Contacts of the helix formed by residues 510 - 522 (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 ASN 510 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D PRO* 4.0 12.1 - - + +
508D SER 3.8 4.0 + - - +
509D PHE* 1.3 72.1 - - - +
511D SER* 1.3 57.9 + - - +
512D ASN* 3.1 13.9 + - - +
513D THR* 2.9 51.0 + - - +
514D PHE* 3.1 8.8 + - - +
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Residues in contact with SER 511 (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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504D PHE* 4.0 15.9 - - - -
509D PHE* 3.1 22.5 + - - -
510D ASN* 1.3 71.0 + - - +
512D ASN* 1.3 64.9 + - - +
514D PHE* 3.4 3.7 + - - +
515D LEU* 3.1 18.4 + - - +
554D PRO* 4.3 8.2 - - - +
557D LEU* 3.7 35.4 - - - +
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Residues in contact with ASN 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ALA* 5.6 3.4 - - - +
132C GLU* 5.7 7.1 - - - +
510D ASN* 3.1 10.6 + - - +
511D SER* 1.3 83.0 + - - +
513D THR* 1.3 54.1 + - - +
515D LEU* 3.7 2.0 + - - +
516D THR* 2.4 46.5 + - - -
557D LEU* 4.0 10.3 - - - +
560D LEU* 4.0 26.3 - - - +
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Residues in contact with THR 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PRO* 4.0 18.2 - - + -
510D ASN* 2.9 35.3 + - - +
512D ASN* 1.3 74.7 - - - +
514D PHE* 1.3 61.8 + - - +
516D THR* 4.2 5.2 - - - -
517D ARG* 2.8 50.2 + - - +
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Residues in contact with PHE 514 (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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468D PRO* 4.0 10.0 - - + +
471D VAL* 3.8 18.8 - - + -
472D VAL* 3.3 40.8 - - + +
475D PHE* 4.4 16.6 - + + -
500D MET* 3.3 29.2 - - + -
504D PHE* 4.1 16.8 - + - -
509D PHE* 3.7 34.3 - + + -
510D ASN 3.1 5.4 + - - +
511D SER 3.5 8.3 - - - +
512D ASN 3.3 0.2 - - - -
513D THR* 1.3 78.1 - - - +
515D LEU* 1.3 59.1 + - + +
518D LEU* 2.6 55.5 + - + +
544D LEU* 6.1 1.3 - - + -
547D VAL* 6.6 0.2 - - + -
553D PHE* 6.1 1.6 - + - -
557D LEU* 5.3 0.9 - - + -
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Residues in contact with LEU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ALA* 6.1 1.3 - - + -
511D SER 3.1 12.7 + - - +
512D ASN 4.0 3.6 - - - +
514D PHE* 1.3 85.5 - - + +
516D THR* 1.3 60.2 + - - +
518D LEU* 3.3 13.7 - - + +
519D LEU* 2.9 42.1 + - + +
544D LEU* 6.0 0.4 - - + -
553D PHE* 5.6 3.6 - - + -
557D LEU* 3.5 38.4 - - + +
560D LEU* 3.3 37.5 - - + -
561D LEU* 3.7 37.7 - - + +
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Residues in contact with THR 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO* 5.2 14.6 - - + -
131C ALA* 4.4 14.4 - - + +
512D ASN* 2.4 35.9 + - - -
513D THR* 3.7 7.1 - - - -
515D LEU* 1.3 74.3 - - - +
517D ARG* 1.3 69.1 + - - +
519D LEU* 3.3 11.5 + - - +
520D ILE* 3.2 35.7 + - + +
525D LEU* 4.0 17.4 - - + +
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Residues in contact with ARG 517 (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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469D GLU* 2.7 45.6 + - - +
472D VAL* 4.0 10.5 - - + -
513D THR* 2.8 38.7 + - + +
514D PHE* 3.6 3.4 - - - +
516D THR* 1.3 73.5 - - - +
518D LEU* 1.3 65.8 + - - +
520D ILE* 3.3 40.1 + - - +
521D HIS* 3.0 41.8 + - + -
529D ASP* 3.5 30.9 + - - -
531D ILE* 4.6 4.8 - - - +
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Residues in contact with LEU 518 (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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472D VAL* 3.7 26.4 - - + +
475D PHE* 4.1 13.5 - - + -
476D LEU* 3.9 24.9 - - + -
514D PHE* 2.6 39.0 + - + +
515D LEU* 3.3 16.8 - - + +
517D ARG* 1.3 74.0 - - - +
519D LEU* 1.3 57.1 + - - +
521D HIS* 3.3 2.8 + - - +
522D MET* 2.9 57.1 + - + +
544D LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 519 (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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131C ALA* 4.6 7.9 - - + -
515D LEU* 2.9 30.2 + - + +
516D THR* 3.6 7.6 - - - +
517D ARG 3.3 0.2 - - - -
518D LEU* 1.3 73.4 - - - +
520D ILE* 1.3 64.2 + - - +
522D MET* 3.2 23.8 + - + +
523D GLY 3.0 3.5 + - - -
524D LEU* 2.9 40.6 + - + -
525D LEU* 3.4 20.8 + - + +
560D LEU 4.3 4.9 - - - +
561D LEU* 3.8 22.0 - - + -
564D PHE* 3.5 42.2 - - + -
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Residues in contact with ILE 520 (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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516D THR* 3.2 30.2 + - + +
517D ARG* 3.5 34.1 - - - +
519D LEU* 1.3 76.9 - - - +
521D HIS* 1.3 58.8 + - - +
523D GLY* 2.8 21.7 + - - -
525D LEU* 3.2 31.6 - - + +
526D LYS 4.2 1.8 - - - +
527D SER* 3.4 37.5 - - - +
531D ILE* 4.1 18.5 - - + +
533D ALA* 4.6 3.6 - - - +
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Residues in contact with HIS 521 (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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469D GLU* 2.9 29.0 + - - -
472D VAL* 3.8 17.8 - - + +
473D SER* 6.3 3.3 - - - -
476D LEU* 3.5 22.8 - - + +
517D ARG* 3.0 43.2 + - + +
518D LEU 3.7 2.0 - - - +
520D ILE* 1.3 77.9 - - - +
522D MET* 1.3 58.3 + - - +
523D GLY 3.2 0.2 - - - -
531D ILE* 4.0 28.8 - - + +
532D LYS* 4.2 5.6 + - + +
533D ALA* 3.3 5.4 - - - -
534D ILE* 3.1 29.8 + - + +
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Residues in contact with MET 522 (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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476D LEU* 4.2 8.7 - - + -
518D LEU* 2.9 48.7 + - + +
519D LEU* 3.8 26.7 - - + +
520D ILE 3.1 0.4 - - - -
521D HIS* 1.3 77.0 - - - +
523D GLY* 1.3 62.1 + - - +
524D LEU* 3.3 25.0 + - + +
533D ALA* 4.0 5.8 - - - +
534D ILE* 4.1 20.8 - - + +
537D LEU* 3.4 25.5 - - + +
540D PRO* 4.0 24.7 - - - -
541D LEU* 5.6 3.8 - - - -
544D LEU* 3.9 19.3 - - + -
561D LEU* 4.5 1.3 - - + -
571D ALA* 5.4 0.7 - - - +
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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
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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