Contacts of the strand formed by residues 505 - 520 (chain D) in PDB entry 3A8P
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 505 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D VAL* 1.3 80.5 - - - +
506D ARG* 1.3 60.1 + - - +
507D LYS 4.3 8.7 - - - +
508D ALA* 5.3 3.1 - - + -
539D THR* 3.5 28.0 - - + -
540D LEU 3.4 4.9 - - - +
541D LYS* 4.1 30.5 - - + +
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Residues in contact with ARG 506 (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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504D VAL* 3.3 27.7 + - + +
505D VAL* 1.3 75.2 - - - +
507D LYS* 1.3 64.3 + - + +
540D LEU* 2.9 20.1 + - + +
542D GLY* 4.8 2.8 + - - -
612D ALA* 3.9 24.5 - - + +
615D SER* 3.6 22.4 + - - -
616D ALA* 3.7 24.6 - - - +
619D SER* 3.7 28.9 + - - -
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Residues in contact with LYS 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D VAL* 3.7 3.8 - - - -
506D ARG* 1.3 82.7 - - + +
508D ALA* 1.3 69.6 + - - +
538D VAL 3.9 0.2 - - - +
539D THR* 3.4 6.0 - - - +
540D LEU* 2.9 29.9 + - + +
605D ASP* 4.0 7.1 + - - -
608D ASN* 3.4 44.4 - - - +
609D TRP* 3.5 57.8 - - + +
612D ALA* 4.2 14.1 - - + -
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Residues in contact with ALA 508 (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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505D VAL* 5.3 3.8 - - + -
507D LYS* 1.3 85.5 + - - +
509D GLY* 1.3 58.3 + - - +
537D TRP* 3.8 23.0 - - + +
538D VAL 3.1 6.7 - - - -
539D THR* 3.6 20.2 - - + +
609D TRP* 4.1 5.1 - - - -
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Residues in contact with GLY 509 (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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508D ALA* 1.3 77.4 - - - +
510D TRP* 1.3 63.7 + - - -
511D LEU 3.7 0.3 + - - -
537D TRP* 3.6 21.6 - - - -
538D VAL* 2.8 33.9 + - - +
609D TRP* 3.8 11.2 - - - -
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Residues in contact with TRP 510 (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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509D GLY* 1.3 72.1 - - - -
511D LEU* 1.3 71.2 + - - +
535D GLN* 3.7 36.6 - - + +
536D TYR* 3.1 41.1 - - - -
537D TRP* 3.5 40.6 - + + -
549D GLU 4.2 16.4 - - - -
599D GLN 4.5 0.7 - - - +
601D THR* 4.0 25.6 - - + +
605D ASP* 4.4 1.9 - - - +
609D TRP* 4.9 0.3 + - - -
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Residues in contact with LEU 511 (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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510D TRP* 1.3 81.0 - - - +
512D PHE* 1.3 70.2 - - - +
513D PHE* 3.9 0.7 + - + +
534D LYS 3.8 0.3 - - - +
535D GLN* 3.5 2.9 - - - +
536D TYR* 2.9 34.4 + - - +
538D VAL* 3.8 21.7 - - + +
586D PHE* 4.1 10.3 - - + -
598D PHE* 3.9 22.4 - - + -
599D GLN 3.3 20.9 - - - +
600D ALA* 3.6 15.5 - - - -
605D ASP* 4.3 0.2 - - - +
609D TRP* 3.6 52.5 - - + +
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Residues in contact with PHE 512 (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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511D LEU* 1.3 76.1 - - - +
513D PHE* 1.3 59.7 + - - +
533D TRP* 3.7 25.8 - + + -
534D LYS* 3.3 10.1 - - - -
535D GLN* 3.4 54.7 - - + -
598D PHE* 3.1 9.4 - - - +
599D GLN* 3.0 59.1 + - + +
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Residues in contact with PHE 513 (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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511D LEU* 4.9 1.6 - - + +
