Contacts of the helix formed by residues 661 - 671 (chain B) in PDB entry 4PP7
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 661 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659B ILE* 3.4 9.2 - - + +
660B ASN* 1.3 81.7 - - - +
662B ARG* 1.3 67.1 + - - +
663B ASP* 3.0 20.7 + - - +
664B GLN* 2.7 55.4 + - + +
665B ILE* 3.3 16.1 + - - +
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Residues in contact with ARG 662 (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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614B SER* 3.0 37.3 + - - +
615B GLY* 5.0 1.8 - - - -
617B ILE* 3.5 19.2 - - - +
618B LEU* 3.7 24.5 - - - +
660B ASN 4.0 3.4 + - - -
661B ASN* 1.3 73.1 + - - +
663B ASP* 1.3 72.6 + - - +
665B ILE* 3.3 10.8 + - - +
666B ILE* 3.3 36.4 + - + +
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Residues in contact with ASP 663 (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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661B ASN* 3.0 16.1 + - - +
662B ARG* 1.3 86.3 - - - +
664B GLN* 1.3 60.2 + - + +
666B ILE* 3.3 16.6 - - + +
667B PHE* 2.9 28.2 + - - +
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Residues in contact with GLN 664 (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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659B ILE* 4.8 8.1 - - + -
661B ASN* 2.7 39.8 + - + +
663B ASP* 1.3 72.2 - - - +
665B ILE* 1.3 57.3 + - - +
667B PHE* 3.0 23.6 + - - +
668B MET* 2.7 55.7 + - - +
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Residues in contact with ILE 665 (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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617B ILE* 3.9 21.3 - - + +
618B LEU* 5.6 2.5 - - + -
625B ILE* 6.4 0.4 - - + -
656B TYR* 3.6 52.0 - - + +
659B ILE* 3.8 31.6 - - + +
661B ASN 3.3 18.2 - - - +
662B ARG* 3.4 11.9 - - - +
664B GLN* 1.3 75.6 - - - +
666B ILE* 1.3 57.6 + - - +
668B MET* 4.8 3.8 - - - -
669B VAL* 2.8 47.0 + - + +
674B LEU* 4.7 2.7 - - + -
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Residues in contact with ILE 666 (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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617B ILE* 3.9 27.1 - - + -
625B ILE* 3.2 38.9 - - + +
662B ARG* 3.3 30.2 + - + +
663B ASP* 3.3 17.0 - - + +
664B GLN 3.2 0.2 - - - -
665B ILE* 1.3 80.4 - - - +
667B PHE* 1.3 67.0 + - - +
669B VAL* 4.1 0.2 - - - +
670B GLY* 3.1 14.4 + - - -
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Residues in contact with PHE 667 (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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663B ASP 2.9 14.2 + - - +
664B GLN* 3.4 29.4 - - - +
666B ILE* 1.3 78.5 - - - +
668B MET* 1.3 64.5 + - + +
670B GLY* 3.3 1.2 + - - -
671B ARG* 2.9 77.5 + - + +
673B TYR* 4.1 14.4 - + - -
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Residues in contact with MET 668 (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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659B ILE* 5.2 10.1 - - + -
664B GLN* 2.7 45.3 + - - +
665B ILE 3.9 0.9 - - - +
667B PHE* 1.3 79.9 - - + +
669B VAL* 1.3 59.8 + - - +
672B GLY 3.0 6.4 + - - -
673B TYR* 2.9 62.8 + - + +
674B LEU* 3.2 33.1 + - + -
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Residues in contact with VAL 669 (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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617B ILE 5.3 3.4 - - - +
620B MET 4.1 12.6 - - - +
622B PRO* 4.1 20.9 - - + +
625B ILE* 4.0 22.7 - - + -
640B TYR* 4.5 10.1 - - - +
656B TYR* 4.0 15.0 - - + +
665B ILE* 2.8 36.5 + - + +
666B ILE* 4.1 3.1 - - - +
668B MET* 1.3 71.2 - - - +
670B GLY* 1.3 63.9 + - - +
672B GLY* 3.2 13.2 + - - -
674B LEU* 3.7 33.9 - - + +
699B LYS* 5.8 0.2 - - - -
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Residues in contact with GLY 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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622B PRO 4.4 7.2 - - - -
625B ILE* 3.9 18.6 - - - +
626B ARG* 2.7 39.5 + - - -
666B ILE 3.1 12.7 + - - -
667B PHE 3.7 3.4 - - - -
669B VAL* 1.3 80.8 - - - +
671B ARG* 1.3 59.2 + - - +
672B GLY* 3.3 0.7 + - - -
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Residues in contact with ARG 671 (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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626B ARG* 5.2 1.1 - - - -
667B PHE* 2.9 56.9 + - + +
670B GLY* 1.3 76.3 - - - +
672B GLY* 1.3 60.3 + - - +
673B TYR* 3.2 52.3 + - + -
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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