Contacts of the helix formed by residues 537 - 550 (chain B) in PDB entry 1KPS
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 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522B MET* 3.4 53.4 - - + +
524B LEU* 4.9 3.6 - - + -
534B ILE* 3.6 14.1 - - + +
535B PRO 5.5 2.2 - - - +
536B SER* 1.3 77.5 + - - +
538B HIS* 1.3 65.0 + - - +
539B GLY 3.3 2.7 - - - -
540B PRO* 3.5 6.7 - - + +
541B LEU* 3.1 40.5 + - + +
571B ALA* 4.3 15.0 - - + -
572B LEU* 4.2 21.3 - - + -
603B SO4 3.3 11.7 + - - +
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Residues in contact with HIS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B PHE* 4.5 12.9 - + - -
483B ARG* 6.4 0.2 - - - -
484B ASP* 5.2 7.9 + - - -
536B SER* 3.5 3.5 + - - +
537B LEU* 1.3 75.8 - - - +
539B GLY* 1.3 67.7 + - - +
541B LEU* 3.9 5.1 - - - +
542B MET* 3.0 62.5 + - + +
576B SER* 5.2 2.0 + - - -
577B PHE* 3.5 40.9 - + + -
578B ALA* 4.1 7.9 - - + +
603B SO4 3.0 24.4 + - - +
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Residues in contact with GLY 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B ALA 3.2 20.4 - - - -
480B SER* 4.9 2.7 - - - -
482B PHE* 4.3 15.0 - - - -
536B SER* 4.8 2.2 + - - -
538B HIS* 1.3 76.9 - - - +
540B PRO* 1.3 73.7 - - - +
542B MET* 3.0 4.0 + - - +
543B VAL* 3.0 25.3 + - - +
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Residues in contact with PRO 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B PHE* 4.9 7.0 - - + -
476B LEU* 4.2 13.0 - - + +
479B ALA* 3.9 24.9 - - + +
480B SER* 4.8 5.4 - - - +
522B MET* 4.2 18.8 - - - -
534B ILE* 3.8 26.7 - - + -
536B SER 4.2 4.3 - - - +
537B LEU* 3.5 21.3 - - + +
539B GLY* 1.3 86.9 - - - +
541B LEU* 1.3 50.1 + - - +
543B VAL* 3.2 2.3 + - + +
544B LEU* 2.6 42.8 + - + +
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B MET* 5.4 5.8 - - - -
524B LEU* 5.9 3.4 - - + -
537B LEU* 3.1 38.9 + - + +
538B HIS* 4.0 2.2 - - - +
539B GLY 3.2 0.8 - - - -
540B PRO* 1.3 74.0 - - + +
542B MET* 1.3 64.9 + - - +
544B LEU* 4.0 12.4 - - + +
545B ASN* 3.4 19.6 + - - +
565B VAL* 4.3 13.2 - - + -
572B LEU* 4.6 18.6 - - + -
576B SER* 4.5 9.0 - - - +
578B ALA* 3.9 18.2 - - + +
579B ARG* 4.5 21.5 - - + +
582B LEU* 3.4 31.9 - - + +
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Residues in contact with MET 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B PHE* 3.5 40.1 - - + -
484B ASP* 4.8 8.1 - - - +
493B LEU* 5.0 1.2 - - - +
538B HIS* 3.0 48.6 + - + +
539B GLY 3.0 5.4 + - - +
541B LEU* 1.3 77.5 - - - +
543B VAL* 1.3 63.1 + - - +
545B ASN* 3.6 11.8 + - - +
546B HIS* 3.6 11.3 + - - +
577B PHE* 5.7 0.4 - - - -
578B ALA* 3.6 24.0 - - + -
581B ASN* 5.7 3.6 - - - +
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B PHE* 4.0 8.1 - - + -
479B ALA* 4.0 22.2 - - + -
482B PHE* 4.3 20.6 - - + -
492B VAL* 4.3 5.8 - - + -
493B LEU* 4.1 14.6 - - + -
496B ILE* 3.6 39.0 - - + -
539B GLY 3.0 16.3 + - - +
