Contacts of the strand formed by residues 619 - 629 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A MET* 5.3 0.4 - - + -
539A LYS* 4.4 13.2 + - - +
540A TYR 3.4 2.7 - - - -
542A LEU* 3.8 42.4 - - + -
574A ILE* 4.5 5.8 - - + -
613A PHE* 3.2 28.9 - - + +
614A SER* 3.8 21.1 - - - +
616A MET* 4.6 1.1 - - + -
617A GLY 3.4 3.1 + - - +
618A PHE* 1.3 102.8 - - + +
620A ASP* 1.3 68.3 - - - +
621A ASN* 3.2 8.5 + - - +
624A ILE* 4.1 5.2 - - + -
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Residues in contact with ASP 620 (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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539A LYS* 4.5 17.6 - - + +
540A TYR 2.8 24.8 + - - +
619A VAL* 1.3 69.7 - - - +
621A ASN* 1.3 59.5 + - - +
622A LYS* 3.0 38.8 + - - +
623A ARG* 3.0 65.7 + - + +
624A ILE* 3.6 5.5 - - - +
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Residues in contact with ASN 621 (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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614A SER* 3.9 28.9 + - - +
619A VAL 3.2 6.8 + - - -
620A ASP* 1.3 72.3 + - - +
622A LYS* 1.3 80.0 + - - +
623A ARG 3.4 0.6 + - - -
624A ILE* 4.1 15.1 - - - +
646A VAL 4.3 14.0 - - - +
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Residues in contact with LYS 622 (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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539A LYS* 6.4 0.2 - - - +
620A ASP* 3.0 24.9 + - - +
621A ASN* 1.3 93.5 + - - +
623A ARG* 1.3 65.0 + - + +
624A ILE 3.9 1.3 - - - -
648A LYS* 3.6 21.8 - - - +
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Residues in contact with ARG 623 (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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539A LYS 4.5 7.7 + - - -
541A PRO* 3.3 39.4 - - + +
542A LEU 3.1 23.2 + - - +
620A ASP* 3.0 35.2 + - - +
622A LYS* 1.3 87.0 - - + +
624A ILE* 1.3 60.8 + - - +
648A LYS* 4.7 4.3 - - + -
762A CYS 4.6 3.4 - - - +
763A PHE* 2.8 66.5 + - + +
764A SER* 5.0 5.0 + - - -
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Residues in contact with ILE 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 3.2 28.9 - - + +
610A ALA* 4.3 10.1 - - + +
613A PHE 5.4 0.2 - - - -
614A SER* 3.6 32.3 - - - -
619A VAL* 4.1 8.5 - - + -
620A ASP 3.6 10.8 - - - +
621A ASN* 4.1 14.1 + - - +
622A LYS 3.9 1.6 - - - -
623A ARG* 1.3 78.8 - - - +
625A ALA* 1.3 62.5 + - - +
646A VAL* 4.0 19.7 + - + +
647A PHE* 3.3 31.1 - - + -
648A LYS* 2.8 34.0 + - - +
763A PHE* 4.1 1.8 - - - -
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Residues in contact with ALA 625 (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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542A LEU 2.8 7.0 + - - +
543A LEU* 3.3 16.6 - - + -
544A LEU* 2.7 30.5 + - - +
624A ILE* 1.3 75.0 - - - +
626A ILE* 1.3 58.3 + - - +
647A PHE* 3.7 4.6 - - - -
649A CYS* 3.4 34.1 - - - +
759A ILE* 4.3 7.0 - - + -
763A PHE* 3.6 18.8 - - + -
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Residues in contact with ILE 626 (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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543A LEU* 4.0 2.2 - - - -
544A LEU* 3.4 31.0 - - + +
546A VAL* 3.8 16.4 - - + -
606A GLN* 5.2 0.4 - - + -
625A ALA* 1.3 77.3 - - - +
627A TRP* 1.3 62.1 + - - +
635A VAL* 5.2 1.1 - - + -
636A THR* 3.6 19.1 - - + +
639A VAL* 3.9 32.8 - - + -
640A LEU* 3.9 25.4 - - + -
647A PHE* 3.6 27.1 - - + -
649A CYS 3.3 2.1 + - - +
650A GLY* 2.9 26.7 - - - -
651A ILE 3.0 1.9 + - - -
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Residues in contact with TRP 627 (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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543A LEU* 3.7 31.4 - - + +
544A LEU 3.1 6.0 + - - +
545A ASP* 3.5 34.3 + - - +
546A VAL* 3.2 24.9 + - - +
563A TRP* 3.6 30.8 - + + -
575A VAL* 5.5 0.8 - - - +
626A ILE* 1.3 75.4 - - - +
628A GLY* 1.3 76.9 + - - +
629A TRP* 3.9 26.5 - + + -
636A THR* 3.2 6.1 - - - -
651A ILE* 3.1 28.7 - - + +
653A VAL* 4.1 6.3 - - + -
752A TYR* 4.1 23.3 - + - -
755A MET* 4.1 23.1 - - + -
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Residues in contact with GLY 628 (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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545A ASP* 5.0 1.1 - - - -
546A VAL 3.5 8.7 - - - -
627A TRP* 1.3 89.1 - - - +
629A TRP* 1.3 58.6 + - - -
632A GLY 3.4 17.0 - - - -
633A GLY* 3.3 11.6 - - - -
636A THR* 3.2 4.2 + - - -
651A ILE 3.2 2.7 + - - +
652A ALA* 3.8 1.2 - - - -
653A VAL* 3.1 25.3 + - - +
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Residues in contact with TRP 629 (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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546A VAL 4.2 2.0 + - - -
547A TYR* 3.6 10.6 - - + -
627A TRP* 3.9 23.5 - + + -
628A GLY* 1.3 73.9 - - - -
630A SER* 1.3 94.5 + - - +
631A TYR 3.2 0.5 + - - -
632A GLY* 2.9 16.8 + - - -
633A GLY 3.5 0.6 - - - +
653A VAL* 3.4 36.4 - - + +
654A ALA* 4.2 4.2 - - - +
740A HIS* 3.0 23.0 + + - -
741A GLY* 3.2 33.6 - - - -
742A ILE* 3.7 16.4 - - + -
748A HIS* 6.2 0.4 - - - -
751A ILE* 4.2 13.9 - - + -
752A TYR* 3.7 29.2 - + - -
755A MET* 5.0 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