Contacts of the helix formed by residues 535 - 557 (chain A) in PDB entry 2K9Y
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 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A SER* 6.3 0.2 - - - -
533A GLY* 3.3 3.3 - - - +
534A ASN* 1.3 88.1 - - + +
536A ALA* 1.3 60.8 + - - +
537A VAL 3.2 0.2 - - - -
538A ILE* 2.9 47.3 - - + +
533B GLY* 6.2 2.9 - - - -
535B LEU* 3.1 36.1 - - + -
536B ALA* 4.9 8.1 - - + +
538B ILE* 4.2 6.4 - - - +
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLU 4.7 1.1 - - - +
531A GLY* 3.3 33.7 - - - -
532A SER 3.8 4.2 - - - +
533A GLY 3.5 16.3 + - - +
534A ASN 3.1 0.2 - - - -
535A LEU* 1.3 74.3 - - - +
537A VAL* 1.3 62.6 + - + +
538A ILE 2.9 6.9 + - - -
539A GLY* 3.2 12.0 + - - -
540A GLY* 3.3 8.3 + - - -
535B LEU* 4.8 0.4 - - - +
538B ILE* 4.7 7.9 - - - +
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY 4.5 3.4 - - - +
534A ASN* 3.4 26.9 - - + +
535A LEU 3.2 0.2 - - - -
536A ALA* 1.3 75.4 - - + +
538A ILE* 1.3 64.7 + - + +
540A GLY* 3.9 3.3 - - - +
541A VAL* 3.2 34.8 + - + +
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ASN 4.6 1.8 - - - +
535A LEU* 2.9 49.6 - - + +
536A ALA 2.9 1.2 + - - -
537A VAL* 1.3 78.9 - - + +
539A GLY* 1.3 57.6 + - - +
541A VAL* 3.9 1.7 - - - +
542A ALA* 2.8 35.3 + - + +
535B LEU 4.2 9.6 - - - +
536B ALA* 4.6 8.7 - - + +
538B ILE* 4.7 1.1 - - + -
539B GLY* 3.1 37.2 - - - +
543B VAL* 5.2 2.9 - - + -
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Residues in contact with GLY 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA 3.2 6.3 + - - -
538A ILE* 1.3 78.8 - - - +
540A GLY* 1.3 58.0 + - - +
542A ALA* 4.3 2.5 - - - -
543A VAL* 2.7 45.2 + - - +
538B ILE* 3.1 30.3 - - - +
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Residues in contact with GLY 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA 3.3 11.3 + - - -
537A VAL* 3.5 4.0 + - - -
538A ILE 3.3 0.6 - - - -
539A GLY* 1.3 74.6 - - - +
541A VAL* 1.3 57.9 + - - +
543A VAL* 4.6 0.8 - - - +
544A GLY* 3.2 22.9 + - - -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A VAL* 3.2 31.6 + - + +
538A ILE* 4.0 1.1 - - - +
540A GLY* 1.3 74.7 - - - +
542A ALA* 1.3 68.2 + - - +
544A GLY* 3.2 1.8 + - - -
545A VAL* 2.9 39.0 + - + +
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Residues in contact with ALA 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ILE* 2.8 26.3 + - + +
541A VAL* 1.3 76.6 - - - +
543A VAL* 1.3 63.4 + - - +
545A VAL* 3.0 15.6 + - - +
546A VAL* 3.2 17.1 + - - +
542B ALA* 3.4 25.6 - - + -
543B VAL* 4.2 21.8 - - + +
546B VAL* 4.2 3.8 - - - +
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A LEU* 5.3 22.9 - - + +
539A GLY* 2.7 35.0 + - - +
540A GLY* 4.6 1.1 - - - +
542A ALA* 1.3 71.5 - - - +
544A GLY* 1.3 62.1 + - - +
546A VAL* 2.9 23.8 + - + +
547A LEU* 3.2 28.8 + - + +
538B ILE* 5.2 2.7 - - + -
542B ALA* 4.2 13.9 - - + -
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Residues in contact with GLY 544 (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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540A GLY 3.2 19.3 + - - -
541A VAL 3.2 1.5 + - - -
543A VAL* 1.3 78.2 - - - +
545A VAL* 1.3 60.6 + - - +
547A LEU* 3.7 12.2 + - - +
548A LEU* 3.3 22.9 + - - +
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Residues in contact with VAL 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A VAL* 2.9 39.6 + - + +
542A ALA* 3.0 8.9 + - - +
544A GLY* 1.3 75.2 - - - +
546A VAL* 1.3 59.2 + - - +
548A LEU* 3.3 7.6 + - + +
549A LEU* 2.9 30.7 + - + +
546B VAL* 4.3 20.6 - - + -
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ALA 3.3 16.6 - - - +
543A VAL* 2.9 14.5 + - + +
545A VAL* 1.3 74.8 - - - +
547A LEU* 1.3 65.7 + - + +
549A LEU* 2.9 23.5 + - - +
