Contacts of the strand formed by residues 655 - 665 (chain A) in PDB entry 6P0D
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 VAL 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A TYR* 4.9 2.7 - - + -
600A ASP* 4.4 7.0 + - - +
601A ILE* 4.4 11.7 - - + -
604A ARG* 3.0 26.0 + - - +
622A ALA* 3.7 24.0 - - + -
623A VAL 3.2 5.6 - - - +
625A TRP* 4.2 3.6 - - - -
627A ARG* 5.1 0.7 + - - -
638A LEU* 3.6 30.5 - - + -
641A ARG* 3.5 31.2 - - - +
653A VAL 3.9 0.2 + - - -
654A GLN* 1.3 79.9 + - - +
656A CYS* 1.3 73.7 + - - +
657A LEU* 4.3 8.5 - - + -
691A GLY 3.9 5.6 - - - +
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Residues in contact with CYS 656 (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 GLU 3.5 1.6 - - - +
623A VAL* 2.8 31.8 + - + +
625A TRP* 3.8 16.5 - - + +
655A VAL* 1.3 77.0 - - - +
657A LEU* 1.3 67.9 + - - +
658A TYR* 3.8 34.0 - - + -
691A GLY* 3.5 37.2 - - - +
692A GLU 3.5 10.3 - - - -
693A PHE 4.1 1.1 - - - -
694A VAL* 4.2 6.7 - - - -
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Residues in contact with LEU 657 (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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574A ALA* 4.7 1.3 - - + -
576A ILE* 3.6 24.9 - - + -
601A ILE* 3.5 42.8 - - + -
604A ARG* 4.7 3.6 - - - +
605A ILE* 5.6 0.2 - - + -
608A ILE* 5.3 5.6 - - + -
620A THR* 3.7 23.3 - - - +
621A GLU 3.5 0.9 - - - -
622A ALA* 4.0 19.3 - - + -
655A VAL* 4.3 2.0 - - + -
656A CYS* 1.3 75.3 - - - +
658A TYR* 1.3 59.9 + - - +
659A ALA 3.9 0.2 - - - -
692A GLU 2.9 16.9 + - - +
693A PHE* 3.3 24.4 - - + -
694A VAL 2.9 27.5 + - - +
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Residues in contact with TYR 658 (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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569A TYR* 3.3 58.8 - + + -
620A THR* 3.3 2.7 - - - -
621A GLU* 2.9 39.5 + - + +
623A VAL* 3.7 35.0 - - + -
625A TRP* 3.6 16.8 - - - -
632A ILE* 3.4 23.4 - - + +
656A CYS* 3.8 21.7 - - + -
657A LEU* 1.3 69.7 - - - +
659A ALA* 1.3 63.0 + - - +
660A PHE* 3.6 5.6 - - - -
694A VAL* 3.2 32.7 - - + +
695A PHE 4.7 1.8 - - - -
696A ALA* 4.7 2.2 - - + -
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Residues in contact with ALA 659 (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 LEU* 4.7 2.2 - - + -
619A ASP 3.7 5.8 - - - +
620A THR* 4.0 9.9 - - + -
657A LEU 3.9 1.0 - - - -
658A TYR* 1.3 72.1 - - - +
660A PHE* 1.3 60.2 + - - +
682A LEU* 4.2 20.0 - - + +
693A PHE* 3.5 36.3 - - + -
694A VAL 2.8 12.2 + - - +
695A PHE* 3.5 9.0 - - + +
696A ALA 3.0 21.4 + - - -
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Residues in contact with PHE 660 (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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566A GLU* 3.5 28.5 - - - +
569A TYR* 5.9 2.9 - + - -
573A ARG* 3.9 17.9 - - + -
619A ASP* 3.0 41.2 + - - -
620A THR* 3.5 25.6 - - - -
621A GLU* 3.6 12.6 - - + -
658A TYR* 3.6 11.2 - - + -
659A ALA* 1.3 74.1 - - - +
661A ASP* 1.3 72.6 + - + +
675A LEU* 4.6 8.1 - - - +
679A ARG* 5.8 2.8 - - - +
682A LEU* 3.9 9.5 - - - +
696A ALA* 4.1 10.3 - - + -
725A LYS* 3.7 19.5 + - - -
742A TRP* 3.9 8.7 - + - -
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Residues in contact with ASP 661 (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 LEU* 3.7 11.8 - - - +
619A ASP* 2.9 47.0 + - + +
660A PHE* 1.3 86.3 - - + +
662A LEU* 1.3 75.8 + - - +
663A ILE* 5.0 0.2 - - + -
675A LEU* 3.9 7.2 - - - +
678A ARG* 2.8 51.4 + - - +
679A ARG* 6.3 0.7 - - - +
682A LEU* 3.8 8.6 - - - +
725A LYS* 5.3 0.2 + - - -
733A TYR* 3.5 9.2 - - + -
742A TRP* 3.2 19.2 - - - -
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Residues in contact with LEU 662 (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 PHE* 4.1 3.6 - - + -
617A ILE 3.5 10.1 - - - +
618A LEU* 3.8 9.6 - - + -
661A ASP* 1.3 80.5 + - - +
663A ILE* 1.3 60.7 + - - +
664A TYR 3.5 19.5 - - - +
665A LEU* 4.1 13.0 - - + -
670A LEU* 3.4 20.0 - - + +
678A ARG* 3.4 35.7 + - - +
681A LEU* 3.6 34.8 - - + +
682A LEU* 3.6 18.4 - - + +
686A PHE* 3.8 24.7 - - + -
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Residues in contact with ILE 663 (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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534A LEU* 4.0 16.0 - - + +
540A LEU* 3.8 30.1 - - + -
575A GLN* 4.8 5.6 - - + +
617A ILE* 2.9 31.7 + - + +
618A LEU 4.8 0.4 - - - -
619A ASP* 4.2 18.4 - - + +
662A LEU* 1.3 79.5 - - - +
664A TYR* 1.3 60.0 + - - +
669A SER* 3.9 1.6 - - - -
670A LEU* 2.9 28.9 + - - +
671A VAL* 4.0 9.8 + - + +
678A ARG* 5.1 1.6 - - - +
733A TYR* 3.7 46.7 - - + +
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Residues in contact with TYR 664 (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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534A LEU* 4.2 26.2 + - + -
535A SER* 5.1 1.6 + - - -
536A PRO* 3.4 42.2 - - + +
580A GLU* 5.9 1.6 - - - +
615A SER* 3.5 11.6 + - - -
616A PHE* 3.2 8.1 - - - -
617A ILE* 3.1 38.6 + - + -
662A LEU* 3.5 9.3 - - - +
663A ILE* 1.3 78.9 - - - +
665A LEU* 1.3 66.4 + - - +
667A GLY* 3.2 45.3 + - - -
668A GLU 3.2 12.1 - - - -
669A SER* 3.8 14.8 - - - -
670A LEU* 4.0 3.0 - - - +
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Residues in contact with LEU 665 (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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613A VAL* 3.9 18.8 - - + -
615A SER 3.5 8.5 - - - +
616A PHE* 4.4 2.7 - - + -
662A LEU* 4.1 9.4 - - + -
664A TYR* 1.3 77.2 - - - +
666A ASN* 1.3 96.1 + - + +
667A GLY 3.2 1.6 - - - -
668A GLU* 2.8 31.0 + - + +
670A LEU* 4.4 7.6 - - + +
681A LEU* 4.1 27.1 - - + -
685A ASN* 3.7 25.8 - - + +
686A PHE* 4.4 17.0 - - + -
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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