Contacts of the helix formed by residues 720 - 735 (chain B) in PDB entry 1P48
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 THR 720 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B LEU* 3.5 7.5 - - - +
718B ILE* 3.2 19.5 - - - +
719B GLN* 1.3 89.7 - - + +
721B ALA* 1.3 64.5 + - - +
722B GLU* 3.4 17.4 + - - +
723B GLU* 3.3 25.5 + - - +
724B ALA 3.4 1.4 + - - -
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Residues in contact with ALA 721 (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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664B LEU* 3.7 11.8 - - + +
666B LEU* 4.0 29.8 - - + -
669B PHE* 4.2 8.7 - - + -
720B THR* 1.3 73.7 - - - +
722B GLU* 1.3 61.7 + - - +
724B ALA* 3.2 2.4 + - - +
725B LEU* 2.8 35.9 + - + +
781B LEU* 6.3 2.7 - - + -
785B LEU* 4.3 17.7 - - + -
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Residues in contact with GLU 722 (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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720B THR* 3.2 20.6 - - - +
721B ALA* 1.3 77.4 + - - +
723B GLU* 1.3 57.0 + - - +
726B ASP* 2.9 38.4 + - - +
781B LEU* 4.1 16.9 - - - +
784B SER* 5.2 3.3 + - - -
785B LEU* 3.9 23.2 - - + +
788B ARG* 3.7 25.8 - - - +
789B TYR* 3.0 17.2 + - + +
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Residues in contact with GLU 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B ARG* 5.8 0.2 + - - -
701B TYR* 2.8 39.4 + - - +
717B ASN 4.7 0.7 - - - +
718B ILE* 3.6 24.9 - - + +
719B GLN* 4.5 11.5 + - - +
720B THR* 3.3 13.9 + - - +
722B GLU* 1.3 79.0 - - - +
724B ALA* 1.3 62.3 + - - +
726B ASP* 3.6 7.5 + - - +
727B LEU* 3.2 23.7 + - - +
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Residues in contact with ALA 724 (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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654B LEU* 3.9 14.8 - - + +
664B LEU* 4.0 8.7 - - + -
669B PHE* 3.8 19.3 - - + -
718B ILE* 3.8 26.0 - - + +
720B THR 3.4 4.7 + - - +
721B ALA 3.2 8.6 + - - +
723B GLU* 1.3 79.6 - - - +
725B LEU* 1.3 62.0 + - - +
727B LEU* 3.2 6.7 + - - +
728B ILE* 3.1 26.4 + - - +
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Residues in contact with LEU 725 (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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669B PHE* 4.0 19.7 - - + -
721B ALA* 2.8 26.0 + - + +
724B ALA* 1.3 74.7 - - - +
726B ASP* 1.3 65.6 + - - +
728B ILE* 3.2 7.4 + - + +
729B VAL* 2.9 28.1 + - - +
743B ILE* 3.9 37.5 - - + -
745B LEU* 4.3 6.1 - - + -
785B LEU* 3.8 17.5 - - + -
789B TYR* 3.4 43.1 - - + -
791B ILE* 4.3 13.7 - - + -
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Residues in contact with ASP 726 (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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700B ARG* 5.2 1.1 - - - +
722B GLU* 2.9 24.7 + - - +
723B GLU* 3.9 7.7 + - - +
725B LEU* 1.3 76.7 - - - +
727B LEU* 1.3 57.3 + - - +
729B VAL* 3.4 5.2 + - - +
730B ASP* 2.9 40.0 + - - +
788B ARG* 3.1 23.7 + - - -
789B TYR* 2.9 22.9 + - - -
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Residues in contact with LEU 727 (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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654B LEU* 4.2 8.3 - - + -
693B LEU* 3.9 16.9 - - + +
696B LEU* 4.3 17.4 - - + +
697B THR* 4.0 17.5 - - - +
700B ARG* 3.7 27.3 - - - +
701B TYR* 3.4 35.9 - - + +
716B PRO* 4.7 1.8 - - + -
718B ILE* 4.2 17.5 - - + -
723B GLU 3.2 8.0 + - - +
724B ALA 3.2 9.2 - - - +
725B LEU 3.1 0.2 - - - -
726B ASP* 1.3 76.4 - - - +
728B ILE* 1.3 64.8 + - - +
730B ASP* 3.2 8.9 + - - +
731B ALA* 3.1 21.0 + - - +
