Contacts of the strand formed by residues 619 - 629 (chain D) in PDB entry 5Y7K
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 VAL 619 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528D MET* 5.3 0.2 - - + -
539D LYS* 4.0 13.0 + - - +
540D TYR 3.4 3.6 - - - +
542D LEU* 4.0 29.6 - - + -
574D ILE* 5.0 2.7 - - + -
613D PHE* 3.3 35.2 - - + +
614D SER* 3.8 14.3 - - - +
617D GLY 3.4 3.7 + - - +
618D PHE* 1.3 97.0 - - + +
620D ASP* 1.3 71.8 + - - +
621D ASN* 3.4 11.6 + - - +
624D ILE* 4.0 20.6 - - + -
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Residues in contact with ASP 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D LYS* 4.1 19.9 - - + +
540D TYR 2.7 25.7 + - - +
619D VAL* 1.3 69.3 - - - +
621D ASN* 1.3 67.7 + - - +
622D LYS* 3.3 20.0 + - - +
623D ARG* 3.0 58.1 + - + +
624D ILE* 3.5 6.9 - - - +
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Residues in contact with ASN 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D SER* 3.5 35.8 + - - +
619D VAL 3.4 8.1 + - - +
620D ASP* 1.3 75.3 + - - +
622D LYS* 1.3 62.1 + - + +
623D ARG 3.2 3.9 + - - -
624D ILE* 3.7 20.6 + - - +
646D VAL 4.2 8.8 - - - +
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Residues in contact with LYS 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D ASP* 3.2 14.1 + - - +
621D ASN* 1.3 79.4 - - + +
623D ARG* 1.3 67.2 + - + +
624D ILE 4.0 0.9 - - - -
648D LYS* 3.6 21.1 - - - +
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Residues in contact with ARG 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D LYS 4.4 9.9 + - - -
541D PRO* 3.4 37.8 - - + +
542D LEU 3.0 23.7 + - - +
620D ASP* 3.0 32.1 + - - +
621D ASN 3.2 0.4 - - - -
622D LYS* 1.3 84.6 - - + +
624D ILE* 1.3 61.5 + - - +
648D LYS* 4.9 4.0 - - + -
762D CYS 4.8 3.6 - - - +
763D PHE* 2.6 69.5 + - + +
764D SER* 4.8 5.6 + - - -
765D LEU* 4.2 10.1 - - - +
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Residues in contact with ILE 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542D LEU* 3.3 21.8 - - + +
610D ALA* 4.5 8.1 - - + +
614D SER* 4.5 11.9 - - - -
619D VAL* 4.0 23.6 - - + -
620D ASP 3.5 11.0 - - - +
621D ASN* 3.7 21.2 + - - +
622D LYS 4.0 0.8 - - - -
623D ARG* 1.3 78.8 - - - +
625D ALA* 1.3 61.7 + - - +
646D VAL* 3.8 27.1 + - + +
647D PHE* 3.3 29.8 - - + -
648D LYS* 3.0 30.1 + - - +
763D PHE* 4.1 1.1 - - - -
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Residues in contact with ALA 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542D LEU 2.7 7.0 + - - +
543D LEU* 3.4 16.7 - - + -
544D LEU* 2.7 30.0 + - - +
624D ILE* 1.3 75.0 - - - +
626D ILE* 1.3 58.6 + - - +
647D PHE* 3.7 5.3 - - - -
649D CYS* 3.5 29.2 - - - +
650D GLY* 5.2 0.2 - - - -
759D ILE* 4.3 6.5 - - + -
763D PHE* 3.6 22.2 - - + -
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Residues in contact with ILE 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D LEU* 3.9 2.0 - - - -
544D LEU* 3.3 24.2 - - + +
546D VAL* 3.7 20.0 - - + -
606D GLN* 5.0 1.1 - - + -
625D ALA* 1.3 78.0 - - - +
627D TRP* 1.3 65.4 + - - +
635D VAL* 5.1 0.2 - - + -
636D THR* 3.5 27.6 - - + +
639D VAL* 3.9 34.5 - - + -
640D LEU* 4.0 11.0 - - + -
647D PHE* 3.5 26.2 - - + -
649D CYS 3.5 8.6 + - - +
650D GLY* 3.0 26.9 - - - -
651D ILE 3.2 1.4 + - - -
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Residues in contact with TRP 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D LEU* 3.7 31.1 - - + +
544D LEU 3.0 6.6 + - - +
545D ASP* 3.5 38.7 + - - +
546D VAL* 3.0 24.9 + - - +
563D TRP* 3.6 34.2 - + + -
575D VAL* 5.2 1.6 - - - +
626D ILE* 1.3 76.0 - - - +
628D GLY* 1.3 76.5 + - - +
629D TRP* 4.1 22.2 - + + -
636D THR* 3.3 6.5 - - - -
651D ILE* 3.3 27.8 - - + +
653D VAL* 4.2 7.2 - - + -
752D TYR* 4.2 18.2 - + - -
755D MET* 4.1 28.0 - - + -
759D ILE* 5.8 0.2 - - + -
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Residues in contact with GLY 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D ASP* 4.9 1.8 - - - -
546D VAL 3.4 15.7 - - - -
627D TRP* 1.3 87.7 - - - +
629D TRP* 1.3 58.5 + - - -
632D GLY 3.5 9.2 - - - -
633D GLY* 3.3 13.9 - - - -
636D THR* 3.3 1.8 + - - -
651D ILE 3.3 6.0 + - - +
653D VAL* 3.2 24.8 + - - +
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Residues in contact with TRP 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D VAL 4.2 2.2 + - - -
547D TYR* 3.7 11.1 - - + -
627D TRP* 4.1 19.6 - + + -
628D GLY* 1.3 74.5 - - - -
630D SER* 1.3 91.8 + - - +
631D TYR 3.1 0.5 + - - -
632D GLY* 2.8 18.1 + - - -
653D VAL* 3.4 40.1 - - + +
654D ALA* 4.0 5.7 - - + +
740D HIS* 3.0 20.7 + + - -
741D GLY* 3.1 33.8 - - - -
742D ILE* 3.8 18.8 - - + -
748D HIS* 6.0 1.6 - + - -
751D ILE* 4.0 15.7 - - + -
752D TYR* 3.9 27.4 - + - -
755D MET* 5.1 0.7 - - + -
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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