Contacts of the helix formed by residues 669 - 679 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A ARG* 3.8 0.7 - - - +
668D LEU* 1.3 75.8 - - - +
670D PRO* 1.3 78.5 - - + +
671D ALA 3.4 2.2 - - - +
672D ALA* 3.1 13.9 + - + +
673D ALA* 3.0 17.8 + - - +
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Residues in contact with PRO 670 (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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627A ASN* 4.2 16.2 - - - +
628A LEU* 4.6 8.5 - - + +
629A ARG* 3.4 50.9 - - + +
669D LYS* 1.3 89.2 - - + +
671D ALA* 1.3 57.2 + - - +
673D ALA* 3.2 5.1 + - + +
674D ALA* 2.8 28.4 + - - +
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Residues in contact with ALA 671 (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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628A LEU* 4.2 22.1 - - + +
636A PHE* 4.8 7.8 - - + -
669D LYS* 3.4 1.5 - - + +
670D PRO* 1.3 77.1 - - - +
672D ALA* 1.3 66.8 + - - +
674D ALA* 3.8 4.6 - - - +
675D ALA* 2.9 26.4 + - - +
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Residues in contact with ALA 672 (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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668D LEU* 4.2 22.9 - - + -
669D LYS* 3.1 18.1 + - + +
671D ALA* 1.3 76.4 - - - +
673D ALA* 1.3 64.0 - - - +
675D ALA* 3.3 4.6 + - - +
676D ASP* 3.0 31.7 + - - +
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Residues in contact with ALA 673 (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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629A ARG* 4.6 14.1 - - + +
665D PHE* 3.9 34.0 - - + -
668D LEU* 4.1 12.4 - - + +
669D LYS 3.0 11.6 + - - +
670D PRO* 3.3 12.3 - - + +
672D ALA* 1.3 75.8 - - - +
674D ALA* 1.3 63.2 + - - +
676D ASP* 3.2 4.1 + - - +
677D MET* 3.0 29.9 + - + +
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Residues in contact with ALA 674 (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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628A LEU* 3.3 28.2 + - + +
631A MET* 5.5 2.0 - - + +
633A PRO* 5.6 0.3 - - - +
636A PHE* 3.8 32.1 - - + +
670D PRO 2.8 16.0 + - - +
671D ALA* 3.3 3.8 + - - +
673D ALA* 1.3 71.9 - - - +
675D ALA* 1.3 57.9 + - - +
677D MET* 3.6 15.1 + - + +
678D ALA* 3.1 30.1 + - - +
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Residues in contact with ALA 675 (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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636A PHE* 4.2 11.3 - - + -
671D ALA 2.9 17.3 + - - +
672D ALA* 3.5 7.0 - - - +
674D ALA* 1.3 74.7 - - - +
676D ASP* 1.3 62.9 + - - +
678D ALA 3.1 0.7 + - - -
679D TYR* 2.6 62.6 + - + +
680D HIS* 4.8 2.5 - - - +
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Residues in contact with ASP 676 (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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665D PHE* 5.5 2.5 - - + -
668D LEU* 4.0 18.8 - - + +
672D ALA* 3.0 19.9 + - - +
673D ALA* 3.7 5.6 - - - +
675D ALA* 1.3 77.7 - - - +
677D MET* 1.3 58.3 + - + +
680D HIS* 3.3 24.8 + - - -
681D HIS 3.0 12.5 + - - -
682D ILE* 2.9 50.6 + - + +
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Residues in contact with MET 677 (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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628A LEU 4.7 0.2 - - - +
629A ARG 3.5 25.4 - - - +
631A MET 4.1 16.8 - - - +
633A PRO* 4.2 5.2 - - + +
649D PHE* 3.8 23.1 - - + -
653D LEU* 4.1 15.5 - - + -
665D PHE* 3.5 32.1 - - + -
673D ALA 3.0 20.0 + - - +
674D ALA* 3.9 14.4 - - - +
676D ASP* 1.3 74.8 - - - +
678D ALA* 1.3 62.3 + - - +
681D HIS* 3.6 8.8 - - - -
682D ILE 3.3 21.3 - - - +
683D ARG* 2.7 29.0 + - - +
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Residues in contact with ALA 678 (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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633A PRO* 3.6 31.4 - - + +
636A PHE* 3.9 20.2 - - + -
637A THR* 4.9 2.5 - - - +
681A HIS* 3.5 21.5 + - - -
674D ALA 3.1 19.4 + - - +
675D ALA 3.9 0.9 - - - +
677D MET* 1.3 79.2 - - - +
679D TYR* 1.3 72.1 + - + +
681D HIS 4.4 0.2 - - - -
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Residues in contact with TYR 679 (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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636A PHE* 3.5 33.9 - + - -
637A THR* 4.9 11.9 + - + +
640A THR* 5.0 10.7 + - - +
681A HIS* 3.4 20.1 + - - -
703A ASN* 5.6 0.2 - - - +
704A ALA* 3.5 33.0 - - + +
705A CYS* 3.8 26.0 - - + +
706A PRO* 3.7 22.6 - - + +
707A GLU* 4.3 6.6 + - - -
634D GLU* 5.8 5.2 - - + +
675D ALA* 2.6 36.4 + - + +
678D ALA* 1.3 80.1 - - + +
680D HIS* 1.3 76.4 + - + +
681D HIS* 3.2 5.3 + - - +
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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