Contacts of the strand formed by residues 802 - 809 (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 MET 802 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C PRO* 4.7 11.9 - - + +
782C LEU* 3.4 25.6 - - - +
783C PRO* 3.8 28.9 - - + -
784C ASP* 4.8 0.5 - - - +
800C TYR* 3.6 27.3 + - + +
801C PRO* 1.3 74.4 - - - +
803C VAL* 1.3 70.8 + - - +
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Residues in contact with VAL 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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780C GLU 4.4 0.7 - - - +
781C PRO* 3.5 3.2 - - - +
782C LEU* 2.8 44.1 + - + +
783C PRO 3.9 3.4 - - - +
784C ASP* 3.6 41.1 - - - +
785C LEU 5.2 0.2 - - - +
802C MET* 1.3 80.1 - - - +
804C GLN* 1.3 63.2 + - - +
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Residues in contact with GLN 804 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778C LEU* 3.5 32.1 - - + +
779C SER 2.9 29.9 + - - +
780C GLU* 4.4 2.4 - - - +
781C PRO* 3.7 31.1 - - + +
803C VAL* 1.3 76.8 - - - +
805C GLN* 1.3 60.7 - - - +
806C TRP* 4.0 1.2 + - - +
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Residues in contact with GLN 805 (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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777C VAL* 3.7 3.9 + - - +
778C LEU* 3.5 5.2 - - - +
779C SER* 2.8 53.7 + - - +
804C GLN* 1.3 73.3 - - - +
806C TRP* 1.3 69.0 + - - +
807C ARG* 4.0 27.1 - - - +
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Residues in contact with TRP 806 (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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776C GLY* 4.0 15.3 - - - -
777C VAL 3.6 17.3 - - - -
778C LEU* 3.8 36.3 - - + -
804C GLN 4.0 2.0 + - - +
805C GLN* 1.3 79.4 - - - +
807C ARG* 1.3 63.1 + - - +
808C VAL* 3.4 29.7 - - + +
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Residues in contact with ARG 807 (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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775C ARG* 4.0 6.6 - - - +
776C GLY* 3.3 1.4 - - - -
777C VAL* 2.9 62.0 + - + +
805C GLN* 4.0 23.1 - - - +
806C TRP* 1.3 77.2 - - - +
808C VAL* 1.3 67.4 + - - +
809C ARG* 3.4 58.7 - - + +
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Residues in contact with VAL 808 (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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774C CYS* 4.9 12.3 - - - -
775C ARG 3.6 14.6 - - - +
776C GLY* 3.9 4.3 - - - -
806C TRP* 3.4 43.5 - - + +
807C ARG* 1.3 79.4 - - - +
809C ARG* 1.3 71.7 + - - +
810C SER* 4.4 9.4 + - - +
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Residues in contact with ARG 809 (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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772C GLU 3.9 3.8 - - - +
774C CYS* 2.9 25.3 + - - -
775C ARG 3.3 12.7 + - - +
807C ARG* 3.4 53.7 - - + +
808C VAL* 1.3 76.1 - - - +
810C SER* 1.3 60.8 + - - +
812C LEU* 3.9 36.0 - - + +
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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