Contacts of the strand formed by residues 530 - 538 (chain A) in PDB entry 2YD0
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 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A MET* 3.7 44.4 - - + -
411A ASP* 4.0 9.0 - - - -
412A ALA* 4.0 15.9 - - + -
524A TRP* 4.6 0.7 - - - -
529A GLY* 1.3 79.9 - - - +
531A PRO* 1.3 80.8 - - + +
548A HIS* 3.7 3.7 - - - -
549A TYR* 3.0 58.5 + + + +
563A TRP* 3.7 10.7 - - - -
607A TYR* 3.7 27.6 - + + +
608A TYR* 4.4 0.7 - - - -
609A ILE* 3.8 22.9 - - + -
645A GLN* 3.9 11.9 - - - -
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Residues in contact with PRO 531 (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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524A TRP* 3.5 25.1 - - + -
530A PHE* 1.3 94.6 - - + +
532A LEU* 1.3 62.4 + - - +
533A ILE* 4.3 8.5 - - + -
546A GLN* 4.5 5.8 - - + +
547A GLU 3.4 11.9 - - - +
549A TYR* 4.4 0.4 - - - -
563A TRP* 3.4 29.4 - - + -
565A VAL* 4.2 14.6 - - + -
607A TYR 3.9 3.1 - - - +
608A TYR* 3.4 15.6 - - + +
609A ILE 3.3 22.0 + - - -
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Residues in contact with LEU 532 (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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530A PHE 4.0 1.0 + - - -
531A PRO* 1.3 70.9 - - - +
533A ILE* 1.3 62.0 + - - +
534A THR* 3.8 17.1 + - - +
545A LYS 3.5 0.7 - - - +
546A GLN* 3.4 4.7 - - - -
547A GLU* 2.8 49.0 + - + +
549A TYR* 4.0 14.1 - - + +
609A ILE* 3.5 26.7 - - + +
611A HIS* 4.0 12.6 - - + +
646A LEU* 3.5 26.9 - - + -
649A ILE* 4.0 26.0 - - + -
651A LYS* 4.2 18.6 - - + -
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Residues in contact with ILE 533 (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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531A PRO* 4.3 9.4 - - + -
532A LEU* 1.3 76.0 - - - +
534A THR* 1.3 62.0 + - - +
535A ILE* 4.0 23.6 - - + -
544A MET* 4.7 0.7 - - + -
545A LYS 3.1 10.8 - - - +
546A GLN* 3.7 26.5 - - + -
565A VAL* 4.4 9.2 - - + -
567A LEU* 3.7 36.1 - - + -
582A LEU* 4.1 10.5 - - + -
600A PHE* 5.3 1.1 - - + -
608A TYR* 3.8 20.6 - - + -
609A ILE 2.8 9.4 + - - +
610A VAL* 3.2 10.6 - - + +
611A HIS 3.0 22.9 + - - -
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Residues in contact with THR 534 (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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532A LEU* 3.8 19.8 + - - +
533A ILE* 1.3 73.2 - - - +
535A ILE* 1.3 64.7 + - - +
536A THR* 4.0 2.4 + - - +
543A HIS 3.5 5.2 - - - +
544A MET* 3.6 0.9 - - - -
545A LYS* 2.9 62.2 + - + +
547A GLU* 4.5 3.1 + - - -
611A HIS* 3.5 20.3 - - + +
613A GLU* 3.5 36.6 - - + +
651A LYS* 5.7 1.7 + - - -
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Residues in contact with ILE 535 (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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533A ILE* 4.0 12.6 - - + -
534A THR* 1.3 70.8 - - - +
536A THR* 1.3 65.0 + - - +
537A VAL* 4.1 21.5 + - + +
542A VAL* 4.1 13.2 - - + -
543A HIS 3.5 1.3 - - - -
544A MET* 3.8 19.7 - - + -
598A ILE* 4.7 1.8 - - + -
600A PHE* 3.7 43.3 - - + -
610A VAL* 3.6 24.7 - - + -
611A HIS 2.9 7.9 + - - -
612A TYR* 3.6 20.9 - - + +
613A GLU* 3.0 26.6 + - - +
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Residues in contact with THR 536 (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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534A THR* 4.7 3.1 + - - +
535A ILE* 1.3 71.9 - - - +
537A VAL* 1.3 60.4 + - - +
538A ARG* 3.4 46.0 - - + +
541A ASN 3.9 0.9 - - - +
542A VAL* 3.6 2.4 - - - +
543A HIS* 2.8 55.2 + - + +
613A GLU* 3.2 25.6 - - + +
614A ASP* 3.7 7.6 - - - +
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Residues in contact with VAL 537 (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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535A ILE* 4.1 12.8 + - + +
536A THR* 1.3 78.8 - - - +
538A ARG* 1.3 76.2 + - - +
539A GLY 3.5 20.7 + - - +
541A ASN 3.6 6.7 - - - +
542A VAL* 4.5 13.5 - - + -
591A LEU* 5.6 0.2 - - + -
595A VAL* 4.9 14.4 - - + -
598A ILE* 3.9 26.9 - - + -
612A TYR* 6.2 0.2 - - + -
613A GLU 5.9 0.6 + - - -
614A ASP* 5.1 2.4 + - - +
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Residues in contact with ARG 538 (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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536A THR* 3.4 24.4 - - + +
537A VAL* 1.3 81.8 + - - +
539A GLY* 1.3 64.9 + - - +
540A ARG 3.3 0.7 + - - -
541A ASN* 3.1 32.7 + - + +
543A HIS* 4.5 16.8 - - + +
614A ASP* 2.9 38.1 + - - -
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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