Contacts of the helix formed by residues 810 - 830 (chain A) in PDB entry 2Y48
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 810 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 5.6 0.2 - - - +
801A GLU* 3.8 1.8 - - - +
807A TYR 3.2 7.8 + - - +
808A PRO 3.0 15.7 + - - +
809A ALA* 1.3 84.0 - - - +
811A VAL* 1.3 62.3 + - - +
812A HIS* 3.1 27.1 + - + +
813A GLY 2.9 19.1 + - - -
814A ALA* 3.2 18.0 + - - +
900A FAD 3.2 32.9 + - - +
1C PRO* 4.5 9.0 - - + -
3C SER* 5.4 3.1 - - - +
4C PHE* 4.0 13.9 - - + -
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Residues in contact with VAL 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 4.4 18.1 - - + +
317A VAL* 3.5 31.6 - - + -
331A ALA* 3.8 17.9 - - + -
342A MET* 3.6 22.0 - - + -
571A TYR* 3.5 27.1 - - + +
574A VAL* 5.9 0.7 - - + -
810A THR* 1.3 67.0 - - - +
812A HIS* 1.3 69.2 + - - +
813A GLY 2.9 1.6 - - - -
814A ALA* 2.8 15.0 + - - +
815A LEU* 2.9 11.1 + - - +
900A FAD 2.8 25.7 + - - +
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Residues in contact with HIS 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 6.3 0.2 - - - -
335A THR* 3.7 19.7 + - + -
340A ASN* 3.3 26.4 + - - +
341A PRO* 3.7 10.0 - - + +
342A MET* 3.8 7.9 - - + +
560A PHE* 3.3 37.0 - + - -
807A TYR* 3.5 23.3 - + - +
810A THR* 3.1 29.6 + - + +
811A VAL* 1.3 83.1 - - - +
813A GLY* 1.3 70.5 + - - +
815A LEU* 3.5 7.2 - - - +
816A LEU* 2.9 34.6 + - + +
900A FAD 4.3 5.4 + - - -
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Residues in contact with GLY 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ILE* 3.2 23.2 - - - +
807A TYR* 3.3 37.7 - - - -
810A THR* 2.9 10.3 + - - -
811A VAL 2.9 1.2 - - - -
812A HIS* 1.3 77.2 - - - +
814A ALA* 1.3 63.6 + - - +
816A LEU* 3.3 2.1 + - - -
817A SER* 3.2 13.5 + - - -
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Residues in contact with ALA 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 4.7 2.5 - - + -
289A SER* 3.4 17.1 - - - +
801A GLU* 4.0 10.0 - - - +
810A THR 3.2 11.3 + - - +
811A VAL* 2.8 7.4 + - - +
813A GLY* 1.3 70.4 - - - +
815A LEU* 1.3 69.5 + - - +
817A SER* 2.7 27.6 + - - -
818A GLY 2.9 6.1 + - - -
900A FAD 3.6 37.5 - - - +
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Residues in contact with LEU 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 5.0 7.9 - - + -
288A VAL* 3.8 23.5 - - + +
292A ALA* 3.7 22.1 - - + +
341A PRO* 4.5 20.2 - - + -
342A MET* 4.8 11.0 - - - -
345A VAL* 4.9 14.8 - - + -
574A VAL* 6.2 0.9 - - + -
578A LEU* 4.5 12.6 - - + -
811A VAL* 2.9 16.7 + - + +
812A HIS* 3.5 8.3 - - - +
814A ALA* 1.3 76.7 - - - +
816A LEU* 1.3 67.9 + - - +
818A GLY* 3.2 2.1 + - - -
819A LEU* 3.1 43.3 + - + +
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Residues in contact with LEU 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.9 39.3 - - - +
341A PRO* 3.9 24.9 - - + -
804A ILE* 3.5 16.9 - - + +
807A TYR* 4.1 31.0 - - + -
812A HIS 2.9 25.6 + - - +
814A ALA 3.2 0.4 - - - -
815A LEU* 1.3 75.8 - - - +
