Contacts of the helix formed by residues 628 - 636 (chain B) in PDB entry 6O81
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 TRP 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B THR 4.3 2.2 - - - -
561B LEU* 3.3 46.0 - - + -
564B GLY* 3.6 18.4 - - - -
565B LYS* 3.6 22.1 - - - +
569B ILE* 5.9 2.5 - - + -
571B CYS* 6.5 0.9 - - - -
574B LEU* 3.6 29.8 - - + -
624B LEU* 3.1 34.4 + - + +
625B LEU* 4.0 5.2 - - - -
627B ALA* 1.3 87.1 - - + +
629B SER* 1.3 60.6 + - - +
630B PRO 3.3 2.9 - - - -
631B VAL* 3.6 17.7 + - + +
632B PHE* 3.2 23.6 + - - +
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Residues in contact with SER 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B LEU 3.4 19.4 + - - -
626B LYS* 3.9 11.0 - - - -
627B ALA 3.3 3.2 + - - -
628B TRP* 1.3 77.2 - - - +
630B PRO* 1.3 59.5 - - - +
632B PHE* 3.5 6.3 + - - +
633B ARG* 2.9 29.1 + - - +
673B LEU* 4.5 22.8 - - - +
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Residues in contact with PRO 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B CYS* 3.8 27.1 - - + -
575B VAL* 6.2 0.2 - - - -
627B ALA 4.7 2.8 - - - +
628B TRP 3.3 0.8 - - - -
629B SER* 1.3 76.8 - - - +
631B VAL* 1.3 60.3 + - - +
633B ARG* 3.3 6.2 + - + +
634B ASN* 2.9 29.9 + - - +
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Residues in contact with VAL 631 (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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571B CYS* 5.1 6.0 - - + +
574B LEU* 5.2 4.5 - - + -
575B VAL* 5.1 20.6 - - + +
628B TRP* 3.6 28.9 + - + +
629B SER 3.4 0.4 - - - -
630B PRO* 1.3 78.8 - - - +
632B PHE* 1.3 57.1 - - - +
634B ASN* 3.8 5.7 - - - +
635B TYR* 2.9 31.0 + - - +
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Residues in contact with PHE 632 (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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628B TRP 3.2 18.4 + - - +
629B SER* 3.8 6.7 - - - +
630B PRO 3.3 0.2 - - - -
631B VAL* 1.3 77.5 - - - +
633B ARG* 1.3 55.8 + - - +
635B TYR* 4.2 4.4 - - - +
636B ILE* 3.0 31.4 + - - +
675B ILE* 5.1 18.1 - - + +
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Residues in contact with ARG 633 (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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629B SER 2.9 18.5 + - - +
630B PRO* 3.7 6.3 - - + +
631B VAL 3.3 0.2 - - - -
632B PHE* 1.3 76.1 - - - +
634B ASN* 1.3 60.8 + - - +
636B ILE 3.0 20.7 - - - +
637B LYS* 4.0 8.1 - - - +
673B LEU 5.9 2.0 - - - +
674B GLU 5.1 11.2 - - - +
675B ILE* 5.8 2.7 - - - +
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Residues in contact with ASN 634 (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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575B VAL* 5.1 12.8 - - + -
630B PRO 2.9 17.9 + - - +
631B VAL* 3.9 6.5 - - - +
633B ARG* 1.3 76.3 - - - +
635B TYR* 1.3 63.6 + - - +
637B LYS* 4.6 7.5 - - - +
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Residues in contact with TYR 635 (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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589B LEU* 5.4 1.7 - - - +
592B VAL 6.1 0.2 - - - -
593B MET* 4.6 21.8 - - + +
596B LEU* 5.2 11.0 - - + -
631B VAL 2.9 18.2 + - - +
632B PHE* 4.2 4.0 - - - +
634B ASN* 1.3 80.4 - - - +
636B ILE* 1.3 60.4 + - + +
637B LYS* 3.6 3.1 + - - +
641B ASP* 4.5 4.9 - - - +
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Residues in contact with ILE 636 (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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593B MET* 5.2 6.3 - - + -
632B PHE 3.0 16.8 + - - +
633B ARG* 3.0 16.7 - - - +
635B TYR* 1.3 74.6 - - + +
637B LYS* 1.3 59.7 + - - +
638B ARG 4.9 0.7 - - - -
641B ASP* 3.8 28.0 - - + +
642B HIS* 4.7 3.8 - - - +
645B ALA* 4.6 11.9 - - + -
675B ILE* 4.8 15.0 - - + +
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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