Contacts of the helix formed by residues 770 - 787 (chain B) in PDB entry 1JQI
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 770 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLN* 3.9 6.1 - - - +
344A GLY* 5.3 1.8 - - - -
537B SER* 4.4 1.5 + - - +
765B GLU 3.5 8.1 - - - -
766B ILE* 3.3 24.5 + - + +
769B GLY* 1.3 76.7 - - - +
771B SER* 1.3 65.3 + - - +
772B GLU* 3.5 6.0 + - - -
773B ILE* 3.0 21.9 + - - +
774B GLN* 3.0 19.6 + - - +
799B FAD 2.6 62.0 + - - +
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Residues in contact with SER 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLN* 3.8 4.3 + - - +
725B LYS* 4.8 1.0 + - - +
726B LEU* 3.6 26.4 - - - +
729B SER* 4.3 2.9 + - - -
730B GLU* 3.9 8.0 + - - +
765B GLU* 3.3 32.0 + - - +
770B THR* 1.3 74.2 - - - +
772B GLU* 1.3 67.1 + - - +
774B GLN* 3.3 7.0 + - - +
775B ARG* 3.0 44.7 + - - +
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Residues in contact with GLU 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.4 31.4 - - - +
289A LYS* 3.0 26.8 + - - -
341A GLN* 3.0 31.1 + - - +
770B THR* 3.5 1.0 + - - -
771B SER* 1.3 82.9 - - - +
773B ILE* 1.3 64.4 + - - +
775B ARG* 3.3 15.3 + - - +
776B LEU* 3.1 25.8 + - - +
799B FAD 3.0 45.9 + - + +
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Residues in contact with ILE 773 (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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537B SER* 3.8 25.1 - - - +
648B ARG* 4.1 13.5 - - - +
769B GLY* 4.3 3.6 - - - -
770B THR* 3.0 26.3 + - - +
772B GLU* 1.3 76.8 - - - +
774B GLN* 1.3 67.3 + - - +
776B LEU* 3.0 11.2 + - + +
777B VAL* 2.9 28.7 + - + +
799B FAD 3.9 27.1 - - + +
800B CAA 3.7 50.9 - - + +
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Residues in contact with GLN 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ARG* 3.5 21.6 + - - +
722B ALA* 3.4 38.9 - - - +
725B LYS* 3.9 21.7 - - + +
726B LEU* 4.1 13.0 - - + -
768B GLU 3.3 14.5 + - - -
769B GLY* 2.7 32.5 + - - +
770B THR 3.0 16.7 + - - +
771B SER* 3.3 9.8 + - - +
773B ILE* 1.3 75.1 - - - +
775B ARG* 1.3 59.2 + - - +
777B VAL* 3.2 4.6 + - - +
778B ILE* 2.9 34.7 + - - +
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Residues in contact with ARG 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 6.4 0.4 - - - +
726B LEU* 3.6 29.5 - - + +
730B GLU* 3.1 39.4 + - - -
771B SER* 3.0 25.9 + - - +
772B GLU* 3.6 16.9 + - - +
773B ILE 3.2 0.2 - - - -
774B GLN* 1.3 78.0 - - - +
776B LEU* 1.3 56.0 + - - +
778B ILE* 3.4 8.4 + - + +
779B ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 776 (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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772B GLU 3.1 15.2 + - - +
773B ILE* 3.0 16.7 + - + +
775B ARG* 1.3 75.5 - - + +
777B VAL* 1.3 59.6 + - + +
779B ALA* 3.3 7.3 + - + +
780B GLY* 2.9 27.4 + - - -
799B FAD 3.5 39.7 - - + +
800B CAA 5.4 12.1 - - + -
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Residues in contact with VAL 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ARG* 4.3 17.3 - - - +
718B THR* 3.7 31.6 - - + +
719B LYS* 5.0 0.6 - - - +
722B ALA* 4.1 17.7 - - + -
773B ILE* 2.9 19.1 + - + +
774B GLN* 3.6 7.4 - - - +
776B LEU* 1.3 75.6 - - - +
778B ILE* 1.3 63.3 + - - +
780B GLY* 3.4 1.7 + - - -
781B HIS* 3.0 37.3 + - + +
800B CAA 3.7 27.6 - - + +
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Residues in contact with ILE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B LYS* 4.3 12.2 - - + +
