Contacts of the helix formed by residues 576 - 589 (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 SER 576 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A CYS* 4.1 7.4 + - - +
538D HIS* 6.1 1.6 - - - -
541D LEU* 5.1 4.0 - - - +
573D GLU* 3.9 18.0 - - - +
575D CYS* 1.3 76.2 - - - +
577D PHE* 1.3 64.8 + - - +
578D ALA* 3.8 8.1 + - - +
579D ARG* 3.3 24.0 + - - +
580D HIS* 3.0 24.3 + - - +
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Residues in contact with PHE 577 (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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138A CYS 4.3 9.4 + - - +
139A GLN 4.4 16.6 - - - -
140A ASN* 5.7 1.1 - - - -
141A ARG* 5.4 15.6 - - + +
538D HIS* 5.9 3.6 - + + -
542D MET* 4.2 29.2 - - + -
576D SER* 1.3 73.2 - - - +
578D ALA* 1.3 55.8 + - - +
580D HIS* 3.1 4.6 + + - +
581D ASN* 2.8 70.7 + - + +
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Residues in contact with ALA 578 (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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538D HIS* 4.1 22.8 - - + +
541D LEU* 3.9 30.1 - - + +
542D MET* 4.1 23.8 - - + +
545D ASN* 5.4 1.0 - - - +
576D SER* 3.3 7.3 + - - +
577D PHE* 1.3 81.0 - - - +
579D ARG* 1.3 57.5 + - - +
581D ASN* 3.6 3.0 + - - +
582D LEU* 3.0 30.7 + - - +
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Residues in contact with ARG 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B THR* 3.5 34.2 + - - +
568B PRO* 3.5 34.3 - - - +
579B ARG* 4.5 2.2 - - - +
587B TYR* 4.7 1.0 + - - -
541D LEU* 4.7 8.9 - - + +
565D VAL* 3.6 13.9 + - + -
566D THR* 4.2 17.4 + - - +
567D LYS 5.5 0.2 + - - -
572D LEU* 3.9 30.8 + - + +
573D GLU* 6.1 1.1 - - - -
574D THR 4.9 3.5 + - - +
575D CYS* 4.7 15.2 - - - +
576D SER* 3.3 18.3 + - - +
577D PHE 3.3 0.4 - - - -
578D ALA* 1.3 75.8 - - - +
580D HIS* 1.3 63.3 + - - +
582D LEU* 3.9 4.3 - - - +
583D LEU* 2.9 64.3 + - + +
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Residues in contact with HIS 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A CYS 4.2 8.5 - - - +
139A GLN* 3.4 63.0 + - - +
562B LEU* 4.9 3.1 - - + -
566B THR* 6.2 0.6 - - - +
587B TYR* 4.2 20.6 + + - -
576D SER 3.0 17.7 + - - +
577D PHE* 3.7 6.7 - + - +
579D ARG* 1.3 79.6 - - - +
581D ASN* 1.3 69.4 + - + +
583D LEU* 3.4 5.5 + - - +
584D GLN* 2.9 50.3 + - - +
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Residues in contact with ASN 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D MET* 6.2 0.9 - - - -
545D ASN* 3.3 21.2 + - + +
549D ARG* 5.3 6.4 + - - -
577D PHE* 2.8 60.2 + - + +
578D ALA* 4.0 3.8 - - - +
580D HIS* 1.3 80.3 - - - +
582D LEU* 1.3 64.7 + - - +
584D GLN* 3.4 9.8 + - - +
585D THR* 3.2 20.8 + - - -
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Residues in contact with LEU 582 (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* 3.5 38.8 - - + +
544D LEU* 4.1 15.9 - - + +
545D ASN* 3.7 38.5 - - + +
548D VAL* 4.5 3.4 - - + -
561D LEU* 4.8 1.3 - - + -
565D VAL* 3.9 22.0 - - + -
578D ALA 3.0 17.9 + - - +
579D ARG* 3.9 3.1 - - - +
581D ASN* 1.3 73.5 - - - +
583D LEU* 1.3 68.8 + - - +
585D THR* 2.8 14.9 + - - -
586D LEU* 2.9 39.3 + - + +
