Contacts of the helix formed by residues 548 - 569 (chain A) in PDB entry 4KSP
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 GLU 548 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A LYS 5.6 0.9 - - - +
547A PHE* 1.3 75.2 - - - +
549A MET* 1.3 57.2 + - - +
550A ILE* 3.1 19.0 - - + +
551A LYS* 2.7 30.0 + - + +
552A LEU* 3.0 10.8 + - - +
681A ARG* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE 3.7 2.0 + - - -
548A GLU* 1.3 71.3 - - - +
550A ILE* 1.3 62.8 + - - +
552A LEU* 3.4 9.6 + - + -
553A ILE* 3.1 46.0 + - + +
649A MET* 3.1 37.5 - - + -
681A ARG* 3.8 31.1 - - + +
683A ASN* 3.3 52.1 - - - +
684A CYS* 3.9 9.4 - - - -
685A PRO* 4.5 2.7 - - + -
720A LEU* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU* 3.0 15.5 + - + +
549A MET* 1.3 79.4 - - - +
551A LYS* 1.3 65.4 + - + +
553A ILE* 3.7 8.8 + - - +
554A ASP* 3.2 23.2 + - - +
720A LEU* 4.3 18.6 - - + +
721A PRO* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 3.7 35.0 - - + -
548A GLU* 2.7 24.8 + - + +
550A ILE* 1.3 77.9 - - + +
552A LEU* 1.3 60.9 + - - +
553A ILE 3.2 1.3 - - - -
554A ASP* 2.9 14.4 + - + +
555A ILE* 2.8 41.3 + - + +
583A LEU* 5.0 2.0 - - - +
586A ASP 3.1 26.8 + - - -
587A LEU* 3.8 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 5.0 3.4 - - + -
547A PHE* 3.7 36.8 - - + +
548A GLU 3.0 7.8 + - - +
549A MET* 3.7 28.0 - - + +
551A LYS* 1.3 76.1 - - - +
553A ILE* 1.3 58.6 + - - +
555A ILE* 3.4 6.7 + - + +
556A ALA* 3.0 27.0 + - - +
648A LEU* 3.2 54.1 - - + +
649A MET* 4.5 9.6 - - + -
681A ARG* 3.4 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A MET* 3.1 37.8 + - + +
550A ILE* 3.9 4.5 - - - +
552A LEU* 1.3 73.3 - - - +
554A ASP* 1.3 60.7 + - - +
556A ALA* 3.3 7.3 + - - +
557A ARG* 2.9 26.6 + - + +
649A MET* 4.9 1.6 - - + -
685A PRO* 4.4 9.0 - - + -
688A MET* 3.8 21.1 - - + -
713A ILE* 4.1 19.4 - - + +
716A LEU* 4.3 19.7 - - + -
717A ALA* 4.4 13.2 - - + -
720A LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ILE 3.2 14.5 + - - +
551A LYS* 2.9 20.1 + - + +
553A ILE* 1.3 74.7 - - - +
555A ILE* 1.3 66.4 + - - +
557A ARG* 3.0 30.5 + - - +
558A GLN* 2.9 47.0 + - - +
587A LEU 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 3.8 27.8 - - + -
547A PHE* 4.4 19.7 - - + -
551A LYS* 2.8 41.7 + - + +
552A LEU* 3.6 9.6 - - - +
554A ASP* 1.3 74.7 - - - +
556A ALA* 1.3 62.5 + - - +
558A GLN* 3.3 5.9 + - - +
559A THR* 2.9 32.8 + - - +
581A ILE* 5.6 0.2 - - + -
583A LEU* 3.9 26.2 - - + -
587A LEU 5.7 1.1 - - - +
589A VAL* 3.8 18.2 - - + +
648A LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU 3.0 14.1 + - - +
553A ILE* 3.4 12.3 - - - +
554A ASP 3.1 0.2 - - - -
555A ILE* 1.3 78.8 - - - +
557A ARG* 1.3 62.1 + - - +
559A THR* 3.5 5.9 + - - -
560A ALA* 3.0 24.4 + - - +
641A PHE* 3.9 4.2 - - - -
645A LEU* 3.7 28.5 - - + -
648A LEU* 3.9 9.4 - - + -
649A MET* 6.1 1.1 - - - -
688A MET* 4.7 7.2 - - + -
713A ILE* 3.9 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ASN* 4.4 3.6 + - - -
553A ILE* 2.9 14.2 + - + +
554A ASP* 3.3 33.3 + - - +
556A ALA* 1.3 75.6 - - - +
558A GLN* 1.3 85.3 + - - +
560A ALA* 3.4 3.5 + - - +
561A GLN* 2.9 61.3 + - - +
710A LEU* 3.7 6.3 - - + +
713A ILE* 3.9 28.0 - - + +
714A GLU* 4.5 24.5 + - + -
717A ALA* 6.0 4.0 - - + -
477B GLY* 5.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ASN* 3.1 24.9 + - - +
554A ASP* 2.9 41.2 + - - +
555A ILE* 3.7 6.4 - - - +
557A ARG* 1.3 96.6 - - - +
559A THR* 1.3 67.8 + - - +
561A GLN* 2.9 18.3 + - - +
562A GLY* 2.9 11.8 + - - -
587A LEU 3.2 19.4 + - - -
588A THR* 3.4 7.5 - - - +
589A VAL* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 5.5 0.2 - - - +
555A ILE* 2.9 22.9 + - - +
556A ALA* 3.7 6.9 - - - -
