Contacts of the helix formed by residues 669 - 680 (chain B) in PDB entry 4YFI
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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629A ARG* 3.9 0.9 - - - +
667B HIS 4.3 0.2 + - - -
668B LEU* 1.3 77.0 - - - +
670B PRO* 1.3 78.6 - - + -
671B ALA* 3.3 2.5 - - + +
672B ALA* 3.1 19.5 + - + +
673B ALA* 3.2 6.9 + - - +
667D HIS 4.8 11.3 + - - +
668D LEU 6.4 0.2 - - - -
669D LYS* 3.8 33.8 - - - +
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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
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627A ASN* 4.0 31.4 - - - +
628A LEU* 4.0 20.5 - - + +
629A ARG* 3.4 29.8 + - + +
669B LYS* 1.3 87.4 - - + -
671B ALA* 1.3 57.7 + - - +
673B ALA* 3.2 6.5 + - + +
674B ASP* 3.0 25.6 + - - +
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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
----------------------------------------------------------
628A LEU* 3.7 22.9 - - + -
636A PHE* 4.3 8.2 - - + -
669B LYS* 3.1 2.7 + - + +
670B PRO* 1.3 77.4 - - - +
672B ALA* 1.3 65.3 + - - +
674B ASP* 3.4 4.5 + - - +
675B MET* 3.1 24.4 + - - +
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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
----------------------------------------------------------
668B LEU* 3.9 25.4 - - + -
669B LYS* 3.1 16.3 + - + +
671B ALA* 1.3 77.8 - - - +
673B ALA* 1.3 58.1 + - - +
675B MET* 3.3 7.3 + - - +
676B ASP* 2.9 33.0 + - - +
668D LEU* 5.2 14.6 - - + -
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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
----------------------------------------------------------
629A ARG* 4.3 17.9 - - + +
665B PHE* 3.9 30.5 - - + -
668B LEU* 3.8 13.2 - - + +
669B LYS 3.2 8.1 + - - +
670B PRO* 3.3 10.8 - - + +
672B ALA* 1.3 81.6 - - - +
674B ASP* 1.3 61.5 + - - +
676B ASP* 3.3 4.8 + - - +
677B MET* 3.0 28.9 + - - +
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Residues in contact with ASP 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LEU* 3.7 22.6 + - + +
631A MET* 5.6 0.4 - - + +
633A PRO* 5.7 0.3 - - - +
636A PHE* 3.3 39.9 - - + +
670B PRO 3.0 10.8 + - - +
671B ALA 3.8 2.9 - - - +
672B ALA 3.3 0.2 - - - -
673B ALA* 1.3 75.5 - - - +
675B MET* 1.3 58.7 + - - +
677B MET* 3.2 14.3 + - + +
678B ALA* 2.8 31.4 + - - +
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Residues in contact with MET 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A PHE* 4.0 9.6 - - + -
671B ALA 3.1 16.1 + - - +
672B ALA* 3.5 6.7 - - - +
674B ASP* 1.3 75.7 - - - +
676B ASP* 1.3 61.9 + - - +
679B TYR* 2.9 59.6 + - + +
680B HIS* 4.2 3.5 - - + +
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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
----------------------------------------------------------
665B PHE* 4.6 6.1 - - + -
667B HIS* 5.5 1.0 + - - -
668B LEU* 3.4 20.5 - - + +
672B ALA 2.9 19.0 + - - +
673B ALA* 3.6 7.9 - - - +
675B MET* 1.3 76.6 - - - +
677B MET* 1.3 61.8 + - - +
680B HIS* 3.3 25.1 + - - +
681B HIS 3.2 8.1 + - - -
682B ILE* 3.1 48.2 + - + +
676D ASP* 5.4 1.7 - - - +
680D HIS* 4.6 3.5 + - - -
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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
----------------------------------------------------------
628A LEU 4.5 0.2 - - - +
629A ARG 3.3 27.8 - - - +
631A MET 3.8 19.5 - - - +
633A PRO* 4.3 4.9 - - + +
649B PHE* 3.9 15.3 - - + -
653B LEU* 3.7 20.4 - - + -
665B PHE* 3.5 38.8 - - + -
673B ALA 3.0 16.5 + - - +
674B ASP* 3.6 13.2 - - - +
675B MET 3.1 0.2 - - - -
676B ASP* 1.3 80.0 - - - +
678B ALA* 1.3 62.5 + - - +
681B HIS* 3.6 8.1 + - - -
682B ILE 3.5 11.4 - - - +
683B ARG* 2.9 27.8 + - - +
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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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633A PRO* 3.8 29.7 - - + +
636A PHE* 3.9 20.9 - - + -
637A THR* 4.7 2.7 - - - +
681A HIS* 3.4 23.7 + - - -
674B ASP 2.8 18.1 + - - +
675B MET 4.1 1.3 - - - +
677B MET* 1.3 78.7 - - - +
679B TYR* 1.3 71.5 + - + +
681B HIS* 4.6 0.9 + - - -
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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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636A PHE* 3.8 27.4 - + - -
637A THR* 4.6 12.4 + - - -
640A THR* 5.0 7.6 + - - +
681A HIS* 3.6 18.8 + - - -
703A ASN* 5.6 0.3 - - - +
704A ALA* 3.3 33.6 - - + +
705A CYS* 3.8 20.0 - - + +
706A PRO* 3.5 24.2 - - + +
707A GLU* 4.3 10.9 + - - -
634B GLU* 5.5 7.1 - - + +
675B MET* 2.9 30.4 + - + +
678B ALA* 1.3 89.3 - - + +
680B HIS* 1.3 83.2 + - + +
681B HIS* 3.5 3.0 - - - -
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Residues in contact with HIS 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ASN* 4.6 4.2 + - - -
705A CYS* 3.6 33.7 - - + +
675B MET* 3.7 6.8 + - + +
676B ASP* 3.3 24.6 + - - +
679B TYR* 1.3 89.2 + - + +
681B HIS* 1.3 65.7 + - - +
682B ILE* 2.9 26.6 + - + +
703C ASN* 3.7 19.1 + - - +
705C CYS* 5.5 0.4 - - + -
708C GLY* 3.8 2.3 - - - -
676D ASP* 4.6 3.7 + - - -
680D HIS* 3.2 66.6 + + + +
682D ILE* 4.9 0.2 - - - +
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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