3 61.6 + - - +
581C TYR* 3.6 17.9 - - + +
583C LEU* 3.8 31.8 - - + +
618C ILE* 5.4 3.6 - - + -
626C LEU* 3.8 31.2 - - + -
627C VAL 3.0 15.9 + - - +
628C ASN* 4.1 1.9 - - - +
629C MET* 3.2 25.0 + - - -
630C ASN* 4.2 4.0 + - - +
637C ARG 5.8 0.2 - - - +
640C LEU* 4.3 12.8 - - + -
641C PHE* 4.0 16.5 - - + -
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Residues in contact with SER 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C VAL* 1.3 77.1 - - - +
553C SER* 1.3 59.1 + - - +
554C ASP* 2.9 32.7 + - - +
555C PHE* 3.7 27.2 - - - -
560C THR* 4.1 7.6 - - - +
581C TYR 3.3 8.7 + - - +
582C ALA* 3.6 3.5 - - - -
583C LEU* 2.9 26.5 + - - -
629C MET* 4.0 17.2 - - - +
630C ASN* 3.4 6.3 + - - -
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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