Contacts of the strand formed by residues 716 - 728 (chain A) in PDB entry 6DBT
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 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A ASP* 3.6 27.6 - - + +
605A SER* 4.9 3.1 - - - +
608A THR* 4.4 8.7 - - + -
711A ILE 3.6 0.7 - - - +
712A SER* 4.3 1.8 - - - -
713A VAL* 2.8 35.2 + - - +
714A GLY 3.7 8.5 - - - +
715A GLY* 1.3 85.5 - - - +
717A LEU* 1.3 62.2 + - - +
718A ARG* 3.4 40.5 + - + +
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Residues in contact with LEU 717 (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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608A THR* 4.1 9.4 + - - -
710A ILE* 4.1 24.5 - - + -
711A ILE 3.3 10.8 - - - +
712A SER* 4.1 8.0 - - - +
715A GLY 4.1 1.8 + - - -
716A LEU* 1.3 73.1 - - - +
718A ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 718 (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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593A ILE* 4.9 3.8 - - - +
594A MET* 3.0 40.4 - - - +
597A LEU* 4.3 15.5 - - - +
604A ASP* 4.7 6.7 + - - +
607A CYS* 3.9 18.2 + - - -
608A THR* 3.2 25.1 - - + +
611A PHE* 4.2 13.2 - - + -
710A ILE* 3.3 8.0 - - - +
711A ILE 2.9 31.1 + - - +
713A VAL* 3.7 30.0 + - + +
714A GLY 4.6 2.0 + - - -
716A LEU* 3.4 39.8 - - - +
717A LEU* 1.3 80.1 - - - +
719A SER* 1.3 60.5 + - - +
720A PHE* 3.5 18.9 - - + -
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Residues in contact with SER 719 (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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608A THR 3.0 7.8 + - - -
609A SER* 2.3 52.9 + - - +
611A PHE* 3.6 13.9 + - - +
708A ARG* 2.9 31.6 + - - -
709A LEU 3.1 6.5 - - - -
710A ILE* 3.5 17.2 - - - +
718A ARG* 1.3 70.7 - - - +
720A PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 720 (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* 3.5 31.9 - - + -
593A ILE* 4.9 8.5 - - + -
609A SER 5.6 0.2 - - - -
611A PHE* 3.4 46.7 - + + +
613A VAL* 4.4 9.9 - - + -
649A ILE* 4.5 4.0 - - + -
708A ARG* 3.4 8.0 - - - +
709A LEU* 2.8 46.2 + - + +
711A ILE* 3.2 33.0 - - + -
713A VAL* 4.7 9.6 - - + -
718A ARG* 3.5 22.2 - - + -
719A SER* 1.3 77.7 - - - +
721A ARG* 1.3 67.7 + - - +
722A PHE* 4.3 9.2 - - + -
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Residues in contact with ARG 721 (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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609A SER 6.0 1.8 - - - +
610A GLY* 6.5 0.9 - - - -
611A PHE 2.9 16.4 + - - +
612A THR* 4.8 8.7 - - - +
613A VAL* 3.6 15.4 + - - +
652A ARG* 6.5 1.6 - - - -
705A MET 4.1 11.0 + - - -
706A GLU* 3.6 19.8 + - - +
707A SER 5.0 3.1 - - - -
708A ARG* 3.1 49.1 - - + +
720A PHE* 1.3 73.7 - - - +
722A PHE* 1.3 81.0 + - - +
723A PHE* 4.5 23.0 - - + -
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Residues in contact with PHE 722 (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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538A TRP* 5.2 8.1 - + - -
582A LEU* 4.3 28.9 - - + -
586A LEU* 4.6 9.0 - - + -
613A VAL* 3.6 39.9 - - + +
615A VAL* 4.9 1.3 - - + -
646A ILE* 5.8 0.4 - - + -
704A MET* 4.9 17.5 - - + +
705A MET* 3.8 27.4 + - - +
707A SER 5.4 5.0 + - - -
709A LEU* 4.1 38.4 - - + -
720A PHE* 4.3 9.9 - - + -
721A ARG* 1.3 94.0 - - - +
723A PHE* 1.3 74.2 + - - +
724A PHE* 3.6 26.9 - + + -
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Residues in contact with PHE 723 (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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612A THR* 3.6 39.7 - - + -
613A VAL 3.2 16.9 + - - +
614A VAL* 3.7 11.6 - - + -
615A VAL 3.4 13.7 + - - -
705A MET* 5.5 2.5 - - - -
721A ARG* 4.5 26.7 - - + -
722A PHE* 1.3 87.8 - - - +
724A PHE* 1.3 69.9 + - - +
725A ARG* 5.2 9.4 - - - +
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Residues in contact with PHE 724 (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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578A TYR* 3.3 39.0 - + - -
582A LEU* 4.4 14.4 - - + -
615A VAL* 3.8 19.5 - - + -
617A GLU* 3.3 24.5 - - + +
701A ARG* 3.4 24.5 - - + +
704A MET* 4.7 12.3 - - + -
705A MET* 4.5 20.7 - - + +
722A PHE* 3.6 31.4 - + + -
723A PHE* 1.3 88.9 - - - +
725A ARG* 1.3 67.3 + - - +
726A GLY 4.0 1.9 + - - -
808A GLU* 4.4 13.7 - - - +
810A GLN* 5.0 0.9 - - - +
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Residues in contact with ARG 725 (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 VAL* 3.6 35.9 - - + +
615A VAL 3.0 10.5 + - - +
616A LYS* 3.3 4.0 - - - -
617A GLU* 3.1 25.7 + - - -
723A PHE* 5.2 7.5 - - - +
724A PHE* 1.3 81.9 - - - +
726A GLY* 1.3 61.9 + - - +
727A THR* 3.5 11.4 + - + +
810A GLN* 2.8 51.5 + - - +
971A ARG* 5.0 7.5 + - - +
972A ASP* 4.4 29.2 + - - +
978A TRP* 4.2 19.0 - - + -
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Residues in contact with GLY 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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617A GLU* 4.4 13.4 + - - +
701A ARG* 5.9 1.1 - - - +
724A PHE 4.0 3.0 + - - -
725A ARG* 1.3 70.3 - - - +
727A THR* 1.3 58.4 + - - -
729A TYR* 3.8 18.2 - - - -
808A GLU* 4.4 12.4 + - - +
809A THR* 3.8 4.3 + - - -
810A GLN* 2.8 41.3 + - - +
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Residues in contact with THR 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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616A LYS* 3.6 9.8 - - + +
617A GLU 4.0 2.0 + - - -
725A ARG* 3.5 24.5 + - + +
726A GLY* 1.3 78.0 - - - +
728A GLY* 1.3 59.4 + - - +
729A TYR* 2.6 29.1 + - - +
810A GLN* 4.3 7.0 - - - +
812A THR* 3.6 28.5 - - + +
978A TRP* 2.9 53.4 + - + +
980A SER* 4.9 1.0 - - - -
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Residues in contact with GLY 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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616A LYS* 5.6 0.9 - - - -
617A GLU 3.2 17.0 + - - -
618A SER* 3.3 10.0 + - - -
619A CYS 3.0 31.4 + - - +
620A ASP* 5.1 0.3 - - - +
727A THR* 1.3 78.1 + - - +
729A TYR* 1.3 61.6 + - - -
980A SER* 3.7 26.5 + - - -
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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