512D PHE* 1.3 75.8 - - - +
514D LYS* 1.3 65.2 + - - +
515D PRO* 3.7 21.1 - - + -
532D LYS 3.2 5.5 - - - +
533D TRP* 3.8 2.2 - - - -
534D LYS* 2.7 39.1 + - + +
536D TYR* 4.0 18.8 - + + -
547D PHE* 3.6 29.6 - + + -
566D LEU* 4.5 2.5 - - + -
596D TYR* 3.4 48.7 - + + -
597D LEU 3.5 6.1 - - - -
598D PHE* 3.4 28.0 - + + -
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Residues in contact with LYS 514 (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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513D PHE* 1.3 80.6 - - - +
515D PRO* 1.3 76.5 - - - +
531D ARG* 3.7 26.6 + - + +
532D LYS* 3.6 24.7 - - - +
533D TRP* 3.2 60.8 - - + +
579D HIS* 5.2 4.8 + - - -
597D LEU* 2.8 49.9 + - + +
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Residues in contact with PRO 515 (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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513D PHE* 3.7 18.6 - - + -
514D LYS* 1.3 88.6 - - + +
516D LEU* 1.3 59.4 + - - +
517D VAL 5.7 0.9 - - - +
528D VAL* 4.0 27.4 - - + -
531D ARG* 3.0 32.0 - - + +
532D LYS 4.7 5.4 - - - +
596D TYR* 3.9 28.5 - - + -
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Residues in contact with LEU 516 (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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514D LYS 3.6 0.4 + - - -
515D PRO* 1.3 75.0 - - - +
517D VAL* 1.3 67.7 + - + +
527D LEU* 3.2 15.6 - - + +
528D VAL* 2.8 26.1 + - - -
531D ARG* 3.7 30.6 - - - +
587D CYS* 5.0 1.8 - - - -
595D VAL* 2.9 34.6 + - + +
597D LEU* 4.2 36.6 - - + -
727D VAL* 4.5 20.9 - - + -
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Residues in contact with VAL 517 (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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515D PRO* 5.7 0.5 - - - +
516D LEU* 1.3 95.2 + - + +
518D THR* 1.3 74.0 + - - +
525D LEU* 4.1 27.8 - - + -
526D GLU 3.6 11.0 - - - +
527D LEU* 4.0 14.8 - - + -
528D VAL* 4.3 3.3 - - - +
593D GLY 4.3 3.4 - - - +
594D ASP* 3.5 3.8 - - - +
595D VAL* 3.0 47.7 + - + +
596D TYR* 5.4 1.9 - - - -
725D LEU* 4.3 18.6 - - + -
727D VAL* 4.9 3.1 - - + -
732D SER* 5.6 2.5 - - - -
735D ALA* 5.0 1.1 - - + -
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Residues in contact with THR 518 (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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517D VAL* 1.3 78.5 - - - +
519D LEU* 1.3 64.5 + - - +
520D GLN* 3.7 30.7 + - - +
525D LEU* 3.7 0.9 - - - -
526D GLU 3.1 34.4 + - - +
527D LEU 5.4 1.6 - - - +
528D VAL* 4.5 13.9 - - + -
593D GLY 4.2 4.3 - - - -
594D ASP* 2.8 19.8 + - - -
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Residues in contact with LEU 519 (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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518D THR* 1.3 77.0 + - - +
520D GLN* 1.3 78.5 + - - +
523D ARG* 3.7 24.0 - - + -
524D LYS 3.8 3.8 - - - +
525D LEU* 4.0 8.5 - - + -
592D CYS 3.3 28.5 - - - +
593D GLY* 3.9 7.9 + - - +
594D ASP* 3.2 8.8 + - - +
738D CYS 5.3 1.3 - - - +
739D SER* 3.5 41.1 - - - +
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Residues in contact with GLN 520 (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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518D THR* 3.7 28.4 + - - +
519D LEU* 1.3 86.6 - - - +
521D LYS* 1.3 72.4 + - + +
523D ARG* 3.2 14.2 + - - -
524D LYS* 2.8 33.4 + - + +
526D GLU* 3.1 29.7 + - + +
527D LEU 5.9 0.4 + - - -
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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