Contacts of the helix formed by residues 822 - 828 (chain A) in PDB entry 5C51
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 822 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ILE* 4.2 27.8 - - + +
285A GLN* 3.7 22.6 - - - +
821A LEU* 1.3 88.4 - - + +
823A ARG* 1.3 57.9 - - - +
824A ALA* 3.0 11.0 - - + +
825A VAL* 2.9 48.4 + - + +
826A ILE 3.6 2.3 + - - -
884A TYR* 4.2 12.8 - - - +
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Residues in contact with ARG 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818A ARG 5.8 2.2 - - - +
821A LEU* 4.0 9.9 - - + +
822A PRO* 1.3 67.3 - - - +
824A ALA* 1.3 55.9 + - - +
825A VAL 3.0 5.6 - - - -
826A ILE* 3.0 15.9 + - + +
827A ARG* 2.9 65.4 + - + +
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Residues in contact with ALA 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A PRO* 3.0 7.4 - - + -
823A ARG* 1.3 77.8 - - - +
825A VAL* 1.3 61.5 + - + +
827A ARG* 3.9 11.5 - - - +
828A HIS* 3.5 15.9 + - - +
883A GLY* 5.8 1.0 - - - -
1142A ARG* 5.0 15.9 - - - +
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Residues in contact with VAL 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 6.1 0.2 - - + -
821A LEU* 5.9 4.3 - - + -
822A PRO* 2.9 26.0 + - + +
824A ALA* 1.3 80.6 - - + +
826A ILE* 1.3 68.6 + - + +
827A ARG 3.2 0.2 - - - -
828A HIS* 3.1 21.9 + - - +
830A ASP 3.8 5.7 - - - +
837A TYR* 6.0 3.1 - - + -
881A PRO* 4.9 4.7 - - + -
882A PRO* 3.3 43.5 - - + +
883A GLY* 5.5 0.9 - - - -
884A TYR* 3.5 33.4 - - + -
1142A ARG* 5.7 0.7 - - - +
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Residues in contact with ILE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818A ARG* 5.0 6.7 - - + +
821A LEU* 3.7 37.2 - - + -
823A ARG* 3.0 18.1 + - + +
825A VAL* 1.3 82.2 - - + +
827A ARG* 1.3 77.0 + - - +
828A HIS 3.2 8.8 - - - +
830A ASP 4.6 6.0 - - - +
831A TYR* 4.5 27.8 - - + +
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Residues in contact with ARG 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A ARG* 2.9 62.6 + - - +
824A ALA* 3.9 10.5 - - - +
825A VAL 3.2 0.2 - - - -
826A ILE* 1.3 94.2 - - - +
828A HIS* 1.3 61.0 + - - +
829A PRO* 3.5 5.4 - - - +
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Residues in contact with HIS 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A ALA 3.5 10.9 + - - +
825A VAL* 3.1 20.3 + - - +
826A ILE 3.2 11.8 - - - +
827A ARG* 1.3 77.5 - - - +
829A PRO* 1.3 72.8 - - + +
830A ASP* 2.4 39.6 + - - +
882A PRO* 3.5 18.0 - - + +
883A GLY* 3.7 27.7 + - - -
1143A GLU* 3.5 23.1 + - - -
1187A ARG* 6.0 0.4 - - - -
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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