Contacts of the helix formed by residues 577 - 587 (chain A) in PDB entry 3KFL
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 THR 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A GLY 3.8 10.0 + - - -
573A GLU* 3.1 16.6 + - - +
576A ASP* 1.3 79.8 + - - +
578A LEU* 1.3 67.3 + - - +
579A GLY 3.5 0.4 - - - -
580A ASN* 3.8 0.2 - - - +
581A LEU* 3.0 13.9 + - - +
637A PHE* 4.4 8.2 - - + -
640A LEU* 3.7 36.1 - - + -
641A ARG* 3.9 22.4 - - + +
644A ASN* 2.8 29.1 + - - +
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Residues in contact with LEU 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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573A GLU 3.1 7.6 + - - +
574A LEU* 3.5 8.1 - - + +
577A THR* 1.3 81.2 - - - +
579A GLY* 1.3 64.6 + - - +
581A LEU* 3.1 6.1 + - - +
582A VAL* 3.1 25.9 + - + +
637A PHE* 4.3 8.1 - - + -
640A LEU* 4.0 21.1 - - + -
674A LEU* 3.7 25.8 - - + -
678A THR* 4.5 3.8 - - - +
681A LEU* 3.7 25.6 - - + -
685A MET* 3.9 17.7 - - + -
692A ILE* 3.8 24.2 - - + -
730A PHE* 4.0 15.7 - - + -
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Residues in contact with GLY 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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574A LEU 2.8 20.7 + - - -
575A ALA* 3.6 5.8 - - - -
577A THR 3.5 0.2 - - - -
578A LEU* 1.3 72.4 - - - +
580A ASN* 1.3 61.4 + - - +
582A VAL* 3.2 10.1 + - - +
583A SER* 3.1 25.7 + - - -
729A VAL* 4.5 11.6 + - - +
730A PHE* 4.4 13.2 - - - -
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Residues in contact with ASN 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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575A ALA 2.9 11.2 + - - +
576A ASP* 3.2 27.8 - - - +
577A THR 3.8 0.9 - - - +
578A LEU 3.3 0.2 - - - -
579A GLY* 1.3 76.3 - - - +
581A LEU* 1.3 61.3 + - - +
583A SER* 3.4 8.7 + - - -
584A ARG* 3.0 50.3 + - - +
644A ASN* 3.6 15.6 - - - +
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Residues in contact with LEU 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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577A THR 3.0 19.1 + - - +
578A LEU 3.1 5.1 + - - +
580A ASN* 1.3 76.6 - - - +
582A VAL* 1.3 63.3 + - - +
584A ARG* 3.3 5.1 + - + +
585A CYS* 3.1 23.8 + - - -
640A LEU* 3.7 32.1 - - + +
643A LEU* 3.5 26.0 - - + -
644A ASN* 3.5 26.7 + - - +
647A VAL* 4.0 10.8 - - + -
670A THR* 3.5 28.5 - - + -
674A LEU* 3.9 18.4 - - + -
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Residues in contact with VAL 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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578A LEU 3.1 18.3 + - - +
579A GLY* 3.2 7.4 + - - +
581A LEU* 1.3 76.4 - - - +
583A SER* 1.3 62.4 + - - +
585A CYS* 3.2 2.9 + - - -
586A VAL* 3.2 30.4 + - + +
674A LEU* 3.7 24.9 - - + -
692A ILE* 3.9 38.4 - - + +
695A ALA* 4.5 15.9 - - + -
696A LEU* 5.3 0.9 - - + -
723A LEU* 4.4 10.1 - - + -
729A VAL* 4.2 19.1 - - + -
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Residues in contact with SER 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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579A GLY 3.1 13.7 + - - -
580A ASN* 3.4 12.9 + - - -
582A VAL* 1.3 75.4 - - - +
584A ARG* 1.3 56.8 + - - +
586A VAL* 3.7 8.3 - - - +
587A ALA* 2.8 34.5 + - - +
723A LEU* 4.3 12.7 - - - +
727A GLN 4.8 4.7 + - - -
728A VAL* 4.9 10.6 - - - +
729A VAL 5.7 0.5 + - - -
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Residues in contact with ARG 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 ASN* 3.0 37.9 + - - +
581A LEU* 3.5 10.5 - - + +
583A SER* 1.3 78.8 - - - +
585A CYS* 1.3 63.3 + - - +
586A VAL 3.2 0.5 + - - -
587A ALA* 3.6 3.7 + - - -
590A ILE* 3.5 38.9 - - + +
644A ASN* 3.0 51.8 + - - +
647A VAL* 3.9 28.2 - - + +
648A THR* 2.7 27.1 + - - +
653A TRP* 4.0 17.9 - - + -
667A LEU* 4.6 0.6 - - - +
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Residues in contact with CYS 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 LEU* 3.1 19.2 + - - +
582A VAL 3.2 7.1 + - - +
584A ARG* 1.3 76.5 - - - +
586A VAL* 1.3 64.6 + - + +
587A ALA 3.6 0.2 - - - -
591A ASN* 3.1 29.1 + - - +
647A VAL* 5.5 0.4 - - - -
667A LEU* 3.8 12.6 - - - +
670A THR* 3.5 32.8 - - - -
671A MET* 3.9 27.9 - - + +
674A LEU* 4.1 13.5 - - + -
696A LEU* 4.5 6.5 - - + -
720A ILE* 4.5 0.2 - - - +
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Residues in contact with VAL 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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582A VAL* 3.2 24.7 + - + +
583A SER* 3.7 7.9 - - - +
585A CYS* 1.3 78.5 - - - +
587A ALA* 1.3 70.3 + - - +
588A PRO* 3.2 8.4 - - + +
591A ASN* 4.4 3.0 - - - +
695A ALA* 4.3 11.7 - - + +
696A LEU* 4.0 21.8 - - + -
720A ILE* 3.8 29.0 - - + +
722A GLY* 4.1 8.8 - - - -
723A LEU* 4.0 33.5 + - + +
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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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583A SER 2.8 16.5 + - - +
584A ARG 3.6 1.6 + - - -
585A CYS 3.6 0.2 - - - -
586A VAL* 1.3 76.5 - - - +
588A PRO* 1.3 66.7 - - + +
589A LYS* 4.3 4.0 - - + +
590A ILE* 3.0 31.4 + - + +
591A ASN* 2.7 32.6 + - - -
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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