Contacts of the helix formed by residues 581 - 599 (chain A) in PDB entry 3KSS
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 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A ILE* 1.3 88.7 - - - +
582A ALA* 1.3 60.8 + - - +
583A ALA* 4.1 4.9 - - - -
584A GLU* 3.7 26.8 + - - +
585A ALA* 3.0 21.0 + - - +
621A LEU* 4.8 1.3 - - - -
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Residues in contact with ALA 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ARG* 5.1 20.1 - - + +
275A ILE* 3.5 10.7 - - + +
580A ILE 4.2 0.6 + - - -
581A SER* 1.3 72.0 - - - +
583A ALA* 1.3 60.8 + - - +
585A ALA* 3.3 2.6 - - - +
586A ALA* 3.0 23.9 + - - +
621A LEU* 3.5 28.6 - - + +
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Residues in contact with ALA 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A SER* 4.1 4.4 - - - -
582A ALA* 1.3 75.5 - - - +
584A GLU* 1.3 60.5 + - - +
585A ALA 3.0 1.3 - - - -
586A ALA* 3.1 7.9 + - - +
587A SER* 2.8 30.6 + - - -
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Residues in contact with GLU 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A ILE* 4.7 5.8 - - + -
581A SER* 3.7 26.8 + - - +
582A ALA 3.4 0.4 - - - -
583A ALA* 1.3 78.5 - - - +
585A ALA* 1.3 56.8 + - - +
587A SER* 3.5 13.0 + - - -
588A MET* 3.0 46.8 + - + +
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Residues in contact with ALA 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 3.9 13.2 - - + -
580A ILE* 3.5 19.0 - - + +
581A SER 3.0 19.5 + - - +
582A ALA* 3.3 10.1 - - - +
584A GLU* 1.3 74.3 - - - +
586A ALA* 1.3 60.6 + - - +
588A MET* 3.2 5.5 + - - +
589A LEU* 2.8 30.9 + - - +
609A THR* 4.1 8.0 + - + +
621A LEU* 4.0 14.6 - - + +
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Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ARG* 5.8 2.0 - - - +
275A ILE* 3.8 18.3 - - + +
277A GLU* 4.8 1.0 - - - +
283A GLU* 4.0 22.1 - - - +
582A ALA 3.0 16.3 + - - +
583A ALA* 3.1 6.7 + - - +
585A ALA* 1.3 75.1 - - - +
587A SER* 1.3 60.7 + - - +
589A LEU* 3.6 9.2 - - - +
590A GLN* 3.2 22.7 + - - +
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Residues in contact with SER 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA 2.8 16.6 + - - -
584A GLU* 3.5 18.0 + - - -
586A ALA* 1.3 74.2 - - - +
588A MET* 1.3 69.0 + - - +
590A GLN* 2.9 17.3 + - - +
591A LYS* 3.0 19.5 + - - +
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Residues in contact with MET 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A ILE* 5.9 5.8 - - - -
584A GLU* 3.0 35.5 + - + +
585A ALA* 3.7 4.9 - - - +
587A SER* 1.3 76.7 + - - +
589A LEU* 1.3 64.8 + - - +
591A LYS* 3.2 18.1 + - - +
592A THR* 2.9 29.2 + - - +
655A LEU* 4.8 18.4 - - + -
656A PRO* 5.2 13.2 - - + +
658A LEU* 4.7 20.9 - - + -
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 3.8 29.4 - - + +
276A ALA 4.2 1.6 - - - -
277A GLU* 2.9 41.6 - - + +
283A GLU* 5.6 0.9 - - - +
585A ALA 2.8 17.4 + - - +
586A ALA* 3.6 6.7 - - - +
588A MET* 1.3 77.1 - - - +
590A GLN* 1.3 56.8 + - - +
592A THR* 3.4 4.9 + - - -
593A ASP* 3.0 27.5 + - - +
607A GLY* 3.5 27.8 - - - +
608A LYS 3.8 2.2 - - - +
609A THR* 3.0 26.2 - - - +
624A VAL* 4.8 7.0 - - + -
626A THR* 4.5 8.7 - - + -
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Residues in contact with GLN 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 2.9 26.0 + - - +
280A GLY 3.8 12.3 + - - +
281A GLU 3.4 21.8 + - - -
282A GLY* 4.0 4.6 - - - -
283A GLU* 4.9 2.6 - - - +
586A ALA 3.2 9.7 + - - +
587A SER* 2.9 11.3 + - - +
589A LEU* 1.3 75.1 - - - +
591A LYS* 1.3 66.0 + - - +
