Contacts of the helix formed by residues 572 - 587 (chain A) in PDB entry 1KWG
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 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LEU* 4.3 1.6 - - - -
532A PHE* 4.4 4.5 - - - +
533A PRO* 4.3 8.6 + - - +
534A LEU* 3.8 18.9 - - - +
571A PRO* 1.3 76.4 - - - +
573A PRO* 1.3 73.9 - - - +
574A GLU* 3.6 13.4 + - - +
575A LEU* 3.0 24.1 + - - +
576A ALA* 3.0 20.3 + - - +
804A ACT 4.0 12.1 - - - -
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Residues in contact with PRO 573 (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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429A LEU* 4.2 25.1 - - + -
572A SER* 1.3 84.4 - - - +
574A GLU* 1.3 75.7 + - - +
576A ALA* 3.4 1.0 + - - +
577A GLY 3.0 24.6 + - - -
803A MPD 3.2 37.6 + - + +
804A ACT 4.9 4.5 - - + +
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Residues in contact with GLU 574 (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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532A PHE* 4.0 13.0 - - + -
572A SER* 3.6 12.0 - - - +
573A PRO* 1.3 97.9 - - - +
575A LEU* 1.3 62.6 - - - +
577A GLY* 3.4 1.6 + - - -
578A ARG* 3.0 30.7 + - + +
803A MPD 3.8 23.1 - - + +
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Residues in contact with LEU 575 (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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529A LEU* 4.8 3.6 - - + -
532A PHE* 3.6 28.4 - - + -
534A LEU* 3.9 31.4 - - + -
549A LEU* 3.6 29.2 - - + -
567A LEU* 4.0 23.8 - - + -
571A PRO* 4.4 10.3 - - + -
572A SER* 3.0 23.6 + - - +
574A GLU* 1.3 75.8 - - - +
576A ALA* 1.3 65.8 + - - +
578A ARG 3.3 0.5 + - - -
579A LEU* 2.9 39.0 + - + +
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Residues in contact with ALA 576 (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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429A LEU* 3.4 32.5 - - + -
430A PHE* 4.3 17.5 - - + -
433A ALA* 3.7 15.5 - - + -
571A PRO* 4.7 2.9 - - + +
572A SER 3.0 8.9 + - - +
573A PRO 3.6 3.8 - - - +
575A LEU* 1.3 77.6 - - - +
577A GLY* 1.3 58.3 + - - +
579A LEU* 4.8 2.5 - - - -
580A LEU* 3.0 39.9 + - - +
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Residues in contact with GLY 577 (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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433A ALA* 3.9 9.8 - - - +
437A LEU* 3.9 12.8 - - - +
573A PRO 3.0 11.5 + - - -
574A GLU 3.8 0.9 - - - -
576A ALA* 1.3 78.1 - - - +
578A ARG* 1.3 56.8 + - - +
580A LEU* 3.9 1.5 - - - -
581A SER* 2.9 31.5 + - - -
803A MPD 3.6 20.4 - - - -
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Residues in contact with ARG 578 (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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529A LEU* 3.1 36.9 + - + +
530A GLY* 3.8 12.1 - - - -
531A ARG 4.8 1.8 + - - +
532A PHE* 3.5 24.1 - - + -
574A GLU* 3.0 20.5 + - + +
575A LEU* 4.0 2.0 - - + +
577A GLY* 1.3 73.7 - - - +
579A LEU* 1.3 60.5 + - - +
581A SER* 3.4 6.0 + - - -
582A ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 579 (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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430A PHE* 5.6 1.8 - - + -
480A LEU* 3.7 39.7 - - + -
529A LEU* 3.9 23.9 - - + +
558A LEU* 4.0 24.7 - - + -
565A LEU* 4.2 17.9 - - + -
567A LEU* 5.2 9.2 - - + -
575A LEU* 2.9 29.8 + - + +
576A ALA* 4.0 2.7 - - - +
578A ARG* 1.3 78.3 - - - +
580A LEU* 1.3 59.0 + - + +
582A ALA* 3.2 2.3 + - - +
583A LEU* 3.0 33.5 + - + +
805A ACT 4.4 8.5 - - + -