550A VAL* 3.2 11.9 + - + +
542B ALA* 4.2 8.7 - - - +
545B VAL* 4.4 17.5 - - + -
546B VAL* 3.3 26.5 - - + +
549B LEU* 4.1 19.2 - - + +
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 3.2 29.7 + - + +
544A GLY* 4.0 10.5 - - - +
546A VAL* 1.3 79.6 - - + +
548A LEU* 1.3 63.4 + - - +
550A VAL* 3.1 18.4 + - + +
551A LEU* 3.2 25.6 - - + +
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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
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544A GLY 3.3 15.8 + - - +
545A VAL* 3.5 7.9 - - - +
546A VAL 3.2 0.6 - - - -
547A LEU* 1.3 79.3 - - - +
549A LEU* 1.3 64.3 + - - +
551A LEU* 3.5 11.4 + - + +
552A ALA* 3.0 29.2 + - + +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A VAL* 2.9 16.1 + - + +
546A VAL* 2.9 13.2 + - - +
548A LEU* 1.3 79.5 - - - +
550A VAL* 1.3 60.1 + - - +
552A ALA* 3.6 4.6 - - - +
553A GLY* 3.1 22.4 + - - +
546B VAL* 4.1 24.5 - - + -
549B LEU* 3.2 45.8 - - + -
550B VAL* 4.3 15.9 - - + -
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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
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546A VAL* 3.5 16.2 - - + +
547A LEU* 3.1 13.2 + - + +
549A LEU* 1.3 75.0 - - - +
551A LEU* 1.3 67.7 + - + +
552A ALA 3.1 0.5 + - - -
554A VAL* 2.8 57.8 + - + +
549B LEU* 4.3 15.0 - - + -
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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 LEU* 3.2 24.2 + - + +
548A LEU* 3.9 14.4 - - + +
550A VAL* 1.3 86.7 - - + +
552A ALA* 1.3 54.2 + - - +
554A VAL* 4.9 2.0 - - - -
555A GLY* 2.7 32.4 + - - +
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Residues in contact with ALA 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* 3.0 27.8 + - + +
549A LEU* 3.6 7.6 - - + +
550A VAL 3.1 0.2 - - - -
551A LEU* 1.3 73.1 - - - +
553A GLY* 1.3 69.8 + - - +
555A GLY* 2.8 10.0 + - - -
556A PHE* 3.2 12.8 + - - +
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Residues in contact with GLY 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 LEU* 3.1 13.2 + - - +
550A VAL 4.0 0.4 - - - -
552A ALA* 1.3 79.2 - - - +
554A VAL* 1.3 53.0 + - - +
555A GLY 3.0 1.4 + - - -
556A PHE* 4.4 1.2 - - - +
557A PHE* 2.7 43.5 + - - +
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Residues in contact with VAL 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* 2.8 45.6 + - + +
551A LEU* 3.8 2.0 - - - +
553A GLY* 1.3 69.7 - - - -
555A GLY* 1.3 56.0 + - - +
557A PHE* 4.4 11.9 - - + -
558A ILE* 2.9 42.6 - - + +
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Residues in contact with GLY 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 2.7 24.5 + - - -
552A ALA 2.8 4.4 + - - -
554A VAL* 1.3 79.7 - - - +
556A PHE* 1.3 55.0 + - - -
558A ILE* 3.1 18.6 - - - +
559A HIS* 4.0 6.4 + - - +
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Residues in contact with PHE 556 (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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552A ALA 3.2 9.2 + - - +
553A GLY* 4.4 1.1 - - - +
555A GLY* 1.3 73.4 - - - +
557A PHE* 1.3 63.7 + - + +
558A ILE 2.9 5.2 - - - -
559A HIS 2.9 7.5 + - - +
560A ARG* 2.7 72.8 + - + -
557B PHE* 4.8 17.7 - + - -
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Residues in contact with PHE 557 (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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553A GLY* 2.7 30.1 + - - +
554A VAL* 4.4 6.7 - - + -
556A PHE* 1.3 78.4 - - + +
558A ILE* 1.3 55.9 + - - +
560A ARG* 2.9 38.5 + - - +
556B PHE* 4.8 20.0 - + - -
557B PHE* 3.7 48.0 - + + -
560B ARG* 4.5 8.1 - - - -
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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