Contacts of the helix formed by residues 835 - 847 (chain i) in PDB entry 5JPQ
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 835 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834i THR* 1.3 71.6 - - - +
836i PHE* 1.3 65.2 + - - +
838i HIS* 3.3 16.9 + - + +
839i LYS* 3.4 10.7 + - - +
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Residues in contact with PHE 836 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623i GLN* 4.8 20.7 - - + +
834i THR* 3.2 5.9 - - - -
835i PRO* 1.3 74.4 - - - +
837i ASP* 1.3 65.9 + - - +
839i LYS* 3.1 9.8 + - - +
840i ARG* 3.1 19.9 + - - +
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Residues in contact with ASP 837 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834i THR* 3.2 28.1 + - - +
836i PHE* 1.3 79.2 - - - +
838i HIS* 1.3 55.9 + - - +
840i ARG* 3.1 4.8 + - - +
841i LEU* 2.8 31.6 + - - +
860i THR* 4.1 25.2 - - - +
863i GLN* 5.7 4.3 - - + -
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Residues in contact with HIS 838 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834i THR 3.2 11.1 + - - +
835i PRO* 3.4 13.2 - - + +
836i PHE 3.2 0.2 - - - -
837i ASP* 1.3 75.8 - - - +
839i LYS* 1.3 59.4 + - - +
841i LEU* 3.6 6.3 - - - +
842i GLU* 2.9 28.8 + - - +
931i ILE* 5.2 3.7 - - + +
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Residues in contact with LYS 839 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623i GLN 5.6 6.1 - - - +
835i PRO 3.4 7.4 + - - +
836i PHE* 3.1 11.7 + - - +
838i HIS* 1.3 80.4 - - - +
840i ARG* 1.3 62.7 + - - +
842i GLU* 3.2 7.5 + - - +
843i SER* 3.0 21.4 + - - -
931i ILE* 5.8 2.7 - - - -
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Residues in contact with ARG 840 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623i GLN* 6.2 5.2 - - + -
836i PHE 3.1 12.9 + - - +
837i ASP* 3.5 9.4 - - - +
839i LYS* 1.3 74.9 - - - +
841i LEU* 1.3 64.0 + - - +
843i SER* 2.9 19.3 + - - -
844i TYR* 3.0 11.8 + - - +
849i LEU* 5.5 0.9 - - - +
854i VAL* 5.2 10.7 - - + +
860i THR* 4.3 14.1 - - - -
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Residues in contact with LEU 841 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837i ASP 2.8 16.9 + - - +
838i HIS* 3.6 8.7 - - - +
840i ARG* 1.3 78.0 - - - +
842i GLU* 1.3 62.2 + - - +
844i TYR* 3.1 7.5 + - - +
845i ALA* 2.9 23.7 + - - +
854i VAL* 5.8 2.0 - - - -
860i THR* 4.9 10.1 - - - +
916i MET* 5.0 5.2 - - + +
920i THR* 5.9 7.6 - - - -
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Residues in contact with GLU 842 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838i HIS 2.9 17.9 + - - +
839i LYS* 3.6 5.8 - - - +
841i LEU* 1.3 76.1 - - - +
843i SER* 1.3 56.8 + - - +
845i ALA* 4.3 6.7 - - - +
846i ASN* 2.6 41.3 + - + +
931i ILE* 3.8 33.7 - - + +
932i ALA 4.9 1.3 - - - +
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Residues in contact with SER 843 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839i LYS 3.0 11.7 + - - -
840i ARG* 2.9 16.0 + - - -
842i GLU* 1.3 78.9 - - - +
844i TYR* 1.4 55.7 + - - +
846i ASN* 5.0 1.3 - - - -
847i GLY* 2.9 32.4 + - - +
849i LEU* 3.7 18.3 + - - -
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Residues in contact with TYR 844 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840i ARG 3.0 10.7 + - - +
841i LEU* 3.1 6.7 + - - +
843i SER* 1.4 78.5 - - - +
845i ALA* 1.3 60.2 + - - +
847i GLY 2.8 18.9 - - - +
849i LEU* 4.1 23.7 - - + +
850i ASP 5.4 1.3 - - - +
851i TYR* 6.2 1.1 - - - -
854i VAL* 4.7 16.4 - - + -
913i MET* 3.9 13.9 - - - +
916i MET* 5.3 7.2 - - + -
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Residues in contact with ALA 845 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841i LEU 2.9 14.6 + - - +
842i GLU* 3.8 6.3 - - - +
844i TYR* 1.3 81.5 - - - +
846i ASN* 1.3 59.6 + - + +
847i GLY 4.5 0.5 - - - +
913i MET* 3.8 22.4 - - - +
916i MET* 4.1 7.1 - - + +
917i ARG* 3.7 38.3 - - + +
920i THR* 6.0 2.2 - - - -
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Residues in contact with ASN 846 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842i GLU* 2.6 23.1 + - + +
843i SER* 5.0 0.9 - - - -
845i ALA* 1.3 74.2 - - - +
847i GLY* 1.3 55.8 + - - +
931i ILE 5.5 0.4 - - - +
932i ALA* 4.4 30.1 - - + +
26r ILE* 4.7 3.1 - - - +
37r GLU* 4.0 24.4 - - + +
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Residues in contact with GLY 847 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843i SER* 2.9 20.1 + - - +
844i TYR 2.8 18.2 - - - +
845i ALA 4.5 0.3 - - - +
846i ASN* 1.3 81.1 - - - +
848i LEU* 1.3 58.7 + - - -
849i LEU 4.7 0.5 - - - +
913i MET* 5.4 1.9 - - - +
26r ILE* 4.3 11.2 - - - +
37r GLU* 5.4 4.5 - - - -
39r ASP* 5.8 5.2 - - - -
40r THR* 4.0 5.2 - - - -
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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