Contacts of the helix formed by residues 716 - 729 (chain B) in PDB entry 1SO2
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 PRO 716 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714B LYS 3.3 10.1 - - - +
715B ILE* 1.3 82.9 - - + +
717B THR* 1.3 66.2 + - - +
718B GLN* 3.2 2.6 + - + -
719B GLN* 3.5 29.7 + - - +
720B PHE* 3.2 18.5 + - - +
870B PHE* 3.5 20.6 - - - +
872B LEU* 3.7 23.1 - - + -
873B HIS* 4.6 3.6 - - + +
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Residues in contact with THR 717 (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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701B TYR* 3.7 36.4 + - + +
710B LEU* 5.4 5.7 - - - +
715B ILE* 3.4 6.1 + - - -
716B PRO* 1.3 71.6 - - - +
718B GLN* 1.3 64.5 + - - +
720B PHE* 3.4 6.1 + - - +
721B MET* 2.9 34.7 + - + +
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Residues in contact with GLN 718 (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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716B PRO* 3.2 1.2 + - + +
717B THR* 1.3 79.4 - - - +
719B GLN* 1.3 71.5 + - - +
721B MET* 3.8 4.1 - - - +
722B ASN* 2.9 65.0 + - - +
725B ARG* 5.6 4.2 - - - +
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Residues in contact with GLN 719 (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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716B PRO* 3.5 28.5 + - - +
718B GLN* 1.3 85.8 - - - +
720B PHE* 1.3 66.7 + - - +
722B ASN* 3.5 2.8 - - - +
723B TYR* 2.9 26.5 + - - +
866B PRO 4.2 5.8 - - - +
867B GLU* 3.4 36.1 - - + +
868B TYR 3.9 1.3 - - - +
869B ASN 4.1 6.2 - - - +
870B PHE* 3.9 22.2 - - + +
872B LEU* 4.6 12.3 - - - +
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Residues in contact with PHE 720 (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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697B SER 4.8 0.4 - - - -
700B MET* 3.9 13.7 - - + -
701B TYR* 3.8 30.5 - + - -
704B PHE* 3.2 48.7 - + + -
710B LEU* 4.4 4.3 - - + -
715B ILE* 3.7 24.2 - - + -
716B PRO 3.2 16.0 + - - +
717B THR* 3.5 6.3 - - - +
719B GLN* 1.3 79.4 - - - +
721B MET* 1.3 80.0 + - + +
723B TYR* 3.8 0.7 - - - +
724B PHE* 3.0 58.5 + + - -
870B PHE* 3.6 16.5 - + - +
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Residues in contact with MET 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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697B SER* 3.8 25.8 - - - +
698B GLN* 3.9 21.5 - - - +
701B TYR* 3.8 28.9 - - + -
717B THR* 2.9 33.7 + - + +
718B GLN* 3.9 4.7 - - - +
720B PHE* 1.3 85.1 - - + +
722B ASN* 1.3 67.7 + - - +
724B PHE* 3.9 1.7 - - - +
725B ARG* 2.9 69.2 + - - +
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Residues in contact with ASN 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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718B GLN* 2.9 56.7 + - - +
719B GLN* 3.2 3.1 + - - +
721B MET* 1.3 77.8 - - - +
723B TYR* 1.3 58.5 + - - +
725B ARG* 3.7 10.2 + - - +
726B ALA* 3.0 27.7 + - - +
867B GLU* 3.1 38.7 + - - +
868B TYR* 3.7 13.2 - - + -
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Residues in contact with TYR 723 (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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719B GLN 2.9 15.7 + - - +
720B PHE 3.8 2.2 - - - +
722B ASN* 1.3 78.4 - - - +
724B PHE* 1.3 82.0 + + - +
726B ALA* 3.1 3.1 + - - +
