Contacts of the strand formed by residues 781 - 789 (chain A) in PDB entry 1ZYC
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 LYS 781 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A ARG* 3.4 52.6 + - + +
632A HIS* 3.7 52.5 + - - +
633A THR* 4.1 9.4 - - + +
769A ARG* 4.8 12.8 + - - +
780A LYS* 1.3 78.7 + - - +
782A SER* 1.3 60.7 + - - +
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Residues in contact with SER 782 (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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632A HIS 3.0 33.0 + - - +
634A GLU* 2.9 39.7 + - - +
637A LEU* 3.4 6.1 - - - +
663A LEU* 3.6 13.5 - - - +
664A GLU 4.1 2.0 - - - -
768A ARG* 3.8 20.6 - - - +
769A ARG* 4.8 0.9 - - - +
780A LYS 5.3 0.2 - - - -
781A LYS* 1.3 75.0 - - - +
783A THR* 1.3 66.1 + - - +
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Residues in contact with THR 783 (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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629A LYS* 5.5 5.8 - - + -
630A ILE 3.2 7.4 - - - +
631A ARG* 3.2 41.7 - - + +
663A LEU* 3.3 7.1 - - - +
664A GLU* 2.9 39.7 + - - +
782A SER* 1.3 74.6 - - - +
784A LEU* 1.3 62.3 + - - +
785A PHE* 2.9 34.0 - - + -
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Residues in contact with LEU 784 (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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628A LYS 3.5 3.6 - - - +
629A LYS* 3.6 0.5 - - - -
630A ILE* 2.6 44.5 + - + +
637A LEU* 4.3 17.5 - - + +
640A ILE* 4.2 25.8 - - + -
641A LEU* 3.8 30.3 - - + -
644A VAL* 4.9 3.8 - - + -
661A ALA* 4.1 9.6 - - + -
662A TRP* 3.0 27.6 - - - +
663A LEU* 4.4 5.8 - - + +
782A SER 4.3 0.2 + - - -
783A THR* 1.3 72.9 - - - +
785A PHE* 1.3 70.4 + - - +
786A ILE* 4.1 17.2 - - + +
645B MET* 4.5 1.1 - - - -
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Residues in contact with PHE 785 (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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595A TYR* 3.2 52.5 - + + -
627A ILE* 3.8 13.5 - - + -
628A LYS 3.3 4.5 - - - +
629A LYS* 3.8 22.0 - - + -
661A ALA* 3.0 25.1 - - - +
662A TRP* 2.8 46.8 + + + -
664A GLU* 3.8 20.2 - - + -
783A THR* 2.9 34.3 - - + -
784A LEU* 1.3 75.2 - - - +
786A ILE* 1.3 66.3 + - - +
787A GLN 4.1 0.4 - - - -
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Residues in contact with ILE 786 (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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626A ALA 3.4 1.2 - - - +
627A ILE* 4.4 1.8 - - - +
628A LYS* 3.0 46.0 + - + +
630A ILE* 4.5 5.6 - - + -
644A VAL* 4.1 13.5 - - + -
658A TYR* 3.6 34.5 - - + -
660A ALA 3.4 8.3 - - - +
661A ALA* 3.9 9.2 - - + -
784A LEU* 4.1 21.3 - - + +
785A PHE* 1.3 81.5 - - - +
787A GLN* 1.3 62.7 + - - +
788A MET* 3.2 10.2 + - + +
856A LEU* 3.2 31.4 - - + -
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Residues in contact with GLN 787 (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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594A ARG* 4.4 7.1 - - - +
599A PHE* 3.9 23.1 - - + -
618A ASN* 4.4 3.6 + - - +
625A TYR* 3.3 51.2 - - + -
626A ALA 3.8 3.4 - - - -
627A ILE* 4.5 6.3 - - + -
658A TYR* 3.8 1.2 - - - -
659A TYR* 2.9 34.7 + - + +
660A ALA* 2.7 34.6 + - - +
662A TRP* 4.1 17.5 - - + -
785A PHE 4.1 0.6 - - - -
786A ILE* 1.3 69.6 - - - +
788A MET* 1.3 61.5 + - - +
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Residues in contact with MET 788 (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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613A VAL* 4.4 9.0 - - + -
625A TYR* 3.3 14.7 - - - +
626A ALA* 2.7 55.2 + - + +
627A ILE 4.4 0.4 - - - -
628A LYS* 3.9 24.5 - - + +
656A VAL* 4.9 3.4 - - + -
657A ARG 3.5 7.0 - - - +
658A TYR* 3.4 52.9 - - + -
659A TYR* 3.8 3.8 - - - -
786A ILE 3.6 12.6 - - - +
787A GLN* 1.3 75.0 - - - +
789A GLU* 1.3 72.1 + - - +
853A ASP* 4.7 15.0 - - - +
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Residues in contact with GLU 789 (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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625A TYR* 4.8 0.9 - - - -
626A ALA* 4.2 5.4 - - - +
655A VAL 4.4 0.3 - - - +
656A VAL* 3.3 26.1 - - + +
657A ARG* 2.6 56.0 + - - +
659A TYR* 3.3 26.2 - - + +
788A MET* 1.3 77.9 - - - +
790A TYR* 1.3 72.1 + - - +
791A CYS* 3.8 10.3 + - - -
850A LYS* 3.6 28.4 + - - +
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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