593A ASP* 3.2 4.9 + - - +
594A LYS* 3.2 41.0 + - - +
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Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A SER* 3.0 16.4 + - - +
588A MET* 3.7 18.6 - - - +
590A GLN* 1.3 76.8 - - - +
592A THR* 1.3 62.7 + - - +
594A LYS* 3.0 24.7 + - + +
595A LEU* 3.1 32.9 + - + +
655A LEU* 3.6 36.7 - - + +
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Residues in contact with THR 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A TYR* 4.7 17.0 + - + -
588A MET* 2.9 19.7 + - - +
589A LEU* 3.7 6.5 - - + -
591A LYS* 1.3 76.8 - - - +
593A ASP* 1.3 63.9 + - - +
594A LYS 3.0 0.2 - - - -
595A LEU* 3.9 7.7 - - - +
596A ILE* 3.0 45.1 + - + +
624A VAL* 5.3 7.9 - - + +
626A THR* 4.6 15.7 - - + -
653A VAL* 4.6 12.0 - - + +
655A LEU* 5.4 5.0 - - - +
658A LEU* 6.0 1.7 - - - +
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Residues in contact with ASP 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 2.9 35.7 - - - +
279A ASN* 3.1 24.8 + - - +
280A GLY 3.6 7.3 + - - -
589A LEU* 3.0 13.7 + - - +
590A GLN 3.2 5.8 + - - +
592A THR* 1.3 77.0 - - - +
594A LYS* 1.3 57.9 + - - +
597A MET* 3.1 25.9 + - - +
605A VAL* 4.0 19.5 - - - +
607A GLY* 3.4 29.8 + - - -
626A THR* 4.2 7.3 - - - +
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Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLY* 3.8 30.3 - - - -
590A GLN* 3.2 31.5 + - - +
591A LYS* 3.0 16.8 + - + +
593A ASP* 1.3 78.4 - - - +
595A LEU* 1.3 65.6 + - + +
597A MET* 3.5 4.6 + - - +
598A SER* 3.0 26.5 + - - -
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Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A LYS* 3.1 30.4 + - + +
592A THR* 3.3 3.6 + - - +
594A LYS* 1.3 78.7 - - + +
596A ILE* 1.3 64.2 + - - +
598A SER* 2.6 30.2 + - - -
599A VAL* 3.8 0.7 + - - +
652A THR* 4.0 28.5 - - + +
653A VAL* 3.5 30.3 - - + -
654A ARG 4.8 0.7 - - - +
655A LEU* 4.6 13.7 - - + -
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Residues in contact with ILE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A TYR* 4.3 4.9 - - + -
592A THR* 3.0 29.5 + - + +
595A LEU* 1.3 75.3 - - - +
597A MET* 1.3 63.5 + - - +
598A SER 3.2 0.7 + - - -
599A VAL* 3.4 11.1 + - - +
602A VAL* 3.1 22.2 - - + +
605A VAL* 3.9 18.4 - - + -
626A THR* 5.7 2.0 - - - +
628A ILE* 3.5 34.1 - - + -
649A LEU* 3.9 12.1 - - + -
653A VAL* 3.6 21.5 - - + -
662A TRP* 3.4 33.4 - - + -
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Residues in contact with MET 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASN* 3.2 45.5 - - + +
280A GLY* 4.9 2.9 - - - +
593A ASP 3.1 22.2 + - - +
594A LYS* 3.5 5.1 + - - +
595A LEU 3.2 0.4 - - - -
596A ILE* 1.3 77.1 - - - +
598A SER* 1.3 66.8 + - - +
599A VAL 3.1 8.3 - - - +
602A VAL* 3.6 10.3 - - - +
603A ALA 3.1 28.5 - - - +
605A VAL* 3.7 10.7 - - + +
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Residues in contact with SER 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A LYS 3.0 12.6 + - - -
595A LEU* 2.6 24.4 + - - -
597A MET* 1.3 78.3 - - - +
599A VAL* 1.3 72.8 + - - +
600A PRO* 3.2 7.8 - - - +
652A THR* 4.1 14.0 - - - +
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A LEU 4.7 0.9 - - - +
596A ILE 3.4 9.5 + - - +
597A MET 3.1 3.6 - - - +
598A SER* 1.3 87.3 + - - +
600A PRO* 1.3 73.4 - - + +
601A GLU* 3.4 25.1 - - + +
602A VAL* 3.0 37.3 - - + +
645A ILE* 4.9 1.1 - - + -
648A GLU* 3.2 31.2 - - + +
649A LEU* 3.5 33.0 - - + -
652A THR* 4.5 7.2 - - + +
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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