817A SER* 1.3 56.9 + - - +
819A LEU* 3.2 21.4 + - + +
820A ARG* 2.9 26.2 + - - +
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Residues in contact with SER 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 3.7 0.2 - - - -
799A ALA* 3.5 2.0 - - - +
800A GLY* 2.7 30.6 + - - -
803A THR* 3.4 21.1 - - - -
804A ILE* 4.2 6.5 - - - -
813A GLY 3.2 10.9 + - - -
814A ALA 2.7 21.0 + - - -
816A LEU* 1.3 68.5 - - - +
818A GLY* 1.3 65.6 + - - +
820A ARG* 3.1 22.6 + - - +
821A GLU* 3.0 27.9 + - - +
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Residues in contact with GLY 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A SER 3.4 25.8 + - - -
293A ALA* 3.4 20.3 - - - +
799A ALA* 4.2 6.3 - - - -
814A ALA 2.9 9.5 + - - -
815A LEU 3.6 4.0 - - - -
817A SER* 1.3 80.0 + - - +
819A LEU* 1.3 61.8 + - - +
821A GLU* 3.2 0.5 + - - -
822A ALA* 3.0 20.3 + - - +
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Residues in contact with LEU 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 6.1 0.2 - - - +
258A ARG 4.9 2.4 - - - +
259A HIS* 4.5 14.7 - - - +
260A GLY* 3.3 29.6 - - - +
264A PHE* 4.1 17.7 - - + -
292A ALA* 4.3 11.6 - - + +
296A GLN* 3.7 30.1 + - + +
341A PRO* 6.0 0.2 - - + -
815A LEU* 3.1 35.9 + - + +
816A LEU* 3.4 20.6 - - + +
818A GLY* 1.3 73.3 - - - +
820A ARG* 1.3 66.8 + - - +
822A ALA* 3.3 5.8 + - - +
823A GLY* 3.1 18.0 + - - -
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Residues in contact with ARG 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A HIS* 5.5 7.3 - - - +
777A ALA* 3.6 13.5 - - - +
798A PHE 2.8 29.3 + - - -
799A ALA* 3.7 4.2 - - - +
803A THR* 3.3 35.4 + - - -
804A ILE* 4.3 10.5 - - + +
816A LEU 2.9 13.9 + - - +
817A SER* 3.1 25.7 + - - +
819A LEU* 1.3 77.1 - - - +
821A GLU* 1.3 83.3 + - - +
823A GLY* 3.2 2.4 + - - -
824A ARG* 3.0 32.0 + - + +
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Residues in contact with GLU 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A LEU* 3.8 21.3 - - + -
777A ALA 3.8 2.4 - - - +
779A PRO* 5.1 0.5 - - - +
797A PHE* 3.6 10.8 - - - +
798A PHE 3.1 47.8 + - - +
799A ALA* 3.8 2.9 - - + -
817A SER 3.0 12.8 + - - +
818A GLY 4.0 2.0 - - - +
820A ARG* 1.3 89.8 + - - +
822A ALA* 1.3 68.5 + - - +
824A ARG* 2.6 44.4 + - - +
825A ILE* 2.7 31.6 + - + +
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Residues in contact with ALA 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ALA* 3.8 13.9 - - - +
296A GLN* 3.3 35.9 - - + -
297A LEU* 3.8 18.6 - - + +
300A PHE* 4.1 4.3 - - + -
622A LEU* 5.2 0.6 - - - +
818A GLY 3.0 12.8 + - - +
819A LEU 3.5 7.6 - - - +
821A GLU* 1.3 74.8 - - - +
823A GLY* 1.3 64.5 + - - +
825A ILE* 3.3 1.2 + - - -
826A ALA* 2.9 24.4 + - - +
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Residues in contact with GLY 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.5 32.7 + - - -
259A HIS* 4.9 9.0 - - - -
819A LEU 3.1 10.6 + - - -
820A ARG 3.5 3.8 - - - -
822A ALA* 1.3 79.6 - - - +
824A ARG* 1.3 55.6 + - - +
826A ALA* 3.3 1.4 + - - +
