Contacts of the strand formed by residues 611 - 622 (chain A) in PDB entry 6DBV
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 PHE 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A ILE* 5.7 4.0 - - + -
597A LEU* 4.2 11.4 - - + -
602A LEU* 6.0 1.1 - - + -
607A CYS 3.9 17.3 - - - -
608A THR* 4.2 8.5 - - - -
609A SER 3.9 1.0 - - - -
610A GLY* 1.3 81.5 - - - +
612A THR* 1.3 61.2 + - - +
613A VAL 4.2 0.4 - - - -
649A ILE* 5.0 3.4 - - + -
650A SER 3.3 5.8 - - - +
651A ILE* 3.4 26.2 - - + -
662A ILE* 3.5 29.4 - - + -
718A ARG* 3.7 42.6 - - + -
719A SER 3.5 14.0 + - - -
720A PHE* 3.4 40.7 - + + -
721A ARG* 3.2 26.0 + - - +
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Residues in contact with THR 612 (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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610A GLY 3.8 5.9 + - - -
611A PHE* 1.3 75.2 + - - +
613A VAL* 1.3 62.7 + - - +
614A VAL* 4.0 11.3 + - + +
648A SER 4.1 0.3 - - - +
649A ILE* 3.6 0.9 - - - -
650A SER* 2.9 47.8 + - - +
651A ILE* 5.8 0.7 - - - -
652A ARG* 5.4 5.4 + - - +
721A ARG* 4.3 17.0 - - + +
723A PHE* 3.5 37.9 - - + -
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Residues in contact with VAL 613 (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 9.0 - - + -
612A THR* 1.3 72.5 - - - +
614A VAL* 1.3 60.7 + - - +
615A VAL* 3.5 25.6 - - + -
646A ILE* 4.4 11.7 - - + -
648A SER 3.3 9.4 - - - +
649A ILE* 3.5 35.7 - - + -
720A PHE* 4.0 20.9 - - + -
721A ARG 3.6 7.0 + - - +
722A PHE* 3.1 48.7 - - + -
723A PHE 3.8 1.6 + - - -
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Residues in contact with VAL 614 (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* 4.4 9.2 - - + +
613A VAL* 1.3 73.1 - - - +
615A VAL* 1.3 65.1 + - - +
647A MET* 3.3 7.0 + - - +
648A SER* 2.9 48.7 + - - +
650A SER* 5.7 1.8 - - - +
723A PHE* 3.8 33.2 - - + +
725A ARG* 3.7 46.9 - - + +
978A TRP* 4.8 5.8 - - + -
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Residues in contact with VAL 615 (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* 5.5 2.7 - - - +
582A LEU* 5.0 5.6 - - + -
613A VAL* 3.5 24.7 + - + +
614A VAL* 1.3 84.7 - - - +
616A LYS* 1.3 61.1 + - - +
617A GLU 4.0 0.9 + - - -
644A PHE* 3.4 32.5 - - + -
645A THR 3.2 20.6 - - - +
646A ILE* 3.5 22.7 - - + -
647A MET 4.1 0.7 - - - +
722A PHE* 4.5 11.0 - - + -
723A PHE 3.7 4.9 + - - +
724A PHE* 3.8 19.3 - - + -
725A ARG* 3.7 15.3 + - - -
978A TRP* 5.6 0.2 - - - -
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Residues in contact with LYS 616 (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* 5.6 0.2 - - - -
615A VAL* 1.3 72.2 - - - +
617A GLU* 1.3 73.8 + - - +
618A SER* 5.0 7.6 - - - -
644A PHE* 3.2 4.9 - - - +
645A THR* 2.9 57.9 + - - +
647A MET* 4.3 17.5 - - + +
668A PRO* 4.5 13.9 + - - +
725A ARG 3.3 17.3 - - - +
727A THR* 3.4 22.9 - - + +
728A GLY* 4.8 2.0 - - - +
977A ALA 4.9 3.4 + - - -
978A TRP* 4.0 30.3 - - + +
979A ALA 3.9 16.4 + - - +
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Residues in contact with GLU 617 (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* 3.5 23.9 + - - +