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Residues in contact with LEU 583 (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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566B THR* 4.5 0.2 - - - +
587B TYR* 3.7 22.2 - - + +
562D LEU* 3.8 14.1 - - + -
565D VAL* 3.4 26.9 - - + -
566D THR* 3.7 28.9 - - - +
579D ARG* 2.9 70.3 + - + +
580D HIS* 3.9 3.1 - - - +
582D LEU* 1.3 72.1 - - - +
584D GLN* 1.3 57.3 + - - +
586D LEU* 3.3 4.6 + - + -
587D TYR* 2.8 41.1 + - + -
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Residues in contact with GLN 584 (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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587B TYR* 3.7 33.7 - - + +
549D ARG* 6.0 0.2 - - - -
580D HIS* 2.9 45.7 + - - +
581D ASN* 3.6 10.3 + - - +
582D LEU 3.1 0.2 - - - -
583D LEU* 1.3 76.7 - - - +
585D THR* 1.3 58.0 + - - +
587D TYR* 4.0 0.9 - - - +
588D ASN* 3.0 32.1 + - + +
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Residues in contact with THR 585 (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* 2.6 29.9 + - - +
548D VAL* 4.5 16.8 - - + +
549D ARG* 3.5 47.1 + - + +
581D ASN* 3.2 7.9 + - - -
582D LEU* 2.8 4.9 + - - -
584D GLN* 1.3 74.6 - - - +
586D LEU* 1.3 58.6 + - - +
588D ASN* 3.0 7.2 + - + +
589D ILE* 2.7 38.3 + - + +
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Residues in contact with LEU 586 (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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548D VAL* 3.5 39.0 - - + -
558D ALA* 4.2 20.2 - - + +
561D LEU* 4.2 12.6 - - + -
562D LEU* 3.4 54.3 - - + +
565D VAL* 4.5 4.5 - - + -
582D LEU* 2.9 40.8 + - + +
583D LEU* 3.8 2.0 - - + +
585D THR* 1.3 76.8 - - - +
587D TYR* 1.3 59.7 + - - +
589D ILE* 2.7 25.5 - - - +
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Residues in contact with TYR 587 (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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580B HIS* 4.1 20.6 + + - -
583B LEU* 3.8 19.5 - - + +
584B GLN* 3.6 46.3 + - + +
587B TYR* 3.4 48.5 - + + -
588B ASN* 3.7 14.3 + - - +
562D LEU* 3.7 31.4 - - + +
566D THR* 3.2 28.9 + - - +
583D LEU* 2.8 35.1 + - + +
584D GLN 4.0 0.4 - - - +
586D LEU* 1.3 70.9 - - - +
588D ASN* 1.3 65.9 + - - +
589D ILE* 3.6 5.7 - - - +
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Residues in contact with ASN 588 (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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587B TYR* 5.5 0.4 - - - +
588B ASN* 4.5 9.6 + - - +
549D ARG* 5.3 8.7 - - - +
584D GLN* 3.0 23.1 + - + +
585D THR* 3.0 7.8 + - + +
587D TYR* 1.3 76.8 - - - +
589D ILE* 1.3 68.7 + - - +
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Residues in contact with ILE 589 (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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548D VAL* 4.4 20.4 - - + +
553D PHE* 5.1 1.1 - - + -
555D LYS* 3.3 53.8 + - + +
558D ALA* 3.8 31.4 - - + -
585D THR* 2.7 18.7 + - + +
586D LEU* 2.7 37.3 - - + +
587D TYR 3.6 7.3 - - - +
588D ASN* 1.3 81.6 + - - +
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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