Contacts of the strand formed by residues 725 - 737 (chain A) in PDB entry 3BJY
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 LEU 725 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A ILE* 3.5 17.2 - - + +
632A ARG* 4.9 1.4 - - - -
633A PHE* 4.0 26.6 + - + -
639A VAL* 4.2 8.7 - - + -
668A LEU* 3.8 18.8 - - + -
669A MET 3.8 5.4 - - - +
715A TYR* 3.8 29.6 - - + +
720A CYS* 3.8 13.2 - - - -
721A PRO 3.4 2.6 + - - -
722A PRO 3.0 18.3 + - - +
724A GLU* 1.3 79.0 - - - +
726A ARG* 1.3 75.7 + - - +
727A GLY 3.5 22.7 - - - +
728A LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 726 (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 ASN 3.8 7.3 - - - +
631A ILE* 3.4 20.1 + - - +
632A ARG* 3.6 45.3 - - - +
633A PHE 5.7 0.2 - - - +
669A MET* 2.9 9.3 + - - +
671A ARG* 4.3 19.1 - - + +
676A PRO 5.6 0.2 + - - -
677A ILE* 2.9 42.4 + - - +
678A GLU* 5.6 0.2 + - - -
679A PRO* 4.8 4.4 - - - +
684A GLY 4.2 0.7 - - - -
685A MET* 3.5 42.1 + - - +
688A CYS* 3.7 18.6 - - - -
723A MET 3.1 24.2 + - - -
724A GLU 3.8 8.6 - - - +
725A LEU* 1.3 90.4 + - - +
727A GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 727 (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 ILE 3.2 12.6 - - - -
628A ASN* 3.2 15.3 - - - -
631A ILE* 3.6 5.4 - - - +
668A LEU* 3.4 3.5 - - - -
669A MET* 3.0 28.3 + - - -
725A LEU* 3.5 10.9 - - - +
726A ARG* 1.3 80.0 - - - +
728A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 728 (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 ILE* 4.3 1.4 - - - +
626A ASP* 3.7 2.2 - - - -
627A ILE* 2.8 38.3 + - - +
628A ASN* 3.9 2.0 + - - -
631A ILE* 5.0 5.1 - - + +
633A PHE* 6.2 0.2 - - + -
639A VAL* 5.4 1.1 - - + -
642A PHE* 4.3 29.7 - - + -
643A ILE* 4.9 8.1 - - + -
666A LEU* 4.2 14.8 - - + -
667A LYS* 3.5 4.3 - - - +
668A LEU* 4.2 13.7 - - + +
715A TYR* 4.2 11.2 - - + -
725A LEU* 4.1 24.9 - - + -
727A GLY* 1.3 75.7 - - - +
729A ALA* 1.3 66.0 + - - +
730A LEU* 3.5 33.2 - - + -
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Residues in contact with ALA 729 (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 ILE 3.2 11.2 - - - +
626A ASP* 3.4 27.1 - - - +
665A THR 3.8 0.3 - - - +
666A LEU* 3.4 5.9 - - - -
667A LYS* 2.7 55.4 + - + +
728A LEU* 1.3 75.7 - - - +
730A LEU* 1.3 65.8 + - - +
731A GLN* 4.1 10.5 - - + +
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Residues in contact with LEU 730 (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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624A SER* 3.0 5.2 - - - -
625A ILE* 2.9 42.6 + - + +
642A PHE* 5.1 3.1 - - + +
643A ILE* 3.8 32.1 - - + +
646A GLY* 3.9 23.3 - - - -
647A CYS* 4.0 8.1 - - - +
650A LEU* 3.6 16.1 - - + +
665A THR 3.8 2.0 - - - -
666A LEU* 3.4 33.4 - - + -
711A MET* 4.0 16.8 - - + -
728A LEU* 3.5 16.2 - - + -
729A ALA* 1.3 72.1 - - - +
731A GLN* 1.3 60.4 + - - +
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Residues in contact with GLN 731 (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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622A SER* 6.4 0.4 - - - -
623A LEU 4.4 0.2 - - - +
624A SER* 3.6 19.8 + - - -
626A ASP* 4.8 6.9 + - - -
664A ILE* 3.2 10.0 - - - +
665A THR* 2.9 59.4 + - - +
667A LYS* 4.7 10.4 - - - +
711A MET* 3.8 1.5 - - - +
729A ALA* 4.5 16.2 - - + +
730A LEU* 1.3 80.1 - - - +
732A PHE* 1.3 66.1 + - - +
733A ASN* 3.2 23.5 - - - +
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Residues in contact with PHE 732 (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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622A SER* 3.3 6.5 - - - -
623A LEU* 2.7 46.4 + - + +
647A CYS* 4.9 3.6 - - - -
650A LEU* 3.6 41.5 - - + -
651A LEU* 4.1 18.4 - - + -
654A LEU* 3.8 25.1 - - + -
661A THR* 3.3 27.6 - - + +
663A GLN 3.5 5.8 - - - -
664A ILE* 3.5 11.7 - - + -
707A ILE* 3.8 33.0 - - + -
711A MET* 4.1 7.6 - - + -
731A GLN* 1.3 80.4 - - - +
733A ASN* 1.3 58.3 + - - +
734A LYS 3.7 1.3 - - - -
735A LEU* 4.0 8.5 - - + +
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Residues in contact with ASN 733 (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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621A LYS* 3.1 14.9 - - - +
622A SER* 3.8 10.9 - - - -
663A GLN* 2.7 37.2 + - - +
664A ILE 3.3 19.2 - - - -
665A THR* 2.6 28.5 + - - +
731A GLN* 3.2 25.0 + - - +
732A PHE* 1.3 73.0 - - - +
734A LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 734 (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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621A LYS 4.1 1.1 - - - -
661A THR* 2.9 22.7 - - - +
662A SER* 3.2 28.7 + - - +
663A GLN* 3.4 23.3 + - + +
696A ARG* 2.7 39.7 - - - +
733A ASN* 1.3 81.3 - - - +
735A LEU* 1.3 61.3 + - - +
736A VAL* 5.5 1.3 - - + -
4P C 5.8 1.2 + - - -
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Residues in contact with LEU 735 (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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620A ARG* 4.1 24.9 - - - +
621A LYS* 3.4 34.1 + - - +
622A SER* 3.6 11.9 - - - +
623A LEU* 4.6 3.4 - - + +
654A LEU* 4.1 14.4 - - + -
657A ILE* 4.5 3.8 - - + -
659A LYS* 4.0 22.9 - - + -
660A THR 3.4 10.5 - - - +
661A THR* 4.2 0.9 - - + -
732A PHE* 4.0 26.7 - - + +
734A LYS* 1.3 80.4 - - - +
736A VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 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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659A LYS* 3.4 8.2 - - - +
660A THR* 2.9 42.3 + - - +
662A SER* 4.0 17.7 - - - +
700A PRO* 3.6 31.2 - - + -
734A LYS* 5.0 1.1 - - + -
735A LEU* 1.3 80.2 - - - +
737A ASP* 1.3 72.2 + - - +
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Residues in contact with ASP 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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658A ASN* 3.7 9.0 - - - +
659A LYS* 4.6 17.5 - - - +
660A THR* 4.6 3.6 + - - +
735A LEU 4.3 0.2 + - - -
736A VAL* 1.3 89.6 - - - +
738A VAL* 1.3 97.9 + - + +
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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