Contacts of the helix formed by residues 578 - 589 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B GLU* 5.5 1.0 + - - -
576B SER 4.4 0.4 + - - -
577B PHE* 1.3 70.2 - - - +
579B ILE* 1.3 63.6 + - - +
580B PRO* 2.7 14.5 - - - +
581B VAL* 2.7 53.5 + - + +
582B VAL* 3.4 10.6 + - + +
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Residues in contact with ILE 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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509B TYR* 4.6 16.2 - - + +
574B LEU* 4.4 26.5 - - + +
577B PHE* 2.9 25.3 + - + +
578B ASP* 1.3 72.2 - - - +
580B PRO* 1.3 70.1 - - + +
582B VAL* 3.2 7.8 + - - -
583B LEU* 2.9 39.6 + - + +
642B LEU* 4.5 28.0 - - + -
647B PHE* 3.6 26.7 - - + -
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Residues in contact with PRO 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASP* 3.1 19.3 - - - +
579B ILE* 1.3 88.7 - - + +
581B VAL* 1.3 62.7 + - + +
583B LEU* 4.0 1.9 - - + +
584B ASN* 3.1 26.2 + - - +
646B ILE* 5.7 4.7 - - + -
647B PHE* 3.8 29.2 - - + -
650B HIS* 4.4 5.0 + - - +
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Residues in contact with VAL 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASP* 2.7 44.5 + - + +
580B PRO* 1.3 74.2 - - + +
582B VAL* 1.3 65.8 + - + +
584B ASN* 3.3 7.1 + - - +
585B ASP* 3.2 21.8 + - + +
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Residues in contact with VAL 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B GLU* 4.4 22.7 - - + -
506B LEU* 3.3 32.7 - - + +
509B TYR* 3.5 30.3 - - + -
577B PHE* 4.7 9.9 - - + -
578B ASP* 3.4 21.0 + - + +
579B ILE* 3.2 9.5 + - - +
581B VAL* 1.3 79.3 - - + +
583B LEU* 1.3 59.4 + - - +
585B ASP* 3.1 7.6 + - - +
586B LEU* 2.9 26.5 + - - +
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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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509B TYR* 3.6 23.1 - - + +
579B ILE* 2.9 38.3 + - + +
580B PRO 4.1 2.5 - - - +
582B VAL* 1.3 74.2 - - - +
584B ASN* 1.3 54.2 + - - +
586B LEU* 4.2 13.2 - - + -
587B ILE* 2.7 48.4 + - + +
633B VAL* 3.6 27.1 - - + -
637B PHE* 3.4 31.9 - - + -
647B PHE* 3.9 10.8 - - + -
650B HIS* 4.2 16.6 - - + -
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Residues in contact with ASN 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B PRO 3.1 19.3 + - - +
581B VAL* 3.4 8.1 - - - +
582B VAL 3.1 0.2 - - - -
583B LEU* 1.3 78.3 - - - +
585B ASP* 1.3 54.5 + - - +
588B ASN* 2.7 66.2 + - - +
589B ASN* 4.3 2.6 + - - -
650B HIS* 4.1 14.7 + - - +
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Residues in contact with ASP 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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493B TRP* 5.1 0.7 - - - -
506B LEU* 3.4 23.5 - - + +
581B VAL* 3.2 10.1 + - + +
582B VAL* 3.1 10.4 + - - +
584B ASN* 1.3 76.7 - - - +
586B LEU* 1.3 61.5 + - - +
589B ASN* 2.4 48.6 + - - +
590B GLN* 2.9 34.7 + - - +
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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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490B VAL* 5.3 1.3 - - + -
493B TRP* 4.9 1.8 - - + -
506B LEU* 3.7 28.4 - - + +
509B TYR* 4.9 0.9 - - + -
510B LEU* 4.2 16.8 - - + -
582B VAL 2.9 16.3 + - - +
583B LEU* 3.7 15.9 - - + +
585B ASP* 1.3 79.7 - - - +
587B ILE* 1.3 62.0 + - + +
590B GLN* 3.5 7.1 + - + -
591B MET* 2.8 51.7 + - + +
629B ILE* 3.9 33.0 - - + -
633B VAL* 4.0 18.2 - - + -
654B LEU* 5.7 1.8 - - + -
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Residues in contact with ILE 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B LEU* 2.7 29.4 + - + +
584B ASN 4.5 0.4 - - - +
586B LEU* 1.3 82.2 - - + +
588B ASN* 1.3 66.8 + - - +
589B ASN 3.6 0.2 - - - -
591B MET* 4.5 7.2 - - - -
592B LYS* 3.3 27.4 + - + +
650B HIS* 3.4 37.5 - - + +
653B THR* 3.8 26.0 - - + -
654B LEU* 3.7 38.6 - - + -
657B LEU* 4.9 7.4 - - + -
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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
----------------------------------------------------------
584B ASN* 2.7 56.4 + - - +
587B ILE* 1.3 86.9 - - - +
589B ASN* 1.3 68.6 + - - +
592B LYS* 4.2 16.4 - - - +
650B HIS* 4.2 9.5 - - - -
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Residues in contact with ASN 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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584B ASN* 4.3 3.2 + - - -
585B ASP* 2.4 45.6 + - - +
587B ILE 3.6 0.2 - - - -
588B ASN* 1.3 90.2 - - - +
590B GLN* 1.3 77.0 + - - +
592B LYS 3.7 10.8 - - - +
593B PRO* 5.3 1.4 - - - +
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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