Contacts of the strand formed by residues 735 - 743 (chain A) in PDB entry 5JZU
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 ARG 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A SER* 3.2 26.1 + - - -
669A ILE* 3.3 2.3 - - - -
670A MET* 2.9 63.3 + - - +
694A VAL 3.3 11.2 - - - +
695A ILE* 3.8 12.3 - - + -
696A PRO* 3.8 4.5 - - + -
700A CYS* 3.7 21.3 - - + -
711A TRP* 3.3 44.4 - - - -
727A VAL* 4.4 0.2 - - - +
729A GLN* 3.6 13.0 - - - +
734A PHE* 1.3 76.6 - - - +
736A LEU* 1.3 60.9 + - - +
737A ILE* 3.8 14.2 - - - +
802A OGA 2.4 35.9 + - - -
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Residues in contact with LEU 736 (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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598A ARG* 4.5 9.9 - - + +
601A GLY 4.5 0.7 - - - -
602A LEU* 4.3 17.3 - - + +
605A MET* 4.2 18.2 - - - -
612A PHE* 4.4 8.7 - - + -
667A TYR* 4.3 15.7 - - + -
668A SER 3.6 18.2 - - - +
669A ILE* 3.9 17.0 - - + -
693A LEU* 3.2 32.0 + - + -
694A VAL* 2.9 37.1 + - + +
695A ILE* 3.7 0.5 - - - +
734A PHE* 4.1 15.1 - - + -
735A ARG* 1.3 72.8 - - - +
737A ILE* 1.3 70.8 + - - +
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Residues in contact with ILE 737 (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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667A TYR* 3.5 6.2 - - - +
668A SER* 2.9 45.7 + - - +
690A HIS* 3.6 34.5 - - + +
691A LEU 3.4 14.1 - - - +
693A LEU* 4.0 6.6 - - - +
695A ILE* 3.8 19.3 - - + -
711A TRP* 4.0 17.3 - - + +
735A ARG* 3.8 15.0 - - - +
736A LEU* 1.3 82.7 - - - +
738A PHE* 1.3 60.5 + - - +
739A ILE* 3.9 7.0 - - + -
802A OGA 3.6 26.2 - - - +
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Residues in contact with PHE 738 (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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590A LEU* 4.3 12.1 - - + -
597A ILE* 3.8 17.7 - - + -
630A LEU* 4.0 6.7 - - + -
647A THR* 3.5 23.8 - - + -
651A LEU* 3.8 9.6 - - + -
665A ILE* 3.5 23.6 - - + -
666A LYS 3.8 13.0 - - - -
667A TYR* 3.7 41.3 - + - -
689A MET 3.4 1.4 - - - +
690A HIS* 3.4 4.2 - - - -
691A LEU* 2.8 47.2 + - + +
693A LEU* 3.9 12.6 - - + -
737A ILE* 1.3 74.2 - - - +
739A ILE* 1.3 60.3 + - - +
740A VAL* 3.6 29.0 + - + +
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Residues in contact with ILE 739 (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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627A GLN* 4.1 12.3 - - - +
664A GLN 5.0 0.4 - - - +
665A ILE* 3.3 6.4 - - - +
666A LYS* 2.8 54.7 + - + +
668A SER* 3.6 14.1 - - - -
688A ARG* 3.8 39.5 - - + +
689A MET 3.2 4.0 - - - +
690A HIS* 3.6 13.2 - - + +
737A ILE* 3.9 7.9 - - + -
738A PHE* 1.3 73.5 - - - +
740A VAL* 1.3 66.6 + - - +
741A ASP* 4.0 4.9 - - - +
802A OGA 3.4 38.4 - - - +
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Residues in contact with VAL 740 (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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586A LEU* 4.3 16.4 - - + -
590A LEU* 4.3 14.8 - - + -
651A LEU* 4.7 5.2 - - + -
657A THR* 3.0 36.1 - - + +
664A GLN 4.0 1.6 - - - -
665A ILE* 4.3 7.9 - - + -
689A MET* 2.8 49.5 + - + +
691A LEU* 6.3 0.2 - - + -
738A PHE* 3.6 34.8 - - + +
739A ILE* 1.3 78.8 - - - +
741A ASP* 1.3 63.6 + - - +
742A VAL* 3.9 0.4 + - + -
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Residues in contact with ASP 741 (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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657A THR* 2.7 34.0 + - - +
660A CYS* 3.9 4.0 - - - +
663A GLY* 3.2 14.1 - - - -
664A GLN 2.7 41.6 + - - +
686A ARG* 3.7 12.5 - - - -
687A LEU 3.4 4.9 - - - +
688A ARG* 2.7 55.1 + - - +
739A ILE* 4.0 2.3 - - - +
740A VAL* 1.3 74.2 - - - +
742A VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 742 (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 THR* 6.0 0.2 - - + -
583A TYR* 3.4 33.7 - - + -
586A LEU* 3.6 30.7 - - + -
656A GLU* 3.4 11.0 - - + +
657A THR* 4.0 8.1 - - - -
660A CYS* 3.7 6.3 - - - -
686A ARG* 3.2 5.9 - - - -
687A LEU* 2.9 50.4 + - + +
689A MET* 4.1 17.9 - - + -
718A ILE* 6.0 0.2 - - + -
740A VAL* 4.7 0.7 - - + +
741A ASP* 1.3 80.8 - - - +
743A TRP* 1.3 61.6 + - - +
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Residues in contact with TRP 743 (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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583A TYR* 2.8 24.8 + - - -
655A PRO 4.8 1.3 + - - -
656A GLU* 3.3 25.1 + - - +
659A GLY 3.0 20.1 + - - -
660A CYS* 3.4 12.4 - - - +
661A ARG* 3.3 38.1 - - + -
662A ARG* 4.1 26.2 - - + -
685A CYS 3.6 13.5 - - - -
742A VAL* 1.3 77.4 - - - +
744A HIS* 1.3 61.8 + - - +
745A PRO* 3.1 1.9 - - - +
747A LEU* 3.5 18.8 - - + -
752A ARG* 3.4 74.3 + - + +
755A LEU* 3.9 23.3 - - + -
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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