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Residues in contact with LEU 580 (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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430A PHE* 3.8 20.9 - - + +
433A ALA* 3.6 20.4 - - + -
434A LEU* 3.4 38.6 - - + +
437A LEU* 3.9 15.6 - - + +
455A PHE* 3.8 10.2 - - + -
457A VAL* 4.4 6.1 - - + -
480A LEU* 3.8 28.0 - - + -
576A ALA 3.0 24.8 + - - +
579A LEU* 1.3 77.3 - - + +
581A SER* 1.3 60.4 + - - +
583A LEU* 3.3 9.9 + - + +
584A ALA* 2.9 28.4 + - - +
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Residues in contact with SER 581 (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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437A LEU* 3.7 19.8 - - - +
577A GLY 2.9 20.8 + - - -
578A ARG* 3.7 7.2 - - - -
580A LEU* 1.3 77.1 - - - +
582A ALA* 1.3 57.7 + - - +
584A ALA* 3.2 6.1 + - - +
585A ALA* 2.9 28.8 + - - +
591A VAL* 3.9 18.5 - - - +
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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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529A LEU* 3.8 20.0 - - + -
578A ARG 3.0 17.3 + - - +
579A LEU 3.5 5.6 - - - +
581A SER* 1.3 78.4 - - - +
583A LEU* 1.3 61.7 + - - +
585A ALA* 3.4 6.4 + - - +
586A GLU* 3.0 24.3 + - - +
805A ACT 3.9 17.1 + - + +
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Residues in contact with LEU 583 (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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455A PHE* 4.1 35.8 - - + +
478A PRO* 4.1 14.2 - - + +
480A LEU* 4.4 31.9 - - + +
560A ARG* 4.1 1.6 - - - +
565A LEU* 4.1 25.4 - - + -
579A LEU* 3.0 29.1 + - + +
580A LEU* 3.7 7.4 - - + +
581A SER 3.3 0.2 - - - -
582A ALA* 1.3 75.7 - - - +
584A ALA* 1.3 63.0 + - - +
586A GLU* 3.4 21.8 + - - +
587A ALA* 3.0 24.6 + - - +
805A ACT 4.1 9.4 - - - +
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Residues in contact with ALA 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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439A LEU* 4.4 5.8 - - + -
455A PHE* 3.8 16.1 - - + -
580A LEU 2.9 14.3 + - - +
581A SER 3.2 5.6 + - - +
583A LEU* 1.3 77.7 - - - +
585A ALA* 1.3 61.4 + - - +
587A ALA 3.1 7.1 + - - -
589A LEU* 2.8 40.1 + - + +
591A VAL* 3.4 31.9 - - + -
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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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581A SER 2.9 16.3 + - - +
582A ALA* 3.7 7.4 - - - +
584A ALA* 1.3 76.0 - - - +
586A GLU* 1.3 63.2 + - - +
588A GLY* 3.0 13.7 + - - -
589A LEU 4.1 8.1 - - - -
591A VAL* 5.3 2.0 - - + +
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Residues in contact with GLU 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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478A PRO* 3.9 13.6 - - + +
560A ARG* 2.9 43.2 + - - -
582A ALA 3.0 17.3 + - - +
583A LEU* 3.6 10.4 - - - +
585A ALA* 1.3 77.4 - - - +
587A ALA* 1.3 61.2 + - - +
588A GLY 3.4 0.9 + - - -
805A ACT 4.5 5.5 + - - +
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Residues in contact with ALA 587 (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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454A ALA* 3.9 38.7 - - + +
455A PHE* 4.7 1.8 - - + -
478A PRO* 5.5 4.5 - - + -
583A LEU 3.0 16.9 + - - +
584A ALA* 3.1 5.5 + - - +
586A GLU* 1.3 76.2 - - - +
588A GLY* 1.3 60.5 + - - +
589A LEU* 3.5 6.6 + - + +
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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