Contacts of the strand formed by residues 513 - 520 (chain A) in PDB entry 1AUQ
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 LEU 513 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A CYS* 4.6 10.3 - - - -
511A ARG* 3.2 9.8 + - + +
512A LEU* 1.3 75.6 - - - +
514A ASP* 1.3 75.8 + - - +
515A LEU* 4.2 8.5 - - + +
544A LEU* 5.4 0.9 - - + -
550A TRP 3.2 3.4 + - - -
551A VAL* 3.2 24.5 - - + -
552A ARG 2.8 25.1 + - - -
611A ARG* 3.3 5.0 + - - -
614A ALA* 3.7 1.2 - - - +
615A SER* 3.6 13.9 - - - +
617A ILE* 3.6 32.1 - - + -
694A LEU* 4.0 31.4 - - + +
698A ALA* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU* 1.3 73.8 - - - +
515A LEU* 1.3 59.2 + - - +
552A ARG* 2.6 51.8 + - - +
568A LEU* 3.8 16.8 - - + +
606A PHE* 4.1 21.1 - - + -
610A ASP* 5.0 0.2 - - - +
611A ARG* 3.2 28.2 + - - +
614A ALA* 4.4 5.6 - - - -
615A SER 2.8 14.2 + - - +
616A ARG* 3.5 4.5 - - + +
617A ILE 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU* 3.9 13.6 - - + -
514A ASP* 1.3 73.7 - - - +
516A VAL* 1.3 66.5 + - - +
517A PHE* 3.6 32.7 - - + -
540A MET* 4.5 2.0 - - + -
544A LEU* 3.9 17.7 - - + -
551A VAL* 4.7 2.5 - - + -
552A ARG 2.8 13.7 + - - +
553A VAL* 3.2 7.9 - - + +
554A ALA 3.0 23.4 + - - +
568A LEU* 4.2 0.6 - - - +
617A ILE* 3.3 24.9 - - + +
619A LEU* 4.3 9.6 - - + -
694A LEU* 3.6 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU* 1.3 77.9 - - - +
517A PHE* 1.3 60.7 + - - +
518A LEU* 3.5 29.1 + - + +
554A ALA* 3.7 16.8 - - + +
556A VAL* 4.5 2.0 - - + -
568A LEU* 4.7 2.7 - - + -
601A THR* 4.7 2.7 - - - +
605A ILE* 3.7 28.7 - - + -
606A PHE* 3.7 35.4 - - + -
617A ILE 2.7 13.5 + - - +
618A ALA* 3.4 8.0 - - + -
619A LEU* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU* 3.6 23.1 - - + -
516A VAL* 1.3 73.0 - - - +
518A LEU* 1.3 60.8 + - - +
519A LEU* 3.8 15.1 - - + +
536A PHE* 5.8 0.4 - + - -
537A VAL* 4.0 20.0 - - + -
540A MET* 3.7 33.2 - - + -
541A MET* 4.0 15.9 - - + -
544A LEU* 4.3 3.1 - - + -
553A VAL* 3.9 25.1 - - + -
554A ALA 2.9 21.6 + - - +
555A VAL* 3.5 14.5 - - + -
556A VAL* 2.9 28.8 + - - +
619A LEU* 3.6 33.9 - - + -
621A LEU* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A VAL* 3.5 28.5 - - + +
517A PHE* 1.3 71.5 - - - +
519A LEU* 1.3 60.6 + - - +
556A VAL* 3.3 22.9 - - + -
558A TYR* 3.4 13.4 - - + -
597A VAL* 4.1 17.0 - - + -
598A LEU* 4.4 7.9 - - + -
600A TYR* 5.8 0.7 - - + -
601A THR* 3.7 23.1 - - - +
618A ALA* 4.3 17.5 - - + -
619A LEU 3.0 15.6 + - - +
620A LEU* 3.5 32.1 - - + -
621A LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 3.8 18.6 - - + +
518A LEU* 1.3 72.6 - - - +
520A ASP* 1.3 63.1 + - - +
521A GLY* 3.2 0.3 + - - -
530A PHE* 4.2 16.6 - - + -
533A LEU* 4.0 21.1 - - + -
534A LYS* 4.0 27.1 - - + -
537A VAL* 3.9 27.1 - - + -
555A VAL* 4.3 14.1 - - + -
556A VAL 2.7 14.1 + - - +
557A GLU* 3.4 7.8 - - - +
558A TYR* 2.8 33.4 + - - -
581A ALA 5.6 0.4 - - - +
584A VAL* 4.7 9.6 - - + -
621A LEU* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 1.3 68.5 - - - +
521A GLY* 1.3 59.6 + - - +
522A SER* 2.6 39.9 + - - +
525A LEU* 3.7 13.8 - - + +
530A PHE* 3.3 20.4 - - - -
533A LEU* 4.3 3.9 - - + +
558A TYR* 3.5 12.3 + - - +
592A ALA* 3.3 6.0 - - - +
594A THR* 6.0 0.3 - - - +
621A LEU 3.2 22.8 + - - +
622A MET* 3.8 2.3 - - - -
623A ALA* 2.7 36.9 + - + +
624A SER* 2.8 19.7 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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