558A GLN* 1.3 77.3 - - - +
560A ALA* 1.3 61.4 + - - +
562A GLY 3.5 0.5 + - - -
563A MET* 3.2 24.6 + - + +
576A LEU* 4.7 5.2 - - + -
581A ILE* 3.5 32.2 - - + +
589A VAL* 4.0 19.3 - - - +
591A ILE* 3.5 13.6 - - + +
641A PHE* 4.1 21.1 - - + -
644A VAL* 5.2 6.4 - - + +
648A LEU* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ALA 3.0 17.5 + - - +
557A ARG 3.5 2.0 - - - +
558A GLN 3.1 0.2 - - - -
559A THR* 1.3 74.0 - - - +
561A GLN* 1.3 60.4 + - - +
563A MET* 3.4 1.7 + - - +
564A ASP* 2.9 30.0 + - - +
641A PHE* 3.9 20.8 - - + -
706A PHE* 4.0 17.3 - - + -
709A ILE* 4.4 3.8 - - + -
710A LEU* 3.4 21.9 - - + +
713A ILE* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A HIS* 4.0 5.3 + - + -
511A ASN* 3.5 16.8 - - - +
557A ARG* 2.9 39.5 + - - +
558A GLN* 3.1 11.0 - - - +
560A ALA* 1.3 77.8 - - - +
562A GLY* 1.3 60.7 + - - +
564A ASP* 3.4 6.8 + - - +
565A TYR* 3.2 19.8 + - - +
710A LEU* 3.3 34.1 - - - +
714A GLU* 4.7 5.7 - - - +
476B HIS* 3.3 42.5 - - - +
477B GLY* 3.5 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A HIS* 4.6 0.7 - - - -
511A ASN* 3.9 14.2 - - - +
512A ILE* 3.5 20.7 - - - +
558A GLN 2.9 10.1 + - - -
559A THR 3.9 2.7 - - - -
561A GLN* 1.3 74.3 - - - +
563A MET* 1.3 64.2 + - - +
565A TYR* 3.2 8.1 + - - +
566A LEU* 3.1 24.2 + - - +
591A ILE* 4.2 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A THR* 3.2 19.8 + - + +
560A ALA 3.8 2.7 - - - +
562A GLY* 1.3 72.1 - - - +
564A ASP* 1.3 68.7 + - - +
566A LEU* 3.1 16.3 + - + +
567A HIS* 2.9 36.4 + - + +
573A HIS* 4.1 11.0 - - + -
576A LEU* 3.9 28.0 - - + -
591A ILE* 3.6 21.1 - - + -
637A ASP* 3.5 38.4 - - + +
706A PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A ALA 2.9 15.1 + - - +
561A GLN* 3.4 13.2 + - - +
563A MET* 1.3 75.7 - - - +
565A TYR* 1.3 56.4 + - - +
567A HIS* 3.9 3.5 - - - +
568A ALA* 3.0 30.5 + - - +
706A PHE* 4.0 12.6 - - + +
707A PRO* 3.4 33.3 - - - +
710A LEU* 4.0 22.4 - - + +
476B HIS* 3.1 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A THR* 4.1 13.0 - - + -
508A ARG 3.1 42.4 + - - -
509A HIS* 3.5 35.0 - + + -
512A ILE* 3.9 9.4 - - + -
561A GLN 3.2 8.1 + - - +
562A GLY 3.2 10.0 + - - +
563A MET 3.1 0.4 - - - -
564A ASP* 1.3 80.0 - - - +
566A LEU* 1.3 68.3 + - + +
568A ALA* 3.3 4.5 + - - +
569A LYS* 3.1 52.7 + - + +
449B TRP* 3.8 8.1 - - - -
475B TRP* 3.9 25.3 - + - -
476B HIS* 3.7 25.7 + + + -
516B MET* 4.7 1.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A THR* 3.9 28.3 - - + -
512A ILE* 4.1 18.6 - - + -
562A GLY 3.1 10.7 + - - +
563A MET* 3.1 33.0 + - + +
565A TYR* 1.3 77.7 - - + +
567A HIS* 1.3 63.8 + - + +
569A LYS* 3.0 12.5 + - - +
571A ILE* 2.8 51.8 + - + +
573A HIS* 4.6 8.7 - - + -
591A ILE* 4.7 4.3 - - + -
901A 1SU 4.3 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A MET* 2.9 25.6 + - + +
564A ASP* 3.9 5.2 - - - +
566A LEU* 1.3 78.8 - - + +
568A ALA* 1.3 61.5 + - - +
570A SER* 3.2 9.2 + - - -
571A ILE 3.4 15.5 - - - -
572A ILE* 4.8 0.2 - - - -
634A PHE* 3.2 79.3 - + + +
637A ASP* 3.2 23.6 + - + +
638A VAL* 5.0 0.4 - - + -
705A LEU* 5.4 2.2 - - - +
706A PHE* 3.6 29.0 + + + +
707A PRO* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 3.0 19.1 + - - +
565A TYR 3.4 6.1 - - - +
567A HIS* 1.3 78.8 - - - +
569A LYS* 1.3 58.6 + - + +
570A SER* 3.2 4.4 + - - -
476B HIS* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LYS* 3.4 37.3 + - + +
565A TYR* 3.1 44.9 + - + +
566A LEU 3.0 9.3 + - - +
568A ALA* 1.3 76.8 - - + +
570A SER* 1.3 67.1 + - - +
571A ILE* 3.6 19.2 + - + +
448B ASP 4.8 7.1 + - - -
449B TRP* 3.5 27.1 - - - +
475B TRP* 5.2 8.0 - - - -
----------------------------------------------------------
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