Contacts of the helix formed by residues 809 - 820 (chain A) in PDB entry 3GTQ
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 809 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802A ASN* 4.6 2.0 - - - +
808A LEU* 1.3 73.2 - - - +
810A PRO* 1.3 66.8 - - + +
811A GLN* 3.5 4.4 + - - -
812A GLU* 2.6 39.7 + - - +
813A PHE* 2.3 38.8 + - - +
728B ARG* 3.6 26.7 - - + +
729B ILE 4.7 1.2 + - - -
730B ARG* 3.2 44.5 - - + +
1047B PHE* 3.6 7.6 - - + -
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Residues in contact with PRO 810 (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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809A THR* 1.3 91.7 - - + -
811A GLN* 1.3 78.8 + - - +
813A PHE* 3.0 3.1 + - - +
814A PHE* 2.9 20.8 + - - +
519B TRP* 3.9 10.6 - - + -
705B MET* 3.7 33.7 - - + -
706B GLN* 6.5 0.4 - - - -
730B ARG* 4.6 8.7 - - - +
745B PRO* 4.0 18.8 - - + -
1047B PHE* 3.4 35.6 - - + -
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Residues in contact with GLN 811 (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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784A LEU* 4.3 13.9 - - + -
786A HIS* 5.2 4.6 - - + +
787A PHE* 3.8 35.0 - - + -
795A GLU 5.2 1.8 - - - +
809A THR* 4.3 4.9 + - - -
810A PRO* 1.3 94.4 - - - +
812A GLU* 1.3 69.9 + - + +
814A PHE* 2.9 10.9 + - - +
815A PHE* 2.9 34.3 + - + -
705B MET* 3.6 28.9 - - + +
730B ARG* 5.0 6.5 - - - +
731B VAL* 4.0 21.2 - - - +
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Residues in contact with GLU 812 (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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799A PHE 4.4 5.0 - - - +
800A VAL* 3.6 30.8 - - + +
801A GLU* 3.1 30.5 + - - +
802A ASN* 3.3 25.6 + - - -
808A LEU* 3.4 5.0 - - + -
809A THR* 2.6 47.2 + - - +
811A GLN* 1.3 80.3 - - + +
813A PHE* 1.3 54.8 + - - +
815A PHE* 2.8 31.2 + - + +
816A HIS* 2.9 15.6 + - - +
729B ILE 4.3 3.6 - - - +
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Residues in contact with PHE 813 (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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808A LEU* 4.2 20.5 - - + +
809A THR 2.3 28.8 + - - +
810A PRO 3.4 4.7 - - - +
812A GLU* 1.3 67.3 - - - +
814A PHE* 1.3 58.4 + - - +
816A HIS* 3.5 1.6 + + - -
817A ALA* 2.7 32.2 + - + +
524B PRO* 5.2 4.9 - - + -
525B ALA* 5.4 3.1 - - + -
748B ILE* 4.5 11.0 - - + -
749B LEU* 4.1 29.2 - - + -
759B PRO* 4.1 20.9 - - + -
760B ASP* 4.8 6.3 - - - -
762B ASN 5.0 3.8 - - - -
764B SER* 4.5 17.9 - - - -
767B ASN* 3.3 31.6 - - + -
1047B PHE* 3.8 29.4 - + + -
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Residues in contact with PHE 814 (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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784A LEU* 3.9 20.6 - - + -
810A PRO 2.9 4.4 + - - -
811A GLN 2.9 11.7 + - - +
813A PHE* 1.3 75.4 - - - +
815A PHE* 1.3 59.6 + + + +
817A ALA* 3.0 6.9 - - - +
818A MET* 2.8 56.0 + - + +
514B LEU* 3.7 26.9 - - + -
515B HIS 3.8 9.0 - - - -
516B ASN* 4.1 17.7 - - - -
518B HIS 4.3 1.6 - - - -
519B TRP* 3.4 61.5 - + + -
520B GLY 5.0 1.1 - - - -
522B VAL 5.3 0.2 - - - -
524B PRO* 4.2 20.0 - - + -
748B ILE* 5.2 3.8 - - + +
