Contacts of the helix formed by residues 576 - 589 (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 SER 576 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538B HIS* 5.2 1.9 + - - -
541B LEU* 4.5 8.0 - - - +
572B LEU* 6.0 2.0 - - - -
574B THR* 3.2 13.8 + - - -
575B CYS* 1.3 83.5 - - - +
577B PHE* 1.3 79.1 + - - +
578B ALA* 3.3 7.6 + - - +
579B ARG* 3.1 35.8 + - - +
580B HIS* 3.7 12.6 + - - +
138C CYS* 3.8 7.1 - - - +
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Residues in contact with PHE 577 (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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538B HIS* 3.5 40.8 - + + -
542B MET* 5.7 0.2 - - - -
575B CYS 4.3 0.9 - - - -
576B SER* 1.3 83.8 + - - +
578B ALA* 1.3 65.5 + - - +
580B HIS* 3.3 12.5 + - - +
581B ASN* 3.2 21.6 + - - +
603B SO4 5.6 6.5 - - - -
137C TYR* 5.2 4.7 - + - -
138C CYS 4.1 10.2 - - - +
141C ARG* 3.2 49.1 - - + +
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Residues in contact with ALA 578 (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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538B HIS* 4.1 11.9 - - - +
541B LEU* 3.9 28.3 - - + +
542B MET* 3.6 31.6 - - + -
545B ASN* 5.5 0.9 - - - +
576B SER* 3.3 6.0 + - - +
577B PHE* 1.3 78.8 - - - +
579B ARG* 1.3 65.9 + - - +
580B HIS 3.2 0.5 + - - -
581B ASN* 3.2 8.0 + - - +
582B LEU* 3.0 25.9 + - - +
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Residues in contact with ARG 579 (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* 4.5 9.9 - - + +
565B VAL* 3.1 22.9 + - + +
566B THR 4.2 12.3 + - - -
567B LYS 4.2 9.1 + - - -
568B PRO* 4.8 1.0 - - - +
572B LEU* 3.3 44.3 - - + +
574B THR 4.5 11.4 + - - -
576B SER* 3.1 28.0 + - - +
578B ALA* 1.3 79.7 - - - +
580B HIS* 1.3 57.0 + - - +
582B LEU* 3.7 5.0 - - - +
583B LEU* 3.0 50.5 + - + +
566D THR* 3.6 24.0 + - - -
568D PRO* 3.8 26.3 - - - +
579D ARG* 4.5 3.8 - - - +
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Residues in contact with HIS 580 (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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576B SER 3.7 6.1 + - - +
577B PHE 3.3 9.3 + - - +
578B ALA 3.2 1.0 - - - -
579B ARG* 1.3 79.3 - - - +
581B ASN* 1.3 73.9 + - - +
583B LEU* 3.8 4.6 - - - +
584B GLN* 2.8 54.6 + - - +
138C CYS* 3.9 13.9 - - + +
139C GLN* 3.6 59.0 + - + +
562D LEU* 4.7 3.4 - - + -
566D THR* 6.1 0.8 - - - +
587D TYR* 4.1 21.5 + + - -
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Residues in contact with ASN 581 (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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542B MET* 5.7 4.2 - - - +
545B ASN* 3.6 22.4 - - + +
577B PHE* 3.2 21.8 + - - +
578B ALA* 3.2 9.0 + - - +
580B HIS* 1.3 83.8 - - - +
582B LEU* 1.3 68.0 + - - +
584B GLN* 3.2 10.7 + - - +
585B THR* 2.8 28.1 + - - +
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Residues in contact with LEU 582 (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 38.1 - - + +
544B LEU* 4.0 21.3 - - + +
545B ASN* 3.5 33.5 + - + +
548B VAL* 4.4 8.1 - - + -
561B LEU* 5.0 1.6 - - + -
565B VAL* 3.7 21.5 - - + -
578B ALA 3.0 16.3 + - - +
579B ARG* 3.7 3.8 - - - +
581B ASN* 1.3 74.8 - - - +
583B LEU* 1.3 66.1 + - - +
585B THR* 2.8 7.0 + - - -