540B PRO* 3.7 5.4 - - + +
542B MET* 1.3 76.7 - - - +
544B LEU* 1.3 60.9 + - - +
546B HIS* 3.1 2.9 + - - +
547B VAL* 2.8 31.2 + - + +
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B PHE* 3.8 26.5 - - + -
514B PHE* 6.0 1.6 - - + -
518B LEU* 4.3 11.2 - - + -
522B MET* 4.2 31.6 - - + -
540B PRO* 2.6 26.1 + - + +
541B LEU* 4.0 9.0 - - + +
542B MET 3.4 0.4 - - - -
543B VAL* 1.3 74.7 - - - +
545B ASN* 1.3 55.4 + - - +
547B VAL* 4.1 11.7 - - + -
548B VAL* 2.8 36.6 + - + +
553B PHE* 5.9 2.5 - - + -
561B LEU* 4.3 28.3 - - + -
582B LEU* 4.0 21.1 - - + -
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Residues in contact with ASN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B LEU 3.4 11.1 + - - +
542B MET* 3.8 10.8 - - - +
543B VAL 3.2 0.8 - - - -
544B LEU* 1.3 77.4 - - - +
546B HIS* 1.3 60.9 + - - +
548B VAL* 3.5 2.6 + - - +
549B ARG* 2.8 43.8 + - - +
578B ALA 5.5 0.4 - - - +
581B ASN* 3.4 21.7 - - + +
582B LEU* 3.5 23.5 - - + +
585B THR* 2.6 32.7 + - - -
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Residues in contact with HIS 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B LYS* 6.2 0.2 - - - -
493B LEU* 3.6 47.5 - - + +
496B ILE* 6.1 0.7 - - + -
497B ASP* 3.3 34.9 + - - -
542B MET 3.6 6.9 + - - +
543B VAL 3.1 8.2 + - - +
545B ASN* 1.3 80.1 - - - +
547B VAL* 1.3 67.9 + - + +
549B ARG* 2.9 19.3 + - - +
550B GLN* 3.1 37.2 + - - +
552B TYR* 4.9 0.7 - - - -
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B PHE* 4.0 11.4 - - + -
496B ILE* 3.7 24.7 - - + -
500B MET* 4.9 1.3 - - + -
504B PHE* 4.7 4.9 - - + -
514B PHE* 6.3 1.8 - - + -
543B VAL* 2.8 27.2 + - + +
544B LEU* 3.6 13.9 - - + +
546B HIS* 1.3 75.0 - - + +
548B VAL* 1.3 59.0 + - - +
550B GLN* 3.0 25.8 + - - +
552B TYR* 3.3 33.4 - - + +
553B PHE* 3.4 29.0 - - + +
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 2.8 29.1 + - + +
545B ASN* 3.9 5.6 - - - +
547B VAL* 1.3 73.9 - - + +
549B ARG* 1.3 57.6 + - - +
550B GLN 3.2 6.3 + - - +
553B PHE* 3.9 38.7 - - + -
555B LYS* 6.0 1.0 - - - +
561B LEU* 4.1 19.1 - - + -
582B LEU* 4.4 3.4 - - + -
585B THR* 4.5 10.0 - - + +
586B LEU* 3.8 15.5 - - + -
589B ILE* 3.4 33.0 - - + +
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Residues in contact with ARG 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B ASN* 2.8 41.1 - - - +
546B HIS* 2.9 12.8 + - - +
548B VAL* 1.3 75.8 - - - +
550B GLN* 1.3 69.9 + - - +
551B ASP* 5.7 0.3 - - - -
585B THR* 3.9 23.3 - - + +
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Residues in contact with GLN 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ASP* 3.7 11.6 - - - +
546B HIS* 3.1 48.6 + - + +
547B VAL* 3.0 11.3 + - - +
548B VAL 3.9 2.3 - - - +
549B ARG* 1.3 92.2 + - - +
551B ASP* 1.3 65.6 + - - +
552B TYR* 3.4 36.0 - - + +
553B PHE* 3.3 17.2 + - - +
555B LYS* 5.7 3.3 - - - -
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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