Contacts of the helix formed by residues 807 - 819 (chain D) 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 807 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784D ILE* 3.5 38.6 - - + -
785D ALA 3.8 8.3 - - - +
786D TYR* 4.2 11.0 - - + +
805D ASN 4.4 0.4 - - - +
806D ILE* 1.3 83.9 - - - +
808D ALA* 1.3 66.2 - - - +
809D LEU* 4.5 7.4 - - + +
810D GLU* 2.9 52.0 + - + +
811D LEU 3.0 11.3 + - - -
925D ARG* 4.0 10.3 - - - +
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Residues in contact with ALA 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709D LEU* 4.0 1.3 - - + +
712D ILE* 4.2 4.0 - - + -
713D PHE* 3.6 22.2 - - + -
785D ALA 2.8 25.2 + - - +
786D TYR* 4.0 2.2 - - - +
787D ILE* 3.5 33.2 - - + +
806D ILE 3.6 2.1 + - - -
807D PRO* 1.3 70.0 - - - +
809D LEU* 1.3 54.1 + - - +
811D LEU* 4.0 2.8 - - - +
812D MET* 2.5 40.0 + - - +
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Residues in contact with LEU 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713D PHE* 3.6 25.1 - - + -
785D ALA 4.6 0.4 + - - -
807D PRO* 3.2 6.2 - - + +
808D ALA* 1.3 78.7 - - - +
810D GLU* 1.3 58.0 + - + +
812D MET* 3.7 6.8 - - + +
813D ALA* 2.9 26.7 + - - +
874D LEU* 3.9 23.3 - - + -
878D GLU* 4.2 29.6 - - + +
881D ARG* 3.8 33.7 - - + +
882D PHE* 3.7 26.4 - - + +
885D LEU* 4.7 3.5 - - + +
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Residues in contact with GLU 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D ILE* 3.3 12.9 - - + +
807D PRO* 2.9 29.3 + - + +
809D LEU* 1.3 77.3 - - + +
811D LEU* 1.3 64.1 + - - +
813D ALA* 2.9 18.2 + - - +
814D LEU* 3.2 7.4 + - - +
881D ARG* 3.0 30.1 + - - +
885D LEU* 3.9 16.6 - - + -
922D GLU* 5.4 0.4 - - - -
925D ARG* 2.7 58.1 + - - +
926D LEU 6.0 0.2 - - - -
929D CYS* 5.1 9.0 - - - -
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Residues in contact with LEU 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D THR* 4.1 28.5 - - + -
754D THR* 5.4 0.2 - - + -
787D ILE* 5.2 11.0 - - + -
803D SER* 3.6 36.8 - - - +
806D ILE* 3.2 50.7 - - + +
807D PRO 3.0 8.4 + - - +
808D ALA* 4.0 4.7 - - - +
810D GLU* 1.3 75.7 - - - +
812D MET* 1.3 64.2 + - - +
814D LEU* 3.2 12.5 + - + +
815D TYR* 3.1 44.0 + - + +
929D CYS* 4.7 2.2 - - - -
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Residues in contact with MET 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704D PHE* 4.2 17.9 - - + -
709D LEU* 3.7 27.7 - - + +
713D PHE* 3.6 45.3 - - + -
715D ILE* 4.4 10.8 - - - -
808D ALA 2.5 24.2 + - - +
809D LEU* 3.7 10.1 - - + +
811D LEU* 1.3 73.8 - - - +
813D ALA* 1.3 61.8 + - - +
815D TYR* 3.9 2.7 - - - +
816D VAL* 2.9 26.5 + - + +
870D PHE* 6.0 0.9 - - - -
871D LEU* 4.3 15.0 - - + -
874D LEU* 5.1 0.4 - - + -
882D PHE* 3.7 25.1 - - + -
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Residues in contact with ALA 813 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809D LEU 2.9 13.8 + - - +
810D GLU 2.9 10.9 + - - +
812D MET* 1.3 76.3 - - - +
814D LEU* 1.3 64.6 + - - +
816D VAL* 2.8 15.2 + - - +
817D ALA* 2.9 15.3 + - - +
