Contacts of the strand formed by residues 618 - 630 (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 LYS 618 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563D GLN* 6.4 1.1 - - - +
564D ILE 3.8 4.7 - - - +
565D ALA* 4.7 16.2 - - + +
598D LYS* 3.6 9.4 - - - +
599D LEU* 3.0 44.4 + - + +
600D ASP* 2.1 35.7 + - - +
601D LYS* 3.7 12.1 + - - +
603D ASN* 3.3 20.6 + - - +
616D GLY 5.6 3.1 - - - +
617D MET* 1.3 75.8 - - - +
619D ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 619 (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* 3.6 1.9 - - - -
564D ILE* 2.7 38.7 + - + +
566D ILE* 3.1 35.7 - - + -
573D LEU* 5.8 0.2 - - + -
592D PHE* 4.9 8.5 - - + -
595D LEU* 4.1 22.2 - - + -
597D HIS 3.1 19.1 - - - +
598D LYS* 4.2 2.0 - - - +
599D LEU* 3.4 9.1 - - - +
610D PRO* 4.6 6.7 - - + -
613D ALA* 4.6 9.2 - - + -
617D MET* 3.8 7.9 - - + +
618D LYS* 1.3 77.5 - - - +
620D ILE* 1.3 63.1 + - - +
621D ALA* 3.6 28.5 - - + +
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Residues in contact with ILE 620 (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* 3.8 26.0 - - + -
562D ALA 3.5 10.8 - - - +
563D GLN* 4.3 11.7 - - + +
596D LEU* 2.8 26.9 + - + +
597D HIS* 3.1 51.4 + - + +
599D LEU* 4.1 12.6 - - + -
605D LYS* 4.9 11.9 - - + +
619D ILE* 1.3 79.2 - - - +
621D ALA* 1.3 61.8 + - - +
658D VAL* 4.8 8.5 - - + -
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Residues in contact with ALA 621 (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 4.2 0.2 - - - +
561D ILE* 3.2 10.1 - - - +
562D ALA 3.1 30.8 + - - +
564D ILE* 4.7 1.8 - - + -
592D PHE* 3.8 26.9 - - + -
594D LYS 3.1 15.7 - - - +
595D LEU* 3.9 4.3 - - - -
596D LEU* 4.0 3.6 - - - +
619D ILE* 3.6 18.9 - - + +
620D ILE* 1.3 73.3 - - - +
622D GLU* 1.3 61.5 + - - +
623D LEU* 4.2 4.7 - - + +
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Residues in contact with GLU 622 (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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559D ARG* 2.8 33.8 + - - -
560D PHE 3.4 10.3 - - - +
561D ILE* 4.3 9.7 - - + +
592D PHE* 3.6 0.3 - - - +
593D ALA* 2.5 43.5 + - + +
594D LYS* 2.7 58.6 + - + +
596D LEU* 4.7 7.2 - - + +
621D ALA* 1.3 72.7 - - - +
623D LEU* 1.3 64.7 + - - +
661D LEU* 4.3 17.2 - - + +
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Residues in contact with LEU 623 (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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558D THR 3.4 1.0 - - - +
559D ARG* 3.3 5.9 - - - +
560D PHE* 2.7 75.2 + - + +
562D ALA* 4.9 2.2 - - + -
564D ILE* 3.9 22.0 - - + -
581D MET* 4.4 3.1 - - + -
590D VAL* 3.9 13.9 - - + -
591D SER 3.6 4.0 - - - +
592D PHE* 3.5 37.2 - - + -
621D ALA* 4.2 5.2 - - + +
622D GLU* 1.3 87.7 - - - +
624D GLU* 1.3 63.8 + - - +
643D PHE* 4.1 13.5 - - + -
645D LEU* 4.8 7.0 - - + -
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Residues in contact with GLU 624 (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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403C LYS* 4.5 16.5 + - - -
558D THR* 3.0 5.2 - - - +
559D ARG* 3.7 44.2 + - + +
589D GLU* 5.6 0.3 - - - +
590D VAL* 3.3 3.2 - - - +
591D SER* 2.8 44.6 + - - +
593D ALA* 3.3 27.1 - - + +
594D LYS* 5.3 1.2 + - - -
622D GLU* 4.3 0.2 - - - +
623D LEU* 1.3 77.5 - - - +
625D THR* 1.3 66.7 + - - +
626D GLN* 5.8 0.3 + - - -
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Residues in contact with THR 625 (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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558D THR* 2.9 35.1 + - - +
560D PHE* 4.6 10.8 - - + -
581D MET* 5.0 4.7 - - - -
588D GLU* 4.6 5.6 - - + -
589D GLU* 3.7 17.0 - - - +
590D VAL* 3.8 14.6 - - + -
624D GLU* 1.3 80.1 - - - +
626D GLN* 1.3 69.3 + - - +
627D THR 2.9 22.0 + - - -
629D VAL* 3.8 20.3 - - + +
631D MET* 5.5 0.2 - - + -
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Residues in contact with GLN 626 (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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558D THR* 4.3 4.4 - - - +
588D GLU* 5.1 4.5 + - - +
589D GLU* 3.5 40.6 + - + +
591D SER* 5.8 1.4 + - - -
624D GLU 5.8 0.6 + - - -
625D THR* 1.3 76.2 - - - +
627D THR* 1.3 71.0 + - + +
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Residues in contact with THR 627 (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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558D THR* 3.5 5.8 - - - -
588D GLU* 3.7 22.7 + - - +
625D THR* 2.9 18.0 + - - -
626D GLN* 1.3 86.6 - - + +
628D PRO* 1.3 80.6 + - + +
629D VAL* 3.4 3.5 + - - +
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Residues in contact with PRO 628 (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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503D PRO* 3.6 36.2 - - + +
545D TYR* 5.2 3.8 - - - -
556D ALA* 4.6 1.6 - - + -
557D THR* 3.6 20.0 - - - +
558D THR* 3.5 11.2 - - + -
588D GLU* 5.8 0.3 - - - +
627D THR* 1.3 94.9 + - + +
629D VAL* 1.3 58.8 + - - +
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Residues in contact with VAL 629 (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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503D PRO* 5.0 1.1 - - - -
556D ALA* 3.5 5.0 - - - -
557D THR 3.2 25.3 + - - +
581D MET* 5.4 2.7 - - - -
583D ILE* 4.7 12.6 - - + -
584D HIS* 4.9 6.3 - - - +
586D ALA* 5.1 9.0 - - + -
588D GLU* 4.2 18.6 - - + +
625D THR* 3.8 25.1 - - + +
627D THR 3.6 10.5 - - - +
628D PRO* 1.3 77.6 - - - +
630D CYS* 1.3 77.2 + - - +
631D MET* 3.5 23.3 + - + +
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Residues in contact with CYS 630 (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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502D MET* 3.4 47.6 - - - -
503D PRO* 3.6 7.6 - - - -
544D GLY 5.2 0.9 - - - -
545D TYR* 4.8 2.0 - - - -
546D VAL* 3.6 28.7 - - + -
554D VAL* 4.1 11.0 - - + -
555D HIS 3.2 12.6 - - - +
556D ALA* 3.9 4.7 - - - -
583D ILE* 4.6 0.3 - - - +
584D HIS* 3.0 25.8 + - + -
629D VAL* 1.3 79.9 - - - +
631D MET* 1.3 61.5 + - - +
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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