Contacts of the strand formed by residues 650 - 660 (chain D) in PDB entry 3E20
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 THR 650 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568D GLU* 4.3 17.8 + - + +
570D PRO* 6.0 6.1 - - + -
646D ARG* 3.3 11.7 - - - +
647D ASP* 3.2 26.8 + - + +
648D GLN* 3.4 0.6 - - - -
649D GLY* 1.3 86.5 - - - +
651D THR* 1.3 78.7 + - - +
652D VAL* 3.4 6.5 + - + +
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Residues in contact with THR 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU* 4.1 11.8 - - + +
568D GLU* 4.0 12.5 + - - +
644D THR* 4.1 15.5 + - - +
645D LEU 3.4 15.0 - - - +
646D ARG* 3.5 21.9 + - - +
650D THR* 1.3 79.3 + - - +
652D VAL* 1.3 61.0 + - - +
653D ALA 3.6 17.0 + - - +
654D VAL* 4.8 6.3 - - + -
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Residues in contact with VAL 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D ILE* 3.6 6.1 - - - +
567D LEU* 2.6 32.3 + - - -
568D GLU 3.3 17.7 - - - +
569D LEU* 3.3 32.9 - - + +
570D PRO* 4.6 3.8 - - + -
573D LEU* 6.2 0.2 - - + -
577D TYR* 4.1 17.9 - - + +
579D CYS* 4.9 0.4 - - - -
645D LEU* 2.9 30.6 + - + +
646D ARG 4.3 0.2 - - - +
647D ASP* 3.7 28.5 - - + +
650D THR* 3.4 6.7 + - + +
651D THR* 1.3 74.3 - - - +
653D ALA* 1.3 59.2 + - + +
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Residues in contact with ALA 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 3.7 20.4 - - + -
565D ALA 3.1 16.4 - - - +
566D ILE* 3.9 7.6 - - + -
567D LEU* 3.8 5.6 - - - -
592D PHE* 6.2 0.2 - - + -
644D THR* 3.5 2.4 - - - -
645D LEU* 2.7 44.3 + - + +
651D THR* 3.4 7.2 - - - +
652D VAL* 1.3 86.8 - - + +
654D VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D ILE* 3.5 7.9 - - - +
565D ALA* 3.0 42.5 + - + +
567D LEU* 3.9 20.9 - - + -
643D PHE* 3.5 13.7 - - - +
644D THR* 4.1 16.2 - - + +
645D LEU* 6.0 0.4 - - - -
651D THR* 4.8 4.3 - - + -
653D ALA* 1.3 80.1 - - - +
655D GLY* 1.3 62.4 + - - +
656D LYS* 6.1 4.7 - - - +
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Residues in contact with GLY 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D GLN 3.2 14.6 - - - -
564D ILE* 4.1 1.8 - - - -
565D ALA 4.7 0.4 - - - -
642D ARG* 3.6 2.6 - - - +
643D PHE* 2.9 47.2 + - - +
654D VAL* 1.3 81.6 - - - +
656D LYS* 1.3 68.3 + - - +
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Residues in contact with LYS 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D ALA* 3.0 18.3 - - - +
563D GLN* 3.0 44.4 + - + +
634D PHE* 3.6 51.3 - - + -
641D GLY 3.1 7.2 - - - +
642D ARG* 4.7 3.5 - - + +
643D PHE* 3.6 1.1 - - - -
654D VAL* 6.1 4.5 - - + +
655D GLY* 1.3 80.4 - - - +
657D VAL* 1.3 63.7 + - - +
658D VAL* 3.5 1.6 + - - +
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Residues in contact with VAL 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D PHE* 4.1 15.3 - - + -
561D ILE 4.3 1.3 - - - +
562D ALA* 3.7 7.6 - - - -
583D ILE* 5.1 1.1 - - + -
631D MET* 4.5 10.3 - - + -
632D GLU 3.0 31.2 - - - +
633D ARG* 3.5 10.1 - - + +
634D PHE* 2.9 28.1 + - - +
640D MET 4.0 4.0 - - - +
641D GLY* 3.0 21.4 + - - +
643D PHE* 3.7 7.4 - - + -
656D LYS* 1.3 73.0 - - - +
658D VAL* 1.3 60.9 + - - +
659D LYS 4.0 10.3 - - - +
660D ILE* 4.0 19.3 - - + -
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Residues in contact with VAL 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D ILE* 2.7 44.1 + - + +
562D ALA* 3.5 12.1 - - - +
563D GLN* 4.2 8.5 - - + +
620D ILE* 4.8 9.2 - - + -
633D ARG* 3.3 21.8 - - - +
656D LYS 3.5 2.0 + - - +
657D VAL* 1.3 74.6 - - - +
659D LYS* 1.3 65.1 + - + +
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Residues in contact with LYS 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D PHE* 3.4 5.0 - - - +
561D ILE* 3.0 45.0 + - + -
633D ARG* 4.2 7.2 - - - +
657D VAL* 3.7 2.1 - - - +
658D VAL* 1.3 82.8 - - + +
660D ILE* 1.3 76.2 + - - +
661D LEU* 3.5 19.9 + - + +
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Residues in contact with ILE 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555D HIS* 4.5 26.5 - - + +
557D THR* 3.8 13.2 - - + -
559D ARG 4.4 1.1 - - - -
560D PHE* 4.4 0.9 - - + -
631D MET* 3.3 53.6 - - + +
632D GLU* 4.8 1.3 - - - +
633D ARG* 4.7 13.5 - - + +
657D VAL* 4.0 14.8 - - + +
659D LYS* 1.3 84.1 - - - +
661D LEU* 1.3 60.3 + - - +
662D ASP* 3.2 30.9 + - - +
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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