727B LEU* 2.8 45.0 + - + +
820B MET* 3.4 22.5 - - + +
858B ALA 2.7 23.5 + - - -
861B LEU* 3.7 14.1 - - + -
862B TYR* 3.2 45.8 - + + -
868B TYR* 3.7 33.6 - + + +
870B PHE* 3.6 21.3 - + + -
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Residues in contact with PHE 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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696B LEU* 5.4 3.1 - - + +
697B SER* 3.9 23.4 - - - +
700B MET* 4.3 18.8 - - + -
704B PHE* 5.4 0.2 - + - -
720B PHE* 3.0 57.9 + + + +
721B MET* 4.5 1.8 - - - +
723B TYR* 1.3 90.7 - + - +
725B ARG* 1.3 60.5 + - - +
727B LEU* 3.7 20.1 - - + +
728B GLU* 3.3 27.9 + - - +
816B VAL* 4.2 20.2 - - + -
819B ALA* 4.1 17.9 - - + -
870B PHE* 3.3 42.4 - + - -
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Residues in contact with ARG 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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694B ARG* 3.3 49.4 - - - +
697B SER* 3.8 15.5 - - - +
698B GLN* 3.9 6.5 - - - +
718B GLN* 5.6 3.8 - - - +
721B MET* 2.9 60.5 + - - +
722B ASN* 3.7 11.4 + - - +
724B PHE* 1.3 75.3 - - - +
726B ALA* 1.3 65.7 + - - +
728B GLU* 3.6 11.8 + - - +
729B ASN* 3.2 32.2 + - - +
776C ASP 5.0 0.2 - - - -
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Residues in contact with ALA 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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722B ASN 3.0 12.3 + - - +
723B TYR* 3.5 7.4 - - - +
725B ARG* 1.3 75.5 - - - +
727B LEU* 1.3 65.6 + - - +
728B GLU 3.4 0.5 + - - -
729B ASN 3.4 5.0 + - - -
730B GLY* 3.5 4.7 + - - -
823B TYR* 4.4 0.2 - - - -
861B LEU* 4.0 15.2 - - + +
868B TYR* 3.4 31.4 - - + +
776C ASP 4.2 3.8 - - - +
777C GLY* 3.3 35.7 - - - +
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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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696B LEU* 4.7 5.2 - - + -
723B TYR* 2.8 40.2 + - + +
724B PHE* 3.8 29.2 - - + +
725B ARG 3.3 0.2 - - - -
726B ALA* 1.3 76.1 - - - +
728B GLU* 1.3 56.4 + - - +
730B GLY* 3.0 16.3 + - - -
731B TYR* 3.6 6.6 - - + -
819B ALA* 3.7 33.4 - - + +
820B MET* 3.8 12.8 - - + -
823B TYR* 3.1 41.9 - - + -
858B ALA* 3.9 14.4 - - + -
861B LEU* 3.8 7.8 - - + +
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Residues in contact with GLU 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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693B GLY 3.4 10.5 - - - +
694B ARG* 2.7 30.2 - - - +
695B ILE* 3.0 0.5 + - - +
696B LEU* 2.5 51.9 + - + -
697B SER* 2.6 27.4 + - - -
724B PHE 3.3 11.0 + - - +
725B ARG* 3.6 15.0 - - - +
727B LEU* 1.3 74.5 - - - +
729B ASN* 1.3 59.2 + - - +
730B GLY 2.9 5.2 - - - -
731B TYR* 3.0 23.2 + - - +
739B ARG* 3.0 26.9 + - + +
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Residues in contact with ASN 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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693B GLY 4.5 4.0 - - - +
694B ARG* 6.0 1.6 - - - +
725B ARG* 3.2 17.1 + - - +
726B ALA 3.4 2.0 + - - -
728B GLU* 1.3 77.9 - - - +
730B GLY* 1.3 58.4 + - - +
731B TYR 3.3 4.8 - - - +
739B ARG* 2.7 29.8 + - - +
776C ASP 3.1 22.8 + - - -
777C GLY* 3.1 28.2 - - - +
778C ARG* 3.8 10.0 - - + +
779C ILE* 4.2 4.9 - - - +
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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