Contacts of the strand formed by residues 651 - 655 (chain B) in PDB entry 1P43
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 LEU 651 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B PRO* 4.0 27.4 - - + +
650B PHE* 1.3 71.6 - - - +
652B ASN* 1.3 59.5 + - - +
653B VAL* 2.9 8.6 + - + +
670B MET* 2.9 3.6 - - - -
671B ILE* 2.8 52.1 + - + +
673B PRO* 4.5 6.5 - - + -
682B ALA 5.1 0.4 - - - +
683B LEU* 4.8 6.5 - - + -
686B GLY* 3.6 34.3 - - - +
897B THR* 5.9 0.9 - - + -
898B GLY 3.3 19.1 - - - +
900B PRO* 4.1 22.7 - - + -
909B LEU* 4.1 20.4 - - + -
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Residues in contact with ASN 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B PHE 3.7 1.8 + - - -
651B LEU* 1.3 67.8 - - - +
653B VAL* 1.3 57.6 + - - +
654B LEU 3.0 28.5 + - - +
655B ASN* 3.2 16.4 - - - +
668B GLN* 3.4 22.8 + - - +
669B PHE 3.3 14.1 + - - +
670B MET* 3.5 17.7 - - + +
711B GLU* 3.2 32.9 - - + +
713B GLY* 3.5 8.5 + - - -
896B LYS* 5.7 1.8 - - + -
898B GLY* 3.7 8.9 + - - -
899B ALA* 3.1 21.9 + - - +
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Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B LEU* 2.9 18.5 + - + +
652B ASN* 1.3 72.1 - - - +
654B LEU* 1.3 60.5 + - + +
669B PHE 3.1 10.8 + - - +
671B ILE* 3.8 41.3 - - + -
689B VAL* 5.9 1.3 - - + -
690B TYR* 3.7 24.7 - - + -
693B LEU* 3.4 25.3 - - + +
713B GLY* 3.2 9.1 - - - -
714B VAL* 2.8 27.7 + - - +
728B ILE* 4.7 7.6 - - + -
899B ALA* 4.1 1.3 - - - -
900B PRO* 4.2 5.4 - - + -
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Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ASN* 3.0 17.9 + - - -
653B VAL* 1.3 83.2 - - + +
655B ASN* 1.3 76.9 + - - +
664B LEU* 4.4 0.7 - - + -
669B PHE* 3.0 49.8 + - + +
693B LEU* 4.5 5.8 - - + -
714B VAL* 3.3 20.0 - - + +
716B PRO* 4.5 2.2 - - + -
718B ILE* 3.6 31.9 - - + -
724B ALA* 3.9 17.7 - - + +
727B LEU* 4.0 20.6 - - + -
728B ILE* 4.6 6.7 - - + -
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Residues in contact with ASN 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ASN* 3.2 24.0 + - - +
654B LEU* 1.3 89.1 - - - +
656B GLY* 1.3 58.5 + - - +
659B HIS* 3.6 34.4 - - + +
660B ALA* 3.8 11.3 - - - +
664B LEU* 4.3 2.4 - - - +
667B GLN* 3.4 5.4 - - - +
668B GLN* 5.2 1.4 + - - +
709B GLY* 3.5 22.6 - - - +
710B ASP 5.4 0.7 - - - -
711B GLU* 5.1 5.1 + - - +
713B GLY* 3.4 30.3 + - - +
714B VAL 2.9 9.3 + - - -
715B ALA* 3.9 11.4 - - + +
716B PRO* 4.7 3.6 - - - +
718B ILE* 5.0 0.5 - - - +
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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