Contacts of the helix formed by residues 537 - 550 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522D MET* 3.4 35.2 - - + +
524D LEU* 3.7 13.7 - - + -
534D ILE* 3.4 33.0 - - + +
535D PRO 5.6 0.7 - - - +
536D SER* 1.3 71.9 - - - +
538D HIS* 1.3 58.9 + - - +
540D PRO* 2.9 10.9 - - + +
541D LEU* 2.9 45.3 + - + +
571D ALA* 5.0 5.2 - - + +
572D LEU* 3.6 30.3 - - + +
601D SO4 3.0 12.0 + - - +
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Residues in contact with HIS 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D PHE* 4.9 12.5 - + - -
483D ARG* 6.4 0.7 - - - -
484D ASP* 4.9 10.7 + - - -
536D SER* 3.5 4.9 + - - +
537D LEU* 1.3 76.7 - - - +
539D GLY* 1.3 60.2 + - - +
541D LEU* 3.7 5.5 - - - +
542D MET* 2.8 63.3 + - + +
576D SER* 6.1 1.6 - - - -
577D PHE* 5.9 3.4 - + + -
578D ALA* 4.1 15.6 - - + +
601D SO4 3.3 27.7 + - - +
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Residues in contact with GLY 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D ALA 3.2 22.4 - - - -
480D SER* 4.9 4.3 - - - -
482D PHE* 4.1 15.5 - - - -
536D SER* 4.7 2.6 + - - -
538D HIS* 1.3 81.4 - - - +
540D PRO* 1.3 62.9 - - - +
542D MET* 3.1 1.9 + - - +
543D VAL* 2.8 33.0 + - - +
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Residues in contact with PRO 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D PHE* 4.7 4.9 - - + -
476D LEU* 4.1 16.8 - - + +
479D ALA* 4.0 18.6 - - + +
480D SER* 5.1 3.6 - - - -
522D MET* 4.0 21.3 - - - -
534D ILE* 3.9 13.0 - - + -
536D SER 3.7 8.5 - - - +
537D LEU* 2.9 33.7 - - + +
539D GLY* 1.3 88.8 - - - +
541D LEU* 1.3 51.5 + - + +
543D VAL* 3.1 1.9 + - + +
544D LEU* 2.5 42.9 + - + +
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Residues in contact with LEU 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D MET* 5.7 3.8 - - - -
524D LEU* 5.8 3.8 - - + -
537D LEU* 2.9 32.5 + - + +
538D HIS* 3.8 4.3 - - - +
540D PRO* 1.3 78.5 - - + +
542D MET* 1.3 64.0 + - - +
544D LEU* 3.4 12.2 + - + +
545D ASN* 3.4 20.3 + - - +
565D VAL* 4.7 12.1 - - + -
572D LEU* 3.4 35.4 - - + -
576D SER* 5.1 3.4 - - - +
578D ALA* 3.9 26.6 - - + +
579D ARG* 4.7 8.7 - - + +
582D LEU* 3.5 30.2 - - + +
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Residues in contact with MET 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D PHE* 3.4 42.4 - - + -
484D ASP* 4.2 13.5 - - - +
489D LYS* 5.8 3.4 - - - -
493D LEU* 5.4 0.7 - - - +
538D HIS* 2.8 46.1 + - + +
539D GLY 3.5 2.7 - - - +
541D LEU* 1.3 78.0 - - - +
543D VAL* 1.3 61.4 + - - +
545D ASN* 3.6 13.3 + - - +
546D HIS* 3.7 9.5 + - - +
577D PHE* 4.2 24.9 - - + -
578D ALA* 4.1 20.2 - - + -
581D ASN* 6.2 1.3 - - - -
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Residues in contact with VAL 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D PHE* 3.9 12.8 - - + -
479D ALA* 3.8 19.1 - - + -
482D PHE* 4.0 26.2 - - + -
492D VAL* 4.2 5.6 - - + -
493D LEU* 4.6 8.5 - - + -
496D ILE* 3.7 39.3 - - + -
539D GLY 2.8 21.6 + - - +
540D PRO* 3.6 3.6 - - + +
542D MET* 1.3 77.6 - - - +
544D LEU* 1.3 65.2 + - - +
546D HIS* 3.2 7.7 + - - +
547D VAL* 3.0 18.5 + - - +
