Contacts of the helix formed by residues 798 - 804 (chain C) in PDB entry 5C0V
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 798 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797C HIS* 1.3 101.1 - - + +
799C SER* 1.3 50.2 + - - +
801C GLU* 3.2 15.4 + - + +
802C LEU* 2.8 40.9 + - + +
812C VAL* 4.3 15.5 - - + -
816C TYR* 4.0 22.4 - - + -
819C ARG* 3.5 31.6 - - - +
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Residues in contact with SER 799 (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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942A ARG 5.2 3.5 + - - -
943A ARG* 6.1 0.3 - - - -
797C HIS* 2.6 26.3 + - - +
798C PRO* 1.3 75.7 - - - +
800C HIS* 1.3 66.2 + - - +
802C LEU* 4.7 0.4 - - - -
803C LEU* 3.2 31.4 + - - +
816C TYR* 3.5 28.6 - - - -
837C THR* 4.4 7.6 - - - +
840C ARG* 5.5 8.0 + - - -
841C PHE* 3.8 21.1 - - - -
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Residues in contact with HIS 800 (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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943A ARG* 3.0 41.3 + - - +
797C HIS* 3.0 18.2 + - + +
799C SER* 1.3 80.2 + - - +
801C GLU* 1.3 63.3 + - - +
803C LEU* 3.1 16.8 + - + +
804C LYS* 3.2 45.6 + - + +
840C ARG* 6.3 0.9 - - - +
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Residues in contact with GLU 801 (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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797C HIS 3.3 6.3 + - - +
798C PRO* 3.2 11.6 + - - +
800C HIS* 1.3 81.4 + - - +
802C LEU* 1.3 61.3 + - - +
803C LEU 3.4 0.7 + - - -
804C LYS* 3.4 23.0 + - + +
807C GLY* 3.5 21.6 - - - +
809C THR* 4.2 9.5 - - - +
812C VAL* 3.9 33.7 - - - +
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Residues in contact with LEU 802 (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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798C PRO* 2.8 26.9 + - + +
799C SER 4.3 0.4 - - - +
800C HIS 3.3 0.4 - - - -
801C GLU* 1.3 74.9 - - + +
803C LEU* 1.3 59.4 + - - +
804C LYS 4.0 0.9 - - - +
807C GLY 3.9 7.6 - - - +
808C PHE* 3.8 25.8 + - + +
809C THR* 3.7 39.0 - - + +
812C VAL* 4.0 21.1 - - + -
813C TYR* 3.8 21.3 - - + +
816C TYR* 3.8 27.8 - - + -
841C PHE* 3.5 21.8 - - + -
845C PHE* 4.1 9.7 - - - -
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Residues in contact with LEU 803 (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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799C SER* 3.2 19.0 + - - +
800C HIS* 3.1 9.2 + - + +
802C LEU* 1.3 76.7 - - - +
804C LYS* 1.3 68.2 + - - +
805C GLU* 3.4 2.1 + - - -
840C ARG* 4.3 20.0 - - - +
841C PHE* 3.6 28.3 - - + +
844C PHE* 3.9 22.2 - - + -
845C PHE* 3.6 34.5 - - + +
849C HIS* 5.1 8.5 + - - -
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Residues in contact with LYS 804 (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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800C HIS* 3.2 49.4 + - + +
801C GLU* 3.4 17.4 + - + +
802C LEU 4.0 2.3 - - - +
803C LEU* 1.3 80.2 - - - +
805C GLU* 1.3 64.4 + - - +
806C ASN 3.3 0.5 + - - -
807C GLY* 2.7 25.9 + - - -
808C PHE* 4.1 0.7 + - - +
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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