Contacts of the helix formed by residues 669 - 679 (chain N) in PDB entry 2PPB
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 ASN 669 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662N GLU* 2.7 22.1 - - - +
667N ALA* 4.0 0.7 - - - +
668N PRO* 1.3 100.5 - - - +
670N VAL* 1.3 58.2 + - + +
671N LYS* 3.5 6.7 - - + +
672N ALA* 3.2 8.8 - - + +
673N ALA* 2.8 27.2 + - - +
1Y G 5.7 3.2 + - - -
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Residues in contact with VAL 670 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067M TYR* 4.9 1.8 - - + +
1071M ILE* 3.5 37.0 - - + -
658N LEU* 3.5 34.3 - - + -
662N GLU* 2.9 20.5 + - - +
669N ASN* 1.3 72.8 - - + +
671N LYS* 1.3 55.1 + - - +
673N ALA* 2.8 5.8 + - - +
674N ARG* 2.7 40.3 + - - +
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Residues in contact with LYS 671 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669N ASN* 3.5 4.1 - - + +
670N VAL* 1.3 77.9 - - - +
672N ALA* 1.3 62.0 + - - +
674N ARG* 3.4 26.0 + - + +
675N ARG* 3.2 24.9 + - + +
2Y A 1.7 68.7 + - - +
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Residues in contact with ALA 672 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667N ALA* 4.7 1.3 - - - -
668N PRO* 3.7 29.2 - - + -
669N ASN* 3.2 19.1 + - + +
671N LYS* 1.3 79.8 - - - +
673N ALA* 1.3 55.7 + - - +
674N ARG 3.2 0.3 + - - -
675N ARG* 3.3 25.7 + - - +
676N MET* 3.0 28.4 + - - +
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Residues in contact with ALA 673 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658N LEU* 3.7 15.0 - - + +
661N MET* 3.3 30.6 - - + +
662N GLU* 3.1 26.2 - - - +
667N ALA* 3.8 7.1 - - + +
669N ASN 2.8 8.4 + - - +
670N VAL 2.8 7.7 + - - +
672N ALA* 1.3 72.4 - - - +
674N ARG* 1.3 59.4 + - - +
676N MET* 3.5 5.7 - - - +
677N LEU* 3.3 27.2 - - - +
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Residues in contact with ARG 674 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067M TYR* 3.4 35.1 + - - -
654N LYS* 5.0 12.8 + - + +
658N LEU* 3.6 24.7 - - + -
670N VAL* 2.7 18.6 + - - +
671N LYS* 3.5 30.2 - - + +
672N ALA 3.1 0.2 - - - -
673N ALA* 1.3 69.4 - - - +
675N ARG* 1.3 66.4 + - - +
676N MET 3.1 1.1 - - - -
677N LEU* 3.0 7.5 + - - +
678N GLU* 3.0 19.7 + - - +
2Y A 6.0 2.6 + - - -
3Y G 4.4 14.8 + - - -
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Residues in contact with ARG 675 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729M LEU* 3.3 47.9 - - + +
671N LYS* 3.2 12.7 + - + +
672N ALA* 3.9 24.3 + - - +
674N ARG* 1.3 79.9 - - - +
676N MET* 1.3 64.2 + - - +
678N GLU* 3.2 36.0 + - + +
679N ARG 4.4 0.7 + - - -
682N ASP* 4.5 4.5 - - - +
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Residues in contact with MET 676 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661N MET* 4.2 9.0 - - + -
666N ILE* 4.9 11.9 - - + +
667N ALA* 5.5 1.1 - - + -
672N ALA 3.0 18.4 + - - +
673N ALA* 3.5 13.2 - - - +
675N ARG* 1.3 80.7 - - - +
677N LEU* 1.3 62.3 + - + +
679N ARG 4.1 0.3 - - - +
682N ASP* 3.0 52.3 - - - +
683N ILE* 3.4 8.1 - - - -
684N LYS* 3.3 37.5 - - + +
687N VAL* 3.6 15.5 - - + -
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Residues in contact with LEU 677 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650N LEU* 4.5 12.9 - - + +
654N LYS* 4.0 31.7 + - - +
657N LEU* 4.1 22.4 - - + -
658N LEU* 4.6 7.4 - - + -
661N MET* 4.2 11.0 - - + -
673N ALA 3.3 17.7 - - - +
674N ARG 3.0 7.6 + - - +
676N MET* 1.3 87.1 - - + +
678N GLU* 1.3 64.5 + - - +
679N ARG 3.0 12.8 + - - +
683N ILE* 3.6 28.8 - - + +
687N VAL* 3.7 21.1 - - + -
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Residues in contact with GLU 678 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751M PRO 4.6 0.9 - - - +
752M GLY* 4.1 13.9 - - - +
791M ARG* 3.1 25.7 + - - -
794M PRO* 6.1 0.5 - - - +
654N LYS* 5.7 1.8 - - - +
674N ARG 3.0 11.5 + - - +
675N ARG* 3.2 33.6 + - + +
677N LEU* 1.3 78.0 - - - +
679N ARG* 1.3 104.9 + - + +
680N GLN* 5.9 0.3 - - - +
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Residues in contact with ARG 679 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726M ILE* 6.0 0.8 - - - +
730M SER* 5.4 0.6 + - - -
733M ALA* 3.0 37.6 - - - +
751M PRO 3.9 7.0 - - - +
752M GLY* 3.5 24.2 + - - +
753M ASP* 3.6 21.1 + - - +
754M ILE* 4.2 7.3 - - - +
791M ARG* 4.0 20.4 - - - +
677N LEU 3.6 6.4 - - - +
678N GLU* 1.3 112.4 + - + +
680N GLN* 1.3 61.8 + - - +
681N ARG* 3.4 7.8 - - + +
682N ASP* 3.1 39.6 + - - +
683N ILE* 3.0 18.9 - - - +
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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