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Residues in contact with PHE 815 (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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768A GLN* 3.5 7.5 - - + +
775A ILE* 4.0 27.4 - - + +
783A THR* 3.8 25.6 - - + -
784A LEU* 3.8 35.0 - - + -
787A PHE* 3.9 13.5 - + - -
795A GLU 4.0 17.0 - - - -
796A SER 4.2 1.1 - - - -
798A GLY* 3.7 26.5 - - - +
799A PHE 6.0 0.9 - - - -
800A VAL* 5.2 2.5 - - + -
811A GLN* 2.9 35.9 + - + -
812A GLU* 2.8 12.2 + - + +
814A PHE* 1.3 77.4 - + - +
816A HIS* 1.3 53.5 + - - +
818A MET* 2.7 38.4 + - - +
819A GLY 3.1 4.7 + - - -
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Residues in contact with HIS 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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760A GLN* 6.3 0.2 - - - -
765A VAL* 5.7 3.5 - - + +
768A GLN* 3.4 35.5 + - - +
800A VAL* 4.5 5.3 - - + +
804A TYR* 3.1 24.4 + - - -
808A LEU* 3.7 28.7 - - + -
812A GLU 2.9 13.7 + - - +
813A PHE* 4.1 4.9 - + - +
815A PHE* 1.3 74.9 - - - +
817A ALA* 1.3 57.2 + - - +
820A GLY* 2.8 33.2 + - - -
762B ASN 3.9 6.3 - - - -
763B GLN* 3.4 7.7 - - + -
764B SER* 2.7 41.9 + - - -
765B PRO* 4.7 2.7 - - + -
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Residues in contact with ALA 817 (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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813A PHE* 2.7 26.9 + - + +
814A PHE* 3.0 13.5 - - - +
816A HIS* 1.3 77.3 - - - +
818A MET* 1.3 54.5 + - - +
820A GLY 2.5 19.9 - - - +
821A ARG* 3.8 4.9 - - - +
514B LEU* 3.6 9.1 - - + +
524B PRO* 3.9 28.4 - - + +
764B SER* 3.4 18.7 + - - +
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Residues in contact with MET 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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770A VAL* 4.0 26.1 - - + +
775A ILE* 3.7 29.6 - - + -
776A ALA* 5.2 3.4 - - + +
814A PHE* 2.8 35.4 + - + +
815A PHE* 2.7 22.0 + - - +
817A ALA* 1.3 71.1 - - - +
819A GLY* 1.3 60.6 + - - +
820A GLY 3.0 9.2 - - - +
821A ARG* 3.7 9.4 - - - +
822A GLU* 3.9 5.2 + - - +
513B GLN* 5.0 5.2 + - - +
514B LEU* 3.6 38.8 + - + +
515B HIS* 5.1 0.2 - - - -
516B ASN* 3.6 26.9 - - - +
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Residues in contact with GLY 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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768A GLN* 4.0 15.4 - - - +
769A SER 3.6 23.1 - - - -
770A VAL* 4.6 0.8 - - - +
815A PHE 3.1 6.9 + - - -
816A HIS 3.4 1.3 + - - -
818A MET* 1.3 74.6 - - - +
820A GLY* 1.3 55.6 + - - +
821A ARG 3.0 0.2 + - - -
822A GLU* 2.7 37.0 + - - +
823A GLY 3.8 2.3 + - - -
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Residues in contact with GLY 820 (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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768A GLN* 4.9 2.0 - - - +
816A HIS* 2.8 24.2 + - - -
817A ALA 2.5 21.4 - - - +
818A MET 3.0 0.3 - - - +
819A GLY* 1.3 69.2 - - - -
821A ARG* 1.3 69.9 + - - +
823A GLY 5.2 0.7 - - - -
824A LEU* 5.5 0.2 - - - -
764B SER* 4.2 5.8 + - - -
765B PRO* 4.1 24.2 - - - -
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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