Contacts of the helix formed by residues 535 - 557 (chain A) in PDB entry 3KSS
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 TRP 535 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A LYS* 3.7 39.7 - - + -
532A VAL* 3.0 15.9 + - - +
533A LEU 3.2 0.2 - - - -
534A HIS* 1.3 90.2 + + + +
536A PRO* 1.3 64.9 - - - +
537A LYS 3.6 0.9 - - - -
538A THR* 2.7 48.8 + - + +
539A THR* 3.2 5.8 - - + +
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Residues in contact with PRO 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A VAL 4.5 0.9 - - - +
533A LEU 3.9 2.2 - - - +
534A HIS 3.0 14.6 - - - +
535A TRP* 1.3 82.4 - - - +
537A LYS* 1.3 66.7 + - + +
538A THR* 3.2 0.6 + - + -
539A THR* 2.6 26.7 + - - +
540A LEU* 3.4 5.3 + - - +
1033A ALA* 4.4 4.0 - - + +
1036A LYS* 3.4 26.2 - - + +
1037A LEU* 3.2 35.6 - - + +
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Residues in contact with LYS 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO* 1.3 82.6 - - + +
538A THR* 1.3 53.4 + - + +
540A LEU* 3.2 34.3 + - + +
541A LEU* 2.7 70.7 + - + +
1037A LEU* 4.8 12.3 - - + +
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Residues in contact with THR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TRP* 2.7 47.0 + - + +
537A LYS* 1.3 75.9 - - + +
539A THR* 1.3 68.4 + - - +
541A LEU* 3.1 7.0 + - - +
542A VAL* 2.6 47.2 + - - +
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Residues in contact with THR 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A VAL* 3.5 30.7 - - + +
535A TRP 3.2 16.8 - - - +
536A PRO* 2.6 19.0 + - + -
538A THR* 1.3 83.7 + - - +
540A LEU* 1.3 61.6 + - - +
542A VAL* 3.3 9.4 + - - +
543A ALA* 2.9 28.8 + - - +
1029A PHE* 4.8 13.6 + - + -
1033A ALA* 3.7 17.9 - - + +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO 3.9 7.4 - - - +
537A LYS* 3.2 45.9 + - + +
538A THR 3.1 0.4 - - - -
539A THR* 1.3 83.2 + - - +
541A LEU* 1.3 63.6 + - + +
543A ALA* 2.9 25.5 + - + +
544A ALA* 2.9 16.1 + - + +
1033A ALA* 6.2 1.1 - - + -
1037A LEU* 5.5 9.6 - - + -
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Residues in contact with LEU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LYS* 2.7 58.2 + - + +
538A THR* 3.8 5.2 - - - +
540A LEU* 1.3 77.8 - - + +
542A VAL* 1.3 61.5 + - + +
544A ALA* 3.3 12.6 + - + +
545A LEU* 3.1 31.7 + - + +
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A THR* 2.6 37.7 + - - +
539A THR* 3.4 9.9 - - - +
541A LEU* 1.3 72.5 - - + +
543A ALA* 1.3 58.2 + - - +
545A LEU* 3.2 11.7 + - + +
546A SER* 3.0 27.9 + - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A THR 2.9 13.9 + - - +
540A LEU* 2.9 15.9 + - + +
542A VAL* 1.3 75.4 - - - +
544A ALA* 1.3 57.5 + - - +
546A SER* 2.6 23.2 + - - +
547A VAL* 2.9 21.7 + - - +
906A PHE* 4.8 21.3 - - + +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 2.9 16.3 + - + +
541A LEU* 3.4 21.3 - - + +
542A VAL 3.2 0.2 - - - -
543A ALA* 1.3 76.0 - - - +
545A LEU* 1.3 63.6 + - + +
547A VAL* 3.3 12.5 + - - +
548A LEU* 3.1 21.5 + - - +
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LEU* 3.1 18.5 + - + +
542A VAL* 3.6 11.7 - - + +
543A ALA 3.2 0.2 - - - -
544A ALA* 1.3 78.8 - - + +
546A SER* 1.3 61.3 + - - +
547A VAL 3.1 0.4 - - - -
548A LEU* 3.0 38.7 + - + +
549A THR* 3.1 6.2 + - - -
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A VAL* 3.0 11.5 + - - +
543A ALA* 2.6 32.1 + - - +
545A LEU* 1.3 75.2 - - - +
547A VAL* 1.3 60.0 + - - +
549A THR* 2.9 31.6 - - - +
550A VAL* 3.4 6.6 + - - +
906A PHE* 5.6 2.3 - - - +
