Contacts of the strand formed by residues 570 - 578 (chain A) in PDB entry 2YA6
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 ILE 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A VAL* 3.6 28.9 - - + -
408A ASP* 3.8 20.2 - - + +
415A PHE* 4.1 16.6 - - + -
559A ILE 3.6 7.9 - - - +
560A VAL* 3.9 15.7 - - + -
568A GLY 4.1 6.3 - - - +
569A ARG* 1.3 73.5 - - - +
571A LEU* 1.3 61.0 + - - +
572A ILE* 4.0 6.7 + - + -
593A TYR* 3.0 29.3 - - - +
594A SER* 2.9 14.1 + - - +
597A HIS* 4.0 3.8 - - - -
598A GLY* 3.8 29.4 - - - +
601A TRP* 3.9 18.7 - - + -
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Residues in contact with LEU 571 (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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558A GLY* 3.5 7.1 - - - -
559A ILE* 2.8 40.5 + - + +
561A LEU* 3.8 30.1 - - + -
569A ARG* 3.6 33.7 - - + -
570A ILE* 1.3 72.0 - - - +
572A ILE* 1.3 64.0 + - - +
573A PRO* 4.0 1.5 - - - +
591A VAL* 4.3 17.7 - - + -
592A ILE 3.8 1.1 - - - -
593A TYR* 3.7 9.0 - - + -
635A VAL* 3.8 28.8 - - + +
643A VAL* 4.0 15.5 - - + -
662A GLY 3.8 9.6 - - - +
663A GLY* 4.6 0.7 - - - -
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Residues in contact with ILE 572 (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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404A VAL* 3.8 36.3 - - + +
406A VAL* 3.8 26.5 - - + -
417A ILE* 3.8 22.7 - - + -
553A VAL* 4.3 11.0 - - + -
570A ILE* 4.0 3.4 - - + -
571A LEU* 1.3 82.5 - - - +
573A PRO* 1.3 76.9 - - - +
574A VAL* 3.4 1.9 + - + -
591A VAL* 3.2 3.6 - - - +
592A ILE* 2.9 47.4 + - + +
601A TRP* 3.7 24.9 - - + -
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Residues in contact with PRO 573 (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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404A VAL* 4.5 2.5 - - + -
553A VAL* 3.5 3.5 - - - +
554A GLY* 2.8 35.8 + - - +
557A THR 5.5 2.5 - - - +
558A GLY* 4.4 9.9 - - - -
571A LEU 4.0 5.8 - - - +
572A ILE* 1.3 93.4 - - + +
574A VAL* 1.3 59.3 + - - +
590A ARG 3.6 7.6 - - - +
591A VAL* 4.1 3.4 - - + -
633A SER* 3.3 40.2 - - - +
634A THR* 4.4 1.1 - - - -
635A VAL* 3.8 30.3 - - + +
645A LEU* 4.8 0.4 - - + -
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Residues in contact with VAL 574 (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 LEU* 4.5 7.2 - - + -
551A LEU* 3.8 21.5 - - + -
552A GLY 3.1 17.3 - - - +
553A VAL* 4.1 6.1 - - + +
554A GLY* 3.8 2.2 - - - +
572A ILE* 3.8 11.9 - - + +
573A PRO* 1.3 79.6 - - - +
575A TYR* 1.3 68.0 + - - +
589A SER* 3.5 2.9 - - - -
590A ARG* 2.9 60.0 + - + +
592A ILE* 4.0 33.2 - - + +
631A THR 4.3 1.9 - - - +
633A SER* 4.8 1.7 + - - -
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Residues in contact with TYR 575 (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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402A ASP* 4.8 1.4 + - - -
427A ILE* 5.1 1.1 - - + -
550A PHE* 3.5 32.4 - + - -
551A LEU* 3.4 2.9 - - - +
552A GLY 2.9 33.3 + - - +
553A VAL 3.3 26.2 - - - -
574A VAL* 1.3 79.2 - - - +
576A THR* 1.3 65.5 + - - +
587A GLN* 3.6 32.5 - - + -
588A SER 3.1 17.7 - - - +
590A ARG* 4.7 0.4 - - - +
631A THR* 3.4 34.3 - - - +
632A GLU* 3.6 19.6 + - + +
1777A DAN 2.7 40.1 + - - -
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Residues in contact with THR 576 (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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547A TRP* 3.5 19.5 - - - -
548A MET* 3.7 35.7 - - + -
550A PHE* 2.9 11.2 - - - +
551A LEU* 3.8 14.4 - - + -
575A TYR* 1.3 78.9 - - - +
577A THR* 1.3 70.2 + - - +
586A SER 3.3 1.0 + - - +
587A GLN* 3.2 7.8 - - - +
588A SER* 3.1 39.2 + - - -
590A ARG* 4.1 15.4 + - - +
620A SER* 4.5 0.5 + - - -
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Residues in contact with THR 577 (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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547A TRP* 3.6 12.0 - - - -
548A MET* 3.8 0.3 - - - -
549A LYS* 2.8 23.7 + - - +
550A PHE* 2.9 33.5 + - + +
576A THR* 1.3 81.0 - - - +
578A ASN* 1.3 60.9 + - - +
582A HIS* 2.7 39.3 + - - +
583A LEU* 4.0 9.4 - - + -
586A SER* 3.3 12.6 - - - +
587A GLN* 3.8 24.5 - - + -
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Residues in contact with ASN 578 (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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547A TRP* 3.8 12.3 - - + +
549A LYS* 3.8 9.4 - - - +
577A THR* 1.3 75.0 - - - +
579A ASN* 1.3 58.7 + - - +
580A VAL* 2.8 26.4 + - - +
581A SER 3.0 12.3 + - - -
582A HIS* 3.0 27.5 + - - +
586A SER* 2.9 17.5 + - - -
620A SER 2.9 25.1 + - - +
621A SER 3.2 22.6 - - - +
622A THR 3.4 0.8 - - - -
623A MET 3.1 32.2 + - - +
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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