Contacts of the strand formed by residues 639 - 651 (chain A) in PDB entry 6DBU
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 ALA 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A GLY* 3.3 4.9 - - - -
622A MET* 2.8 39.1 + - + +
625A VAL* 4.7 3.8 - - + -
638A LYS* 1.3 79.7 - - - +
640A VAL* 1.3 68.7 + - - +
641A ARG* 6.4 0.2 - - + -
679A LEU* 6.3 0.7 - - + -
680A MET 3.5 9.0 - - - +
681A PHE* 4.2 11.7 - - + -
682A VAL 3.5 5.4 - - - -
684A GLU 5.5 0.9 + - - -
990A PHE* 4.3 24.7 - - + -
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Residues in contact with VAL 640 (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* 3.7 22.7 - - - -
620A ASP 3.3 14.8 - - - +
621A GLY* 4.5 1.8 - - - -
622A MET* 4.7 0.4 - - - +
639A ALA* 1.3 82.7 - - - +
641A ARG* 1.3 67.0 + - - +
642A PHE* 5.0 1.3 - - + +
678A CYS 4.1 0.6 - - - +
679A LEU* 3.6 6.2 - - - +
680A MET* 2.9 59.6 + - + +
682A VAL* 4.1 14.1 - - + +
683A ASP 4.4 3.1 - - - +
684A GLU* 4.4 22.0 - - + +
690A LEU* 4.2 11.2 - - + -
694A LEU* 5.4 0.4 - - + -
733A MET* 6.3 0.9 - - + -
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Residues in contact with ARG 641 (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 3.8 2.4 - - - +
619A CYS* 3.7 2.3 - - - -
620A ASP 3.0 30.1 + - - +
622A MET* 3.3 20.3 - - + +
640A VAL* 1.3 77.4 - - - +
642A PHE* 1.3 63.8 + - - +
643A SER* 3.8 3.1 + - - -
674A CYS* 5.5 2.2 + - - -
676A PRO* 4.7 4.7 - - + +
678A CYS 3.7 2.5 - - - -
679A LEU* 4.2 29.8 - - + -
983A ASN* 2.5 46.0 + - - +
986A GLY* 3.8 12.8 - - - -
987A ASN* 2.0 55.0 + - - +
990A PHE* 4.3 5.7 - - - +
1013A HIS* 4.5 22.3 + - - -
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Residues in contact with PHE 642 (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* 3.9 24.7 - + - -
617A GLU* 3.6 33.0 - - + -
618A SER 3.8 2.0 - - - -
619A CYS* 3.4 33.0 - - + +
640A VAL* 4.2 1.9 - - + +
641A ARG* 1.3 71.2 - - - +
643A SER* 1.3 63.4 + - - +
644A PHE* 5.3 1.3 - - + -
676A PRO* 3.7 2.1 - - - +
677A LEU* 2.9 43.0 + - + -
678A CYS* 3.0 29.7 + - + +
680A MET* 6.3 0.4 - - + +
694A LEU* 4.5 20.0 - - + -
697A VAL* 4.1 14.4 - - + -
701A ARG* 5.2 1.1 - - - -
729A TYR* 4.3 11.0 - - - -
807A MET* 4.6 12.8 - - - -
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Residues in contact with SER 643 (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 4.3 0.2 - - - +
617A GLU 3.6 0.3 - - - -
618A SER* 2.8 38.9 + - - -
641A ARG* 4.7 3.6 - - - -
642A PHE* 1.3 78.5 - - - +
644A PHE* 1.3 60.7 + - - +
674A CYS* 3.2 21.3 - - - -
675A ARG 3.2 19.3 - - - -
676A PRO* 3.9 4.3 - - - -
677A LEU* 4.4 0.7 - - - +
983A ASN* 2.3 35.9 + - - +
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Residues in contact with PHE 644 (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* 4.1 15.7 - + + +
581A ALA* 4.2 13.7 - - + -
582A LEU* 3.7 33.4 - - + -
585A ALA* 4.5 8.5 - - + -
615A VAL* 3.8 24.2 - - + -
616A LYS 3.5 9.6 - - - +
617A GLU* 4.0 5.4 - - + +
642A PHE* 5.4 1.1 - - + -
643A SER* 1.3 73.7 - - - +
645A THR* 1.3 68.7 + - - +
646A ILE* 3.6 26.0 - - + -
675A ARG* 2.9 49.9 + - + +
677A LEU* 3.6 39.0 - - + +
1014A TRP* 4.8 2.5 - + - -
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Residues in contact with THR 645 (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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615A VAL* 3.7 1.4 - - - -