615A VAL 4.0 1.2 + - - -
616A LYS* 1.3 84.4 - - - +
618A SER* 1.3 67.9 + - - +
642A PHE* 4.2 20.6 - - + -
643A SER 4.2 3.8 - - - +
644A PHE* 3.7 7.9 - - + -
697A VAL* 5.4 1.0 - - - +
701A ARG* 3.1 48.5 + - - +
724A PHE* 4.1 12.5 - - + +
725A ARG 3.5 5.8 + - - +
726A GLY* 4.4 10.4 + - - -
727A THR 3.9 9.5 + - - -
729A TYR* 3.8 18.3 + - - +
807A MET* 5.0 5.9 - - - +
808A GLU 5.4 0.3 - - - +
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Residues in contact with SER 618 (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* 4.9 9.2 - - - -
617A GLU* 1.3 79.0 - - - +
619A CYS* 1.3 67.3 + - - +
642A PHE* 3.8 4.4 - - - -
643A SER* 2.7 35.6 + - - +
644A PHE* 5.5 0.9 - - - -
728A GLY* 2.9 28.0 + - - -
729A TYR* 4.3 7.2 + - - -
980A SER* 5.1 3.4 + - - -
983A ASN* 3.7 26.2 + - - +
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Residues in contact with CYS 619 (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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618A SER* 1.3 82.4 + - - +
620A ASP* 1.3 66.4 + - - +
640A VAL* 3.8 26.7 - - - -
641A ARG 3.7 7.0 - - - +
642A PHE* 3.3 29.6 - - + -
680A MET* 5.8 0.7 - - - -
690A LEU* 6.0 2.9 - - - -
694A LEU* 5.6 5.2 - - - -
728A GLY 3.2 6.8 + - - +
729A TYR* 3.6 21.1 - - + -
730A ASP* 4.7 0.2 - - - +
733A MET* 3.4 28.0 - - - +
737A MET* 5.6 4.7 - - + -
983A ASN* 4.0 2.0 - - - +
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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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619A CYS* 1.3 78.8 - - - +
621A GLY* 1.3 83.9 + - - +
640A VAL* 4.4 4.5 - - - -
641A ARG* 2.9 29.3 + - - +
684A GLU* 2.9 13.9 - - - +
728A GLY 5.2 2.5 - - - +
729A TYR* 5.7 0.2 - - - -
730A ASP* 3.8 18.9 + - - +
733A MET* 4.5 5.5 - - - +
817A HIS* 5.4 0.3 - - - -
983A ASN* 3.4 21.5 + - - +
984A GLU* 2.6 19.1 - - + +
987A ASN* 5.6 0.3 - - - +
1102A CA 2.6 29.5 - - - -
17E C 2.9 7.6 + - - -
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Residues in contact with GLY 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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620A ASP* 1.3 90.9 + - - +
622A MET* 1.3 66.0 + - - +
623A GLY 4.3 0.2 - - - -
639A ALA 3.3 9.9 - - - -
640A VAL* 3.9 9.2 - - - -
641A ARG* 5.0 0.7 - - - -
684A GLU* 3.1 21.8 + - - +
984A GLU* 3.9 15.4 - - - +
987A ASN* 4.3 6.7 + - - -
17E C 5.6 1.6 - - - -
18E A 4.3 1.8 + - - -
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Residues in contact with MET 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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621A GLY* 1.3 74.1 - - - +
623A GLY* 1.3 56.7 + - - +
625A VAL* 4.0 7.3 - - + +
638A LYS* 3.3 2.8 - - - -
639A ALA* 2.5 48.6 + - + +
640A VAL* 5.6 0.2 - - - -
641A ARG* 5.9 1.6 - - + +
684A GLU* 4.7 0.6 + - - -
984A GLU* 6.1 0.7 - - - +
987A ASN* 2.5 40.2 - - + +
988A LYS* 5.3 1.3 - - - +
990A PHE* 4.6 9.6 - - + -
991A ARG* 3.1 55.4 - - + +
18E A 3.3 37.9 - - - +
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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