882D PHE* 3.4 18.4 - - + -
885D LEU* 3.6 35.2 - - + +
886D VAL* 3.9 8.7 - - + +
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Residues in contact with LEU 814 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749D VAL* 4.0 20.0 - - + -
753D THR* 3.8 28.5 - - + -
810D GLU 3.2 6.3 + - - +
811D LEU* 3.2 17.4 + - + +
813D ALA* 1.3 77.9 - - - +
815D TYR* 1.3 60.3 + - + +
817D ALA* 3.2 6.5 + - - +
818D ALA* 3.0 30.0 + - - +
889D ALA* 4.8 8.3 - - + -
929D CYS* 3.6 39.5 - - + +
932D CYS* 4.2 9.2 - - + -
933D ILE* 3.8 24.0 - - + +
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Residues in contact with TYR 815 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700D MET* 3.6 7.6 - - - +
703D LEU* 5.5 2.2 - - + -
704D PHE* 3.9 22.2 - + + -
707D THR* 4.4 9.8 - - + +
709D LEU* 3.9 24.9 - - + -
746D LEU* 4.1 15.4 - - + +
749D VAL* 3.9 14.6 - - + -
750D TRP* 3.8 32.3 - + - -
753D THR* 2.4 33.0 + - - -
754D THR* 3.5 13.0 - - - +
787D ILE* 5.9 2.3 - - + +
811D LEU* 3.1 31.9 + - + +
812D MET 3.9 3.1 - - - +
814D LEU* 1.3 84.4 - - + +
816D VAL* 1.3 63.2 + - - +
818D ALA* 3.7 3.8 + - - +
819D ALA* 3.2 21.7 + - - +
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Residues in contact with VAL 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700D MET* 5.1 1.8 - - - -
704D PHE* 4.2 12.8 - - + -
724D PHE* 4.7 16.4 - - + -
812D MET* 2.9 24.4 + - + +
813D ALA 2.8 7.2 + - - +
815D TYR* 1.3 78.9 - - - +
817D ALA* 1.3 52.9 + - - +
819D ALA* 3.3 8.9 + - - +
820D MET* 2.8 57.2 + - + +
859D TRP* 5.5 2.0 - - + -
870D PHE* 5.4 9.4 - - + -
882D PHE* 3.5 23.6 - - + -
886D VAL* 4.1 9.9 - - + -
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Residues in contact with ALA 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813D ALA 2.9 10.6 + - - +
814D LEU 3.2 7.6 + - - +
816D VAL* 1.3 72.7 - - - +
818D ALA* 1.3 55.3 + - - +
819D ALA 3.0 1.1 - - - -
820D MET* 2.6 30.1 + - - -
821D HIS* 2.6 22.7 + - - +
886D VAL* 3.9 9.4 - - - +
889D ALA* 3.5 31.2 - - + -
890D ILE* 3.9 14.8 - - + -
933D ILE* 4.2 4.0 - - + -
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Residues in contact with ALA 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D ALA* 4.1 10.0 - - - +
745D VAL* 4.2 9.9 - - + -
746D LEU* 3.8 30.1 - - - +
749D VAL* 4.1 11.0 - - + -
814D LEU 3.0 16.1 + - - +
815D TYR 3.8 4.3 - - - +
817D ALA* 1.3 75.8 - - - +
819D ALA* 1.3 63.5 + - - +
820D MET 3.0 1.7 + - - -
821D HIS* 3.1 25.0 + - - -
933D ILE* 3.9 14.8 - - + +
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Residues in contact with ALA 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696D LEU* 3.8 23.9 - - + +
700D MET* 3.5 28.9 - - + -
724D PHE* 4.2 12.6 - - + -
727D LEU* 3.1 16.9 - - - +
731D TYR* 3.6 9.7 + - - -
742D ALA* 4.8 0.2 - - - -
746D LEU* 4.9 1.1 - - + -
815D TYR 3.2 11.7 + - - +
816D VAL 3.4 10.8 - - - +
817D ALA 3.0 1.0 - - - -
818D ALA* 1.3 81.3 - - - +
820D MET* 1.3 57.3 + - - +
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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