Contacts of the helix formed by residues 838 - 850 (chain C) in PDB entry 5J67
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 SER 838 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836C GLU* 3.0 15.4 + - - -
837C SER* 1.3 74.3 - - - +
839C ARG* 1.3 59.2 + - - +
840C GLU* 4.0 4.3 + - - +
841C GLU* 3.5 37.3 + - - +
842C LEU* 3.2 35.8 + - - +
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Residues in contact with ARG 839 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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838C SER* 1.3 71.0 + - - +
840C GLU* 1.3 74.2 + - + +
841C GLU 3.1 1.5 + - - -
842C LEU* 3.2 11.2 + - - +
843C LEU* 3.1 45.3 + - + +
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Residues in contact with GLU 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838C SER* 4.0 4.4 + - - +
839C ARG* 1.3 84.8 - - + +
841C GLU* 1.3 60.1 + - - +
843C LEU* 3.7 15.6 + - - +
844C SER* 3.4 23.9 + - - -
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Residues in contact with GLU 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832C ILE* 4.9 1.0 - - - +
833C LEU* 3.2 38.1 - - + +
836C GLU* 3.2 39.0 - - - +
838C SER* 3.5 21.8 + - - +
839C ARG 3.1 0.4 - - - -
840C GLU* 1.3 76.3 - - - +
842C LEU* 1.3 65.2 + - + +
843C LEU 3.2 0.2 - - - -
844C SER* 3.3 9.8 + - - -
845C PHE* 3.2 19.6 + - - +
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Residues in contact with LEU 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833C LEU* 4.5 22.2 - - + +
836C GLU 5.3 3.1 - - - +
837C SER* 5.5 3.6 - - - -
838C SER 3.2 29.2 + - - +
839C ARG* 3.2 13.5 + - - +
841C GLU* 1.3 78.4 - - + +
843C LEU* 1.3 60.5 + - + +
845C PHE* 3.5 12.7 - - + +
846C ILE* 3.4 29.5 + - + +
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Residues in contact with LEU 843 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839C ARG* 3.1 41.1 + - + +
840C GLU* 3.9 18.4 - - - +
841C GLU 3.2 0.2 - - - -
842C LEU* 1.3 73.6 - - + +
844C SER* 1.3 61.2 + - - +
845C PHE 3.2 1.3 - - - -
846C ILE* 3.1 18.0 + - + +
847C GLN* 2.9 38.0 + - - +
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Residues in contact with SER 844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840C GLU 3.4 12.6 + - - -
841C GLU* 3.3 12.4 + - - -
843C LEU* 1.3 75.3 - - - +
845C PHE* 1.3 63.3 + - - +
847C GLN* 3.7 17.4 + - - +
848C HIS* 3.4 21.5 + - - +
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Residues in contact with PHE 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C PHE* 3.7 31.0 - + - -
829C VAL* 3.9 20.2 - - + -
830C LEU* 4.4 19.1 - - + -
833C LEU* 3.8 32.1 - - + -
841C GLU 3.2 5.4 + - - +
842C LEU* 3.5 15.5 - - + +
843C LEU 3.2 0.2 - - - -
844C SER* 1.3 74.6 - - - +
846C ILE* 1.3 65.7 + - + +
848C HIS* 3.2 2.9 + - - -
849C TYR* 2.7 66.0 + + + +
850C GLY 4.9 4.5 - - - -
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Residues in contact with ILE 846 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731C ASN* 4.6 13.1 + - - +
842C LEU* 3.4 19.7 + - + +
843C LEU* 3.1 21.1 + - + +
845C PHE* 1.3 80.8 - - + +
847C GLN* 1.3 61.2 + - - +
850C GLY* 2.7 53.9 + - - +
851C SER* 4.6 10.1 - - - +
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Residues in contact with GLN 847 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731C ASN* 5.6 3.0 + - - +
739C GLN* 3.0 22.0 - - - +
843C LEU* 2.9 22.6 + - + +
844C SER* 3.7 20.0 + - - +
845C PHE 3.3 0.2 - - - -
846C ILE* 1.3 76.8 - - - +
848C HIS* 1.3 57.0 + - + +
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Residues in contact with HIS 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739C GLN* 3.2 24.8 - - - +
740C GLY* 3.2 22.2 + - - -
844C SER 3.4 13.4 + - - +
845C PHE* 3.2 4.1 + - - +
847C GLN* 1.3 83.2 - - - +
849C TYR* 1.3 91.6 + + + +
850C GLY 3.5 0.2 - - - -
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Residues in contact with TYR 849 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729C GLY* 4.3 10.9 - - - -
730C TYR 4.4 0.2 + - - -
739C GLN* 3.3 18.1 - - - +
740C GLY* 4.1 2.2 - - - -
741C GLN 3.8 33.4 - - - -
742C VAL* 4.6 6.4 - - + +
825C GLY* 3.4 23.2 + - - -
826C PHE* 3.6 27.8 - + + -
829C VAL* 3.6 28.4 - - + +
845C PHE* 2.7 54.6 + + + +
848C HIS* 1.3 97.4 + + + +
850C GLY* 1.3 59.8 + - - +
851C SER 5.5 0.3 - - - -
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Residues in contact with GLY 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730C TYR 4.1 8.5 - - - -
731C ASN* 4.3 9.4 - - - -
739C GLN* 3.9 12.8 - - - +
845C PHE* 4.9 4.5 - - - -
846C ILE* 2.7 45.0 + - - +
848C HIS 3.5 1.6 + - - -
849C TYR* 1.3 79.4 - - - +
851C SER* 1.3 59.8 + - - -
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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