909A VAL* 4.1 12.4 - - - +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ALA 2.9 16.3 + - - +
544A ALA* 3.4 13.0 - - - +
546A SER* 1.3 77.4 - - - +
548A LEU* 1.3 63.0 + - - +
550A VAL* 2.8 31.9 - - + +
551A LEU* 3.1 13.4 + - + +
905A PRO* 4.8 9.2 - - + -
906A PHE* 4.1 31.9 - - + +
909A VAL* 4.3 6.3 - - + -
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ALA 3.1 9.4 + - - +
545A LEU* 3.0 29.0 + - + +
547A VAL* 1.3 78.2 - - - +
549A THR* 1.3 63.2 + - - +
551A LEU* 2.5 38.1 + - + +
552A TRP* 3.1 9.8 + - + +
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Residues in contact with THR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A LEU 3.1 7.2 + - - -
546A SER* 2.9 28.3 - - - +
548A LEU* 1.3 88.5 - - - +
550A VAL* 1.3 55.0 + - - +
552A TRP* 4.2 6.8 - - - +
553A PRO* 2.9 17.2 - - - +
909A VAL* 4.9 2.9 - - + -
913A TRP* 2.8 54.8 + - + +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A SER 3.4 2.4 + - - +
547A VAL* 2.8 29.8 + - + +
548A LEU 3.0 0.6 - - - -
549A THR* 1.3 78.8 - - - +
551A LEU* 1.3 60.6 + - + +
553A PRO* 3.3 20.5 - - - +
554A LEU* 3.4 17.5 + - + +
905A PRO 5.8 0.9 - - - +
909A VAL* 3.4 39.0 - - + -
912A ILE* 3.1 45.4 - - + +
913A TRP* 3.3 6.1 - - + +
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A VAL* 3.1 17.1 + - + +
548A LEU* 2.5 27.0 + - + +
550A VAL* 1.3 72.7 - - + +
552A TRP* 1.3 67.4 + - - +
553A PRO 3.1 1.6 - - - -
554A LEU* 3.1 20.6 + - + +
555A ASN* 3.4 14.0 + - + +
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Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A LEU* 3.1 11.5 + - + +
549A THR* 4.2 11.4 - - - +
551A LEU* 1.3 80.0 - - - +
553A PRO* 1.3 74.0 - - + +
555A ASN* 3.6 6.1 + - - +
556A LYS* 3.5 36.4 + - + +
913A TRP* 4.6 12.6 - + - -
916A TRP* 3.1 37.9 - + - -
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Residues in contact with PRO 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A THR 2.9 26.9 - - - +
550A VAL 3.3 7.0 - - - +
552A TRP* 1.3 92.3 - - + +
554A LEU* 1.3 55.2 + - - +
555A ASN 3.0 2.2 - - - -
556A LYS* 2.6 25.1 + - - -
557A VAL* 2.7 16.4 + - - -
912A ILE* 3.2 30.5 - - + -
913A TRP* 4.0 4.3 - - + +
916A TRP* 3.0 42.9 - - + +
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A VAL* 3.5 20.4 - - + +
551A LEU* 3.1 15.6 + - + +
553A PRO* 1.3 77.6 - - - +
555A ASN* 1.3 57.9 + - - +
557A VAL* 3.2 21.5 - - - +
912A ILE* 3.6 30.5 - - + -
915A LEU* 5.4 4.0 - - + -
930A PHE* 5.2 9.2 - - + -
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Residues in contact with ASN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 3.4 12.6 + - + +
552A TRP* 3.9 9.2 - - - +
553A PRO 3.0 0.8 - - - -
554A LEU* 1.3 78.8 - - - +
556A LYS* 1.3 60.9 + - - +
557A VAL* 3.7 6.6 - - - +
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Residues in contact with LYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A TRP* 3.5 32.6 + - + +
553A PRO 2.6 13.3 + - - +
555A ASN* 1.3 72.9 - - - +
557A VAL* 1.3 64.5 - - - +
558A GLY* 2.8 42.5 + - - +
916A TRP* 3.5 28.0 - - + +
919A GLY* 6.0 2.2 - - - -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO 2.7 17.7 + - - -
554A LEU* 3.2 21.8 - - - +
555A ASN 3.7 7.2 - - - +
556A LYS* 1.3 78.1 - - - +
558A GLY* 1.3 62.3 + - - +
559A GLY* 3.1 3.9 + - - +
560A GLU 5.3 5.8 - - - +
561A PHE* 5.5 12.8 - - + -
915A LEU* 6.0 3.1 - - - -
916A TRP* 4.2 6.1 - - - -
920A PHE 3.8 1.6 - - - +
921A HIS 2.7 33.4 - - - +
922A LEU* 5.1 13.7 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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