586B LEU* 2.8 45.1 + - + +
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Residues in contact with LEU 583 (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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562B LEU* 3.4 31.4 - - + +
565B VAL* 4.2 12.6 - - + +
566B THR* 3.5 23.6 - - - +
579B ARG* 3.0 56.0 + - + +
580B HIS* 3.8 3.8 - - - +
582B LEU* 1.3 78.8 - - - +
584B GLN* 1.3 64.4 + - - +
586B LEU* 3.1 5.0 + - + +
587B TYR* 3.0 33.6 + - + -
566D THR* 4.3 3.6 - - - +
587D TYR* 3.8 24.0 - - + +
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Residues in contact with GLN 584 (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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580B HIS* 2.8 47.1 + - - +
581B ASN* 3.5 11.0 - - - +
583B LEU* 1.3 72.4 - - - +
585B THR* 1.3 64.8 + - - +
587B TYR* 3.4 0.9 + - - +
588B ASN* 3.0 45.4 + - - +
562D LEU* 6.1 0.6 - - - +
587D TYR* 3.6 30.1 + - + +
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Residues in contact with THR 585 (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* 2.6 26.1 + - - +
548B VAL* 4.5 14.8 - - + -
549B ARG* 3.9 32.1 - - + +
581B ASN 2.8 18.3 + - - -
582B LEU* 3.3 7.0 - - - -
584B GLN* 1.3 72.8 - - - +
586B LEU* 1.3 59.4 + - - +
588B ASN* 3.3 11.2 + - + +
589B ILE* 3.1 29.6 + - + +
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Residues in contact with LEU 586 (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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548B VAL* 3.8 33.9 - - + -
558B ALA* 4.0 27.0 - - + +
561B LEU* 4.2 12.1 - - + +
562B LEU* 3.7 46.0 - - + +
565B VAL* 4.5 3.6 - - + -
582B LEU* 2.8 38.9 + - + +
583B LEU* 3.1 12.5 + - + +
585B THR* 1.3 73.9 - - - +
587B TYR* 1.3 65.2 + - - +
589B ILE* 3.2 21.2 + - + +
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Residues in contact with TYR 587 (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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562B LEU* 3.3 32.9 - - + +
566B THR* 2.9 24.8 + - - +
583B LEU* 3.0 38.7 + - + +
584B GLN 4.1 0.4 - - - +
586B LEU* 1.3 77.5 - - - +
588B ASN* 1.3 64.0 + - - +
589B ILE* 3.1 9.7 + - - +
579D ARG* 4.7 0.9 + - - -
580D HIS* 4.2 22.5 + + - -
583D LEU* 3.7 16.2 - - + +
584D GLN* 3.7 47.8 - - + +
587D TYR* 3.4 46.7 - + + -
588D ASN 5.5 0.4 - - - +
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Residues in contact with ASN 588 (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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584B GLN* 3.0 38.2 + - - +
585B THR* 3.3 10.8 - - + +
586B LEU 3.2 0.2 - - - -
587B TYR* 1.3 78.9 - - - +
589B ILE* 1.3 61.9 + - - +
587D TYR 3.7 25.7 + - - -
588D ASN* 4.5 7.1 + - - +
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Residues in contact with ILE 589 (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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548B VAL* 3.4 38.1 - - + +
553B PHE* 5.1 2.9 - - + -
555B LYS* 4.6 27.4 - - + +
558B ALA* 3.9 29.2 - - + -
559B PRO* 5.8 0.2 - - + -
585B THR* 3.1 21.2 + - + +
586B LEU* 3.4 14.9 - - + +
587B TYR 3.0 11.4 - - - +
588B ASN* 1.3 80.4 - - + +
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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