Contacts of the helix formed by residues 774 - 786 (chain J) in PDB entry 5IJO
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 GLY 774 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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772J GLU* 3.9 3.6 + - - +
773J ALA* 1.3 71.4 - - - +
775J GLN* 1.3 53.3 + - - +
776J THR 3.2 0.9 - - - -
777J VAL* 2.7 34.0 + - - +
778J ILE* 2.8 13.4 + - - +
840J ALA* 5.6 10.5 - - - -
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Residues in contact with GLN 775 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719J HIS* 4.9 16.4 - - + -
773J ALA* 3.2 8.3 - - + -
774J GLY* 1.3 76.5 - - - +
776J THR* 1.3 63.4 + - - +
778J ILE* 3.8 9.1 - - - +
779J ASN* 2.7 25.5 + - - +
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Residues in contact with THR 776 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715J LEU* 4.0 28.3 - - - -
716J PRO* 5.4 2.7 - - - -
718J TYR* 5.0 6.7 - - - -
719J HIS* 5.6 6.8 - - - +
773J ALA* 4.2 8.6 + - - +
774J GLY 3.0 1.0 + - - -
775J GLN* 1.3 79.5 - - - +
777J VAL* 1.3 63.6 + - - +
779J ASN* 3.2 12.2 + - - +
780J ILE* 3.4 11.3 + - - +
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Residues in contact with VAL 777 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773J ALA 5.0 0.2 + - - -
774J GLY* 2.7 18.7 + - - +
776J THR* 1.3 74.8 - - - +
778J ILE* 1.3 62.0 + - - +
780J ILE* 3.2 8.9 + - - +
781J MET* 3.2 18.8 + - - +
817J ALA* 5.4 8.9 - - + +
821J THR* 5.9 7.2 - - - -
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Residues in contact with ILE 778 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774J GLY 2.8 12.8 + - - +
775J GLN* 3.8 11.0 - - - +
777J VAL* 1.3 73.0 - - - +
779J ASN* 1.3 60.2 + - - +
781J MET* 2.9 10.6 + - + +
782J GLY* 2.8 27.9 + - - -
844J HIS* 6.1 4.5 - - + -
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Residues in contact with ASN 779 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775J GLN 2.7 17.4 + - - +
776J THR* 3.4 9.2 - - - +
778J ILE* 1.3 77.0 - - - +
780J ILE* 1.3 62.7 + - - +
782J GLY* 3.2 1.5 + - - -
783J ILE* 2.9 24.4 + - - +
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Residues in contact with ILE 780 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776J THR 3.4 6.4 + - - +
777J VAL* 3.2 10.1 + - - +
778J ILE 3.2 0.4 - - - -
779J ASN* 1.3 78.6 - - - +
781J MET* 1.3 65.1 + - - +
783J ILE* 3.1 6.2 + - - +
784J GLY* 3.0 22.3 + - - -
813J THR* 4.9 13.5 - - - +
814J VAL* 5.1 9.7 - - - +
817J ALA* 4.3 21.5 - - + -
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Residues in contact with MET 781 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777J VAL 3.2 9.6 + - - +
778J ILE* 2.9 14.1 + - + +
780J ILE* 1.3 78.5 - - - +
782J GLY* 1.3 60.7 + - - +
784J GLY* 3.5 1.0 + - - -
785J VAL* 3.2 20.6 + - - +
814J VAL* 6.3 1.3 - - - -
844J HIS* 6.1 4.9 - - + -
850J ASN* 5.3 14.7 - - + +
851J LEU* 6.5 1.1 - - - -
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Residues in contact with GLY 782 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778J ILE 2.8 13.0 + - - -
779J ASN* 3.7 2.7 - - - -
781J MET* 1.3 74.8 - - - +
783J ILE* 1.3 64.4 + - - +
785J VAL* 3.1 17.8 + - - +
786J ASP* 3.1 14.0 + - - +
850J ASN* 6.3 1.6 - - - -
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Residues in contact with ILE 783 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779J ASN 2.9 16.0 + - - +
780J ILE* 3.1 6.9 + - - +
782J GLY* 1.3 75.5 - - - +
784J GLY* 1.3 63.5 + - - +
786J ASP* 2.9 26.5 + - - +
787J THR* 3.5 2.8 + - - -
810J LEU* 6.2 0.9 - - - -
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Residues in contact with GLY 784 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780J ILE 3.0 15.0 + - - -
781J MET 4.0 1.3 - - - -
783J ILE* 1.3 74.2 - - - +
785J VAL* 1.3 68.6 + - - +
786J ASP 3.3 0.3 + - - -
787J THR* 3.6 13.8 + - - -
810J LEU* 5.4 11.0 - - - -
814J VAL* 5.2 11.9 - - - -
857J LYS* 5.1 7.6 - - - +
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Residues in contact with VAL 785 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781J MET 3.2 13.2 + - - +
782J GLY* 3.1 14.4 + - - +
784J GLY* 1.3 79.4 - - - +
786J ASP* 1.4 57.1 + - + +
787J THR 3.4 3.8 + - - +
850J ASN* 5.9 8.5 - - + +
853J ALA* 6.1 5.2 - - + -
854J VAL* 6.0 6.3 - - - +
857J LYS* 5.2 10.1 - - - +
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Residues in contact with ASP 786 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782J GLY 3.1 8.8 + - - +
783J ILE* 2.9 13.5 + - - +
785J VAL* 1.4 78.1 - - + +
787J THR* 1.3 63.5 + - - +
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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