Contacts of the helix formed by residues 669 - 679 (chain B) in PDB entry 4YFF
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 LYS 669 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B LEU* 1.3 75.5 - - - +
670B PRO* 1.3 79.0 - - + +
671B ALA* 3.3 4.3 - - + +
672B ALA* 3.0 21.1 + - + +
673B ALA* 3.1 9.8 + - - +
629C ARG* 4.3 0.4 - - - +
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Residues in contact with PRO 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LEU 3.8 0.6 - - - -
669B LYS* 1.3 89.6 - - + +
671B ALA* 1.3 58.2 + - - +
673B ALA* 3.0 9.6 + - + +
674B ALA* 2.9 28.2 + - - +
624C GLN 3.9 13.5 - - - +
625C PRO 3.3 20.4 - - - +
626C GLY* 3.3 28.9 - - - +
628C LEU* 3.7 14.1 - - + +
629C ARG* 4.3 18.8 + - + +
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Residues in contact with ALA 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LYS* 3.3 2.6 - - + -
670B PRO* 1.3 80.2 - - - +
672B ALA* 1.3 57.2 - - - +
674B ALA* 3.6 4.8 + - - +
675B ALA* 3.0 28.4 + - - +
624C GLN 4.9 11.2 - - - +
628C LEU* 3.8 20.6 - - + +
636C PHE* 3.7 10.1 - - + -
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Residues in contact with ALA 672 (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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668B LEU* 4.2 21.5 - - + -
669B LYS* 3.0 17.0 + - + +
671B ALA* 1.3 75.8 - - - +
673B ALA* 1.3 66.4 + - - +
675B ALA* 3.1 8.8 + - - +
676B ASP* 3.0 27.6 + - - +
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Residues in contact with ALA 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PHE* 3.8 33.3 - - + -
668B LEU* 4.1 12.5 - - + +
669B LYS 3.1 9.6 + - - +
670B PRO* 3.0 12.7 + - + +
672B ALA* 1.3 74.0 - - - +
674B ALA* 1.3 66.4 + - - +
676B ASP* 3.2 4.5 + - - +
677B MET* 3.1 30.4 + - + +
629C ARG* 4.5 16.8 - - + +
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Residues in contact with ALA 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B PRO 2.9 12.5 + - - +
671B ALA* 3.6 4.7 - - - +
673B ALA* 1.3 74.6 - - - +
675B ALA* 1.3 53.6 + - - +
677B MET* 3.3 14.2 + - - +
678B ALA* 2.7 38.5 + - - +
628C LEU* 3.9 15.4 + - + +
631C MET* 5.9 0.4 - - + -
633C PRO* 5.7 0.3 - - - +
636C PHE* 3.2 43.8 - - + -
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Residues in contact with ALA 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ALA 3.0 15.8 + - - +
672B ALA* 3.1 13.6 + - - +
674B ALA* 1.3 75.8 - - - +
676B ASP* 1.3 59.3 + - - +
679B TYR* 2.7 56.5 + - + +
680B HIS* 4.5 2.9 - - + +
636C PHE* 3.3 13.0 - - + -
707C GLU* 5.9 0.7 - - - +
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Residues in contact with ASP 676 (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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665B PHE* 4.5 9.0 - - + -
668B LEU* 3.4 22.9 - - - +
672B ALA* 3.0 15.8 + - - +
673B ALA 3.2 7.4 + - - +
675B ALA* 1.3 75.0 - - - +
677B MET* 1.3 61.9 + - - +
680B HIS* 3.2 25.4 + - - -
681B HIS 2.9 26.2 + - - -
682B ILE* 2.9 33.9 + - + +
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Residues in contact with MET 677 (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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649B PHE* 4.0 15.3 - - + -
653B LEU* 3.9 22.7 - - + -
665B PHE* 3.5 29.2 - - + -
673B ALA 3.1 19.5 + - - +
674B ALA* 3.7 12.8 - - - +
676B ASP* 1.3 77.9 - - - +
678B ALA* 1.3 62.5 + - - +
681B HIS* 3.4 9.2 + - - -
682B ILE 3.3 21.3 - - - +
683B ARG* 2.9 29.1 + - - +
628C LEU 4.4 0.4 - - - +
629C ARG 3.5 24.2 - - - +
631C MET 3.7 21.5 - - - +
633C PRO* 4.6 5.6 - - + +
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Residues in contact with ALA 678 (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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674B ALA 2.7 21.5 + - - +
675B ALA 3.8 2.0 - - - +
677B MET* 1.3 78.2 - - - +
679B TYR* 1.3 74.5 + - + +
681B HIS* 4.0 15.4 + - - -
633C PRO* 4.1 23.3 - - + +
636C PHE* 3.5 23.3 - - + -
637C THR* 4.6 6.7 - - - +
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Residues in contact with TYR 679 (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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634B GLU* 4.5 19.2 - - + +
675B ALA* 2.7 35.3 + - + +
678B ALA* 1.3 81.8 - - + +
680B HIS* 1.3 64.1 + + + +
681B HIS* 3.2 10.7 - - - -
636C PHE* 4.2 22.7 - + - -
637C THR* 4.5 9.4 + - - -
640C THR* 3.9 23.2 - - - +
704C ALA* 3.2 34.6 - - - +
705C CYS* 3.8 21.7 + - + -
706C PRO* 3.5 32.0 - - + +
707C GLU* 4.0 18.4 - - - -
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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