Contacts of the helix formed by residues 816 - 822 (chain C) in PDB entry 1P3A
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 THR 816 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814C ALA 4.8 3.8 - - - +
815C LYS* 1.3 76.7 - - - +
817C ARG* 1.3 59.2 + - - +
818C SER* 3.3 11.1 + - - -
819C SER* 2.9 42.9 + - - +
820C ARG* 3.1 11.8 + - - +
30I A 5.1 2.0 - - - +
31I G 3.7 18.2 - - - -
265J T 5.6 2.0 - - - +
266J T 5.0 16.8 - - - +
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Residues in contact with ARG 817 (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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815C LYS 5.4 0.2 - - - +
816C THR* 1.3 71.9 - - - +
818C SER* 1.3 60.6 + - - +
819C SER 3.2 0.2 - - - -
820C ARG* 3.3 17.9 + - - +
821C ALA* 2.9 30.5 + - - +
827C VAL* 3.8 28.0 - - + +
828C GLY* 3.8 12.3 + - - -
831C HIS* 3.0 48.4 + - - +
845C ALA* 4.3 7.9 + - - +
848C PRO* 4.2 3.8 - - - +
1318D TYR* 3.1 39.3 + - + -
31I G 2.8 33.9 + - - +
32I T 5.7 2.5 - - - +
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Residues in contact with SER 818 (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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816C THR* 3.2 9.5 + - - -
817C ARG* 1.3 79.7 + - - +
819C SER* 1.3 52.8 + - - +
821C ALA* 3.3 2.1 + - - -
822C GLY 2.9 7.8 + - - -
823C LEU* 2.7 41.5 + - - +
824C GLN 4.6 2.7 - - - -
825C PHE 3.0 17.1 + - - -
826C PRO* 3.4 5.5 - - - +
827C VAL* 2.9 34.7 + - - +
828C GLY 4.7 1.2 + - - -
31I G 5.5 0.2 + - - -
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Residues in contact with SER 819 (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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815C LYS* 3.2 32.9 + - - -
816C THR* 2.9 27.1 + - - -
818C SER* 1.3 73.8