616A LYS* 2.9 58.5 + - - +
644A PHE* 1.3 84.7 + - - +
646A ILE* 1.3 74.9 + - - +
647A MET* 3.2 2.3 + - + -
665A GLU* 5.4 5.4 - - + -
668A PRO* 5.0 3.4 - - + +
673A SER* 3.2 33.3 + - - +
674A CYS* 3.2 25.3 - - - -
675A ARG* 4.6 3.6 - - + -
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Residues in contact with ILE 646 (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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582A LEU* 3.6 31.0 - - + -
585A ALA* 4.5 17.9 - - + +
586A LEU* 4.9 11.9 - - + -
589A LEU* 4.6 23.8 - - + -
613A VAL* 4.1 24.7 - - + -
614A VAL 3.9 2.7 - - - +
615A VAL* 4.3 7.0 - - + -
644A PHE* 3.6 15.3 - - + -
645A THR* 1.3 80.6 - - - +
647A MET* 1.3 63.4 + - - +
648A SER 4.8 7.0 - - - +
649A ILE* 5.4 2.5 - - + -
663A PHE* 4.5 8.4 - - + -
665A GLU* 4.0 11.1 - - - +
673A SER* 4.9 1.4 + - - -
675A ARG* 4.9 6.4 - - - +
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Residues in contact with MET 647 (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* 2.9 29.2 + - + +
616A LYS* 3.8 32.1 - - + -
645A THR* 3.2 4.4 + - + +
646A ILE* 1.3 74.3 - - - +
648A SER* 1.3 71.0 + - - +
663A PHE* 4.5 1.4 - - - -
664A GLN* 5.1 13.2 - - + +
665A GLU* 3.2 32.8 + - - +
668A PRO* 3.6 32.1 - - + -
977A ALA* 4.1 12.8 - - + +
978A TRP* 4.3 26.9 - - + +
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A THR 3.7 1.0 - - - +
613A VAL* 3.7 0.4 - - - -
614A VAL* 2.9 46.9 + - - +
646A ILE* 3.8 3.1 - - - -
647A MET* 1.3 90.8 - - - +
649A ILE* 1.3 59.9 + - - +
650A SER* 4.2 1.5 + - - -
661A THR* 5.9 1.1 - - - -
663A PHE* 3.4 12.1 - - - -
664A GLN* 4.4 13.2 - - - -
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Residues in contact with ILE 649 (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* 6.1 2.7 - - + -
589A LEU* 5.2 2.7 - - + -
593A ILE* 4.8 13.0 - - + -
611A PHE* 3.5 28.7 - - + -
612A THR 3.2 21.1 - - - +
613A VAL* 3.5 25.4 - - + -
646A ILE* 5.4 3.4 - - + -
648A SER* 1.3 73.2 - - - +
650A SER* 1.3 73.7 + - - +
661A THR* 4.0 1.0 - - - -
662A ILE* 2.9 18.7 + - + +
663A PHE* 2.9 66.1 + - + +
720A PHE* 4.2 3.8 - - + -
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Residues in contact with SER 650 (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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611A PHE* 3.7 1.7 - - - -
612A THR* 2.9 49.6 + - - +
614A VAL* 5.8 1.6 - - - +
648A SER* 5.3 1.6 + - - -
649A ILE* 1.3 79.4 - - - +
651A ILE* 1.3 64.6 + - - +
659A GLY* 5.3 3.7 - - - -
660A ILE 3.1 29.4 - - - -
661A THR* 4.3 3.1 - - - -
662A ILE* 3.9 3.1 - - - +
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Residues in contact with ILE 651 (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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597A LEU* 4.8 4.0 - - + -
602A LEU* 4.2 23.8 - - + -
607A CYS* 4.9 4.3 - - + -
610A GLY* 3.1 18.8 - - - +
611A PHE* 3.5 44.6 - - + -
612A THR* 5.3 1.9 - - - -
650A SER* 1.3 79.1 + - - +
652A ARG* 1.3 59.9 + - - +
653A LEU* 4.2 19.7 - - + +
657A ASP* 2.9 14.4 - - + +
659A GLY* 5.5 0.2 - - - -
660A ILE* 3.1 42.4 + - + +
662A ILE* 3.7 16.6 - - + -
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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