827A ASP* 2.9 36.9 + - - +
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Residues in contact with ARG 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A HIS* 5.6 0.6 - - - -
777A ALA* 3.2 22.2 + - - +
778A GLN* 4.5 11.9 + - - +
779A PRO* 3.5 34.3 - - - +
797A PHE* 4.0 12.7 - - + -
820A ARG* 3.0 28.3 + - + +
821A GLU* 2.6 41.5 + - - +
823A GLY* 1.3 72.1 - - - +
825A ILE* 1.3 62.6 + - - +
827A ASP* 3.5 8.9 + - + +
828A GLN* 3.2 22.8 + - + +
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Residues in contact with ILE 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 4.3 19.3 - - + -
297A LEU* 3.9 21.3 - - + -
302A MET* 4.2 9.6 - - - -
620A ALA* 5.0 0.9 - - + -
622A LEU* 4.4 21.1 - - + -
797A PHE* 3.5 53.4 - - + -
821A GLU* 2.7 26.6 + - + +
822A ALA 3.8 2.2 - - - +
824A ARG* 1.3 69.5 - - - +
826A ALA* 1.3 65.9 + - - +
828A GLN* 2.9 17.8 + - - +
829A PHE* 3.0 26.4 + - + +
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Residues in contact with ALA 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.2 26.6 + - - +
297A LEU* 4.8 1.6 - - + -
300A PHE* 3.4 34.3 - - + -
302A MET* 4.7 3.6 - - - -
822A ALA 2.9 14.6 + - - +
825A ILE* 1.3 75.0 - - - +
827A ASP* 1.3 63.1 + - - +
830A LEU* 2.9 36.2 + - + +
831A GLY 3.4 1.4 + - - -
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Residues in contact with ASP 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A CYS* 5.9 0.3 - - - -
258A ARG* 2.7 35.7 + - - +
259A HIS* 4.1 9.5 + - - -
823A GLY 2.9 19.3 + - - +
824A ARG* 3.8 8.6 - - + +
825A ILE 3.2 0.2 - - - -
826A ALA* 1.3 75.4 - - - +
828A GLN* 1.3 62.1 + - - +
831A GLY* 3.3 21.7 - - - -
832A ALA* 4.0 12.7 + - + +
834A TYR* 2.7 32.1 + - - -
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Residues in contact with GLN 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A ILE* 3.3 24.3 - - + +
794A PRO* 2.6 37.6 + - + +
797A PHE* 4.6 6.0 - - + -
824A ARG* 3.2 11.6 + - - +
825A ILE* 2.9 11.2 + - - +
827A ASP* 1.3 82.1 - - - +
829A PHE* 1.3 86.4 + - + +
831A GLY* 4.4 2.3 + - - -
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Residues in contact with PHE 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A THR* 5.2 4.2 - - - +
279A GLY* 5.7 3.4 - - - -
302A MET* 4.1 21.8 - - + -
619A ASP* 3.8 29.2 - - + -
620A ALA* 3.9 18.6 - - + -
793A ILE* 3.8 16.6 - - + -
794A PRO 3.8 17.3 - - - -
795A ARG* 3.8 18.8 - - - -
797A PHE* 4.2 6.1 - + - -
825A ILE* 3.0 25.2 + - + +
828A GLN* 1.3 98.9 - - + +
830A LEU* 1.3 68.3 + - + +
831A GLY 3.4 1.3 - - - -
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Residues in contact with LEU 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 4.6 9.4 + - - +
278A THR* 3.7 47.1 - - + +
300A PHE* 3.3 41.7 - - + +
301A GLY 4.9 0.2 - - - +
302A MET* 3.9 18.8 - - + -
826A ALA* 2.9 19.0 + - + +
829A PHE* 1.3 79.6 - - + +
831A GLY* 1.3 67.2 + - - +
833A MET* 4.0 16.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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