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Residues in contact with LEU 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D PHE* 4.0 16.8 - - + -
514D PHE* 6.1 1.3 - - + -
515D LEU* 6.0 0.2 - - + -
518D LEU* 3.9 21.8 - - + -
522D MET* 3.9 31.9 - - + -
540D PRO 2.5 28.9 + - - +
541D LEU* 3.9 12.6 - - + +
542D MET 3.4 0.2 - - - -
543D VAL* 1.3 70.9 - - - +
545D ASN* 1.3 67.4 + - - +
547D VAL* 3.2 8.2 + - + -
548D VAL* 2.8 33.7 + - + +
553D PHE* 6.1 2.5 - - + -
561D LEU* 4.1 27.6 - - + -
565D VAL* 5.5 0.4 - - + -
582D LEU* 4.1 17.0 - - + -
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Residues in contact with ASN 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541D LEU 3.4 9.9 + - - +
542D MET* 3.8 12.1 - - - +
543D VAL 3.2 0.6 - - - -
544D LEU* 1.3 79.3 - - - +
546D HIS* 1.3 60.0 + - - +
548D VAL* 3.7 1.5 + - - +
549D ARG* 2.9 38.7 + - - +
578D ALA 5.4 0.9 - - - +
581D ASN* 3.3 26.0 + - + +
582D LEU* 3.7 28.8 - - + +
585D THR* 2.6 35.8 + - - +
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Residues in contact with HIS 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D LEU* 3.6 45.2 - - + +
496D ILE* 5.4 1.1 - - + -
497D ASP* 2.6 43.6 + - - -
542D MET 3.7 6.1 + - - +
543D VAL 3.2 9.6 + - - +
544D LEU 3.1 0.6 - - - -
545D ASN* 1.3 78.6 - - - +
547D VAL* 1.3 69.7 + - + +
549D ARG* 2.9 17.8 + - - +
550D GLN* 3.1 34.3 + - - +
552D TYR* 4.6 0.4 - - - -
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Residues in contact with VAL 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D PHE* 4.0 15.0 - - + -
496D ILE* 3.6 23.6 - - + -
500D MET* 4.8 3.6 - - + -
504D PHE* 4.5 6.1 - - + -
514D PHE* 6.6 0.2 - - + -
543D VAL* 3.0 14.8 + - + +
544D LEU* 3.6 12.6 - - + +
546D HIS* 1.3 77.3 - - + +
548D VAL* 1.3 59.1 + - + +
550D GLN* 2.8 28.1 + - - +
552D TYR* 3.6 38.1 - - + +
553D PHE* 3.5 24.7 - - + +
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Residues in contact with VAL 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D LEU* 2.8 28.3 + - + +
545D ASN* 4.1 4.7 - - - +
547D VAL* 1.3 72.2 - - + +
549D ARG* 1.3 59.7 + - - +
550D GLN 3.5 5.8 + - - +
553D PHE* 3.7 38.1 - - + -
555D LYS* 5.2 3.8 + - - +
561D LEU* 3.8 27.8 - - + -
582D LEU* 4.5 2.9 - - + -
585D THR* 4.5 11.7 - - + +
586D LEU* 3.5 27.6 - - + -
589D ILE* 4.4 17.7 - - + +
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Residues in contact with ARG 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D ASN* 2.9 29.8 + - - +
546D HIS* 2.9 12.1 + - - +
548D VAL* 1.3 75.3 - - - +
550D GLN* 1.3 70.5 + - - +
551D ASP* 5.2 2.1 - - - +
581D ASN* 5.3 6.4 + - - -
585D THR* 3.5 40.0 + - + +
588D ASN* 5.3 8.9 - - - +
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Residues in contact with GLN 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D ASP* 3.9 7.3 + - - +
546D HIS* 3.1 44.0 + - - +
547D VAL 2.8 16.4 + - - +
548D VAL 3.8 3.5 - - - +
549D ARG* 1.3 89.2 + - - +
551D ASP* 1.3 65.8 + - - +
552D TYR* 3.5 37.8 - - + -
553D PHE* 3.7 15.5 + - - +
555D LYS* 5.5 5.2 + - - +
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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