Contacts of the strand formed by residues 579 - 584 (chain A) in PDB entry 3APO
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 TRP 579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A VAL* 4.1 22.9 - - + -
561A LEU* 4.1 17.0 - - + -
569A LEU* 3.2 43.8 + - + -
570A VAL* 3.7 30.5 - - + -
573A ARG* 4.1 19.5 - - + +
577A GLU* 5.1 1.6 + - - +
578A VAL* 1.3 83.4 - - - +
580A MET* 1.3 64.9 + - - +
581A VAL* 4.3 2.9 - - + -
609A ILE* 4.4 0.9 - - - -
610A ASN* 3.3 37.8 + - + +
611A VAL 3.5 22.7 - - - -
612A GLY* 3.6 20.2 - - - -
636A PHE* 3.4 4.5 - - - -
637A TYR* 2.7 43.2 + - + +
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Residues in contact with MET 580 (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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579A TRP* 1.3 71.6 - - - +
581A VAL* 1.3 63.9 + - - +
598A TRP* 3.7 32.2 - - + -
601A MET* 3.8 20.2 - - - +
605A LEU* 4.3 7.4 - - - -
609A ILE* 3.8 17.3 - - + -
610A ASN 2.9 10.2 + - - +
611A VAL* 3.5 5.0 - - + -
612A GLY 2.8 26.9 + - - +
634A ILE* 4.4 0.4 - - + -
635A ARG 3.3 6.7 - - - +
636A PHE* 3.7 20.9 - - + -
660A LEU* 3.7 21.3 - - + +
663A TRP* 3.8 22.9 - - + -
664A GLY* 4.0 17.7 - - - -
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Residues in contact with VAL 581 (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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561A LEU* 4.2 17.3 - - + -
566A PHE* 4.6 2.5 - - + -
570A VAL* 4.3 12.6 - - + -
579A TRP* 4.3 5.2 - - + -
580A MET* 1.3 79.8 - - - +
582A ASP* 1.3 62.6 - - - +
583A PHE* 3.5 31.6 + - + -
598A TRP* 3.8 4.2 - - - -
612A GLY 3.5 10.1 - - - +
614A VAL* 3.9 21.3 - - + -
633A GLU 3.3 6.1 - - - +
634A ILE* 3.5 1.7 - - - -
635A ARG 2.9 33.2 + - - -
637A TYR* 3.6 24.0 - - + -
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Residues in contact with ASP 582 (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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581A VAL* 1.3 71.3 - - - +
583A PHE* 1.3 70.3 + - - +
584A TYR* 3.5 15.8 + - - +
591A SER 5.3 1.0 - - - +
594A LEU* 3.4 25.3 - - + +
595A MET* 3.5 22.7 + - - +
598A TRP* 3.5 32.2 - - + +
612A GLY 3.0 8.4 + - - +
613A SER* 3.2 3.5 - - - -
614A VAL 2.7 31.9 + - - -
632A PRO* 3.6 11.4 - - - +
633A GLU 3.8 4.1 - - - +
634A ILE* 4.9 0.9 - - + +
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Residues in contact with PHE 583 (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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566A PHE* 3.9 11.2 - + - -
581A VAL* 3.5 29.2 - - + -
582A ASP* 1.3 72.5 - - - +
584A TYR* 1.3 58.1 + - - +
614A VAL* 3.6 31.9 - - + -
616A CYS* 4.0 9.9 - - - -
622A PHE* 4.3 11.9 - + - -
623A CYS* 4.0 4.9 - - - -
626A GLU* 4.6 7.2 - - + -
628A VAL* 3.7 31.6 - - + -
631A TYR* 4.1 4.8 - - - -
632A PRO* 3.4 4.9 - - - +
633A GLU* 2.9 42.1 + - + +
635A ARG* 3.8 22.2 - - + -
637A TYR* 3.5 25.4 - - - -
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Residues in contact with TYR 584 (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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560A SER* 5.2 3.8 + - - -
582A ASP* 3.5 23.6 - - - +
583A PHE* 1.3 74.8 - - - +
585A SER* 1.3 70.4 + - - +
586A PRO* 4.0 9.9 - - + -
591A SER* 3.6 22.7 - - - +
595A MET* 3.7 24.3 - - + +
613A SER* 3.5 27.0 + - - -
614A VAL 3.0 21.9 + - - +
615A ASP* 3.7 32.0 + - + +
616A CYS* 2.7 35.0 + - - +
631A TYR* 4.1 6.5 - - - -
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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