Contacts of the helix formed by residues 578 - 589 (chain D) in PDB entry 3F7F
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 ASP 578 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505D GLU* 5.5 0.8 + - - -
576D SER 4.4 0.2 + - - -
577D PHE* 1.3 70.4 - - - +
579D ILE* 1.3 63.6 + - - +
580D PRO* 2.8 15.5 - - - +
581D VAL* 2.7 52.6 + - + +
582D VAL* 3.4 10.4 + - + +
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Residues in contact with ILE 579 (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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509D TYR* 4.6 15.3 - - + +
574D LEU* 4.4 27.1 - - + +
577D PHE* 2.9 25.9 + - + +
578D ASP* 1.3 72.0 - - - +
580D PRO* 1.3 71.7 - - + +
582D VAL* 3.2 7.5 + - - +
583D LEU* 2.9 38.8 + - + +
642D LEU* 4.5 27.1 - - + -
647D PHE* 3.6 26.7 - - + -
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Residues in contact with PRO 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D ASP* 3.1 19.3 - - - +
579D ILE* 1.3 89.6 - - + +
581D VAL* 1.3 61.3 + - + +
583D LEU* 3.6 2.3 + - + +
584D ASN* 3.1 26.0 + - - +
646D ILE* 5.7 4.9 - - + -
647D PHE* 3.8 28.3 - - + -
650D HIS* 4.4 6.0 + - + +
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Residues in contact with VAL 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D ASP* 2.7 43.6 + - + +
580D PRO* 1.3 73.3 - - + +
582D VAL* 1.3 66.1 + - + +
584D ASN* 3.3 7.8 + - - +
585D ASP* 3.2 22.6 + - + +
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Residues in contact with VAL 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D GLU* 4.4 21.5 - - + +
506D LEU* 3.3 32.6 - - + +
509D TYR* 3.5 30.3 - - + -
577D PHE* 4.7 10.1 - - + -
578D ASP* 3.4 21.5 + - + +
579D ILE* 3.2 10.2 + - - +
581D VAL* 1.3 78.2 - - + +
583D LEU* 1.3 62.0 + - - +
585D ASP* 3.1 8.1 + - - +
586D LEU* 2.9 26.0 + - - +
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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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509D TYR* 3.6 22.4 - - + +
579D ILE* 2.9 39.3 + - + +
580D PRO 4.1 2.7 - - - +
582D VAL* 1.3 73.5 - - - +
584D ASN* 1.3 53.4 + - - +
586D LEU* 4.2 13.7 - - + -
587D ILE* 2.7 47.5 + - + +
633D VAL* 3.6 27.4 - - + -
637D PHE* 3.5 32.3 - - + -
647D PHE* 3.9 11.2 - - + -
650D HIS* 4.2 16.4 - - + -
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Residues in contact with ASN 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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580D PRO 3.1 19.1 + - - +
581D VAL* 3.4 8.1 - - - +
582D VAL 3.1 0.2 - - - -
583D LEU* 1.3 78.4 - - - +
585D ASP* 1.3 54.5 + - - +
588D ASN* 2.7 70.3 + - - +
589D ASN* 4.3 2.8 + - - -
650D HIS* 4.1 15.9 + - - +
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Residues in contact with ASP 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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493D TRP* 5.1 0.7 - - - -
506D LEU* 3.4 23.5 - - + +
581D VAL* 3.2 10.3 + - + +
582D VAL* 3.1 10.3 + - - +
584D ASN* 1.3 76.2 - - - +
586D LEU* 1.3 62.7 + - - +
589D ASN* 2.4 47.0 + - - +
590D GLN* 2.9 34.0 + - - +
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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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490D VAL* 5.3 1.3 - - + -
493D TRP* 4.9 1.8 - - + -
506D LEU* 3.7 28.4 - - + +
509D TYR* 4.9 0.7 - - + -
510D LEU* 4.2 17.3 - - + -
582D VAL 2.9 16.5 + - - +
583D LEU* 3.7 15.9 - - + +
585D ASP* 1.3 78.5 - - - +
587D ILE* 1.3 63.1 + - + +
590D GLN* 4.1 7.9 - - + -
591D MET* 2.8 51.5 + - + +
629D ILE* 3.9 34.5 - - + -
633D VAL* 4.1 18.2 - - + -
654D LEU* 5.7 1.8 - - + -
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Residues in contact with ILE 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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583D LEU* 2.7 30.1 + - + +
584D ASN 4.5 0.2 - - - +
586D LEU* 1.3 83.2 - - + +
588D ASN* 1.3 66.5 + - - +
591D MET* 4.6 6.7 - - - -
592D LYS* 3.3 28.0 + - + +
650D HIS* 3.4 37.5 - - + +
653D THR* 3.8 26.0 - - + -
654D LEU* 3.7 39.5 - - + -
657D LEU* 4.9 7.2 - - + -
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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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584D ASN* 2.7 57.7 + - - +
587D ILE* 1.3 86.5 - - - +
589D ASN* 1.3 67.4 + - - +
592D LYS* 4.2 16.8 - - - +
650D HIS* 4.2 9.1 - - - -
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Residues in contact with ASN 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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584D ASN* 4.3 3.4 + - - -
585D ASP* 2.4 45.8 + - - +
587D ILE 3.6 0.4 - - - -
588D ASN* 1.3 88.6 - - - +
590D GLN* 1.3 76.6 + - - +
591D MET 3.8 0.2 - - - -
592D LYS 3.7 10.4 - - - +
593D PRO* 5.3 0.9 - - - +
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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