722B ALA* 3.7 15.9 - - + -
723B MET* 3.7 57.2 - - + +
726B LEU* 3.9 23.6 - - + -
774B GLN 2.9 22.6 + - - +
775B ARG* 3.6 6.5 - - - +
777B VAL* 1.3 74.4 - - - +
779B ALA* 1.3 60.8 + - - +
781B HIS* 3.4 2.4 + - - +
782B LEU* 2.9 33.8 + - + +
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Residues in contact with ALA 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B ARG 2.9 17.5 + - - +
776B LEU* 3.7 8.7 - - + +
778B ILE* 1.3 78.5 - - - +
780B GLY* 1.3 63.4 + - - +
782B LEU* 3.7 8.4 - - - +
783B LEU* 3.0 37.5 + - + +
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Residues in contact with GLY 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU 2.9 16.5 + - - -
777B VAL* 3.9 2.2 - - - -
778B ILE 3.2 0.2 - - - -
779B ALA* 1.3 79.1 - - - +
781B HIS* 1.3 62.6 + - - +
783B LEU* 3.7 6.2 + - - +
784B ARG* 3.2 28.8 + - - +
787B ARG* 5.0 2.4 + - - -
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Residues in contact with HIS 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B THR* 3.5 36.6 + - + -
719B LYS* 3.8 30.5 - - + -
777B VAL* 3.0 30.8 + - + +
780B GLY* 1.3 75.4 - - - +
782B LEU* 1.3 66.4 + - - +
784B ARG* 3.2 37.8 + - - +
785B SER* 3.1 25.0 + - - -
800B CAA 5.6 6.4 + + - -
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Residues in contact with LEU 782 (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 LYS* 4.3 17.8 - - + +
723B MET* 6.1 1.6 - - + -
778B ILE* 2.9 24.6 + - + +
779B ALA* 3.7 9.0 - - - +
781B HIS* 1.3 76.7 - - - +
783B LEU* 1.3 68.4 + - + +
785B SER* 2.9 25.1 + - - -
786B TYR* 3.4 33.5 - - + +
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Residues in contact with LEU 783 (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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779B ALA* 3.0 23.5 + - + +
780B GLY* 4.0 4.7 - - - +
782B LEU* 1.3 84.9 - - + +
784B ARG* 1.3 61.7 + - - +
786B TYR* 3.1 21.8 + - + +
787B ARG* 3.2 50.0 + - + +
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Residues in contact with ARG 784 (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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780B GLY* 3.2 17.9 + - - +
781B HIS* 3.4 43.4 + - - +
782B LEU 3.2 0.6 - - - -
783B LEU* 1.3 79.0 - - - +
785B SER* 1.3 60.1 + - - +
786B TYR 3.6 0.3 + - - -
787B ARG* 3.7 25.4 + - - +
800B CAA 5.5 5.9 + - - -
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Residues in contact with SER 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B LYS* 5.6 5.0 + - - +
781B HIS 3.1 12.3 + - - -
782B LEU* 2.9 17.3 + - - -
784B ARG* 1.3 77.5 - - - +
786B TYR* 1.3 64.7 + - - +
787B ARG 3.5 1.1 - - - -
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Residues in contact with TYR 786 (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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782B LEU* 3.4 47.6 + - + +
783B LEU* 3.1 15.3 + - + +
785B SER* 1.3 83.6 - - - +
787B ARG* 1.3 64.9 + - + +
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Residues in contact with ARG 787 (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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780B GLY 5.0 2.4 + - - -
783B LEU* 3.2 52.1 + - + +
784B ARG* 3.7 18.5 + - - +
785B SER 3.5 2.1 - - - -
786B TYR* 1.3 84.7 - - + +
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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