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Residues in contact with ILE 728 (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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653B VAL* 4.5 8.7 - - + -
654B LEU* 4.2 16.8 - - + -
669B PHE* 3.3 48.0 - - + +
671B ILE* 3.6 30.1 - - + -
689B VAL* 5.5 1.3 - - + -
693B LEU* 4.5 5.8 - - + -
724B ALA 3.1 14.7 + - - +
725B LEU* 3.2 13.2 + - + +
727B LEU* 1.3 76.0 - - - +
729B VAL* 1.3 58.7 + - - +
731B ALA* 3.2 8.4 + - - +
732B ILE* 3.0 34.2 + - + +
743B ILE* 4.2 13.7 - - + -
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Residues in contact with VAL 729 (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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725B LEU 2.9 20.6 + - - +
726B ASP* 3.8 6.1 - - - +
728B ILE* 1.3 73.0 - - - +
730B ASP* 1.3 66.7 + - - +
732B ILE* 3.4 10.6 + - + +
733B LYS* 3.1 54.2 + - + +
738B ASP* 5.7 0.4 - - - +
743B ILE* 4.0 17.9 - - + -
789B TYR* 4.0 21.8 - - + -
790B PRO* 4.4 11.9 - - + -
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Residues in contact with ASP 730 (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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696B LEU* 4.0 13.2 - - + +
700B ARG* 2.8 37.8 + - - +
726B ASP* 2.9 27.1 + - - +
727B LEU* 3.5 7.0 - - - +
728B ILE 3.2 0.4 - - - -
729B VAL* 1.3 80.1 - - - +
731B ALA* 1.3 57.4 + - - +
733B LYS* 3.5 8.7 + - - +
734B ALA* 2.8 31.2 + - - +
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Residues in contact with ALA 731 (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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689B VAL* 3.7 14.6 - - + +
692B ASN* 3.9 3.7 - - - +
693B LEU* 3.7 37.5 - - + +
696B LEU* 3.9 9.8 - - + +
727B LEU 3.1 12.4 + - - +
728B ILE* 3.2 10.1 + - - +
730B ASP* 1.3 75.8 - - - +
732B ILE* 1.3 65.2 + - - +
734B ALA* 3.9 2.2 - - - +
735B ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 732 (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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671B ILE* 4.3 2.5 - - + -
689B VAL* 3.8 23.1 - - + -
728B ILE* 3.0 33.2 + - + +
729B VAL* 3.7 15.9 - - + +
731B ALA* 1.3 76.1 - - - +
733B LYS* 1.3 61.5 + - + +
735B ALA* 3.5 2.3 + - - +
736B GLY 3.3 3.5 + - - -
737B HIS* 3.0 51.8 + - + +
738B ASP* 3.7 10.5 - - - +
739B GLY 4.9 0.2 - - - +
741B VAL* 3.9 42.0 - - + +
743B ILE* 4.6 10.5 - - + -
790B PRO* 5.5 2.2 - - + -
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Residues in contact with LYS 733 (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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729B VAL* 3.1 39.0 + - + +
730B ASP* 3.9 8.5 + - - +
732B ILE* 1.3 74.7 - - + +
734B ALA* 1.3 60.9 + - - +
735B ALA 3.0 1.6 - - - -
736B GLY* 2.8 22.0 + - - -
738B ASP* 3.9 40.8 - - + +
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Residues in contact with ALA 734 (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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692B ASN* 3.8 19.7 - - - +
696B LEU* 4.5 12.8 - - + -
730B ASP 2.8 22.2 + - - +
731B ALA* 3.9 4.5 - - - +
733B LYS* 1.3 73.6 - - - +
735B ALA* 1.3 60.7 + - - +
736B GLY 3.5 0.7 + - - -
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Residues in contact with ALA 735 (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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688B GLU* 4.1 5.2 - - + +
689B VAL* 4.0 13.9 - - + +
692B ASN* 3.5 24.4 - - - +
731B ALA 2.9 18.5 + - - +
732B ILE 3.7 2.5 - - - +
733B LYS 3.0 0.2 - - - -
734B ALA* 1.3 76.9 - - - +
736B GLY* 1.3 60.2 + - - +
737B HIS* 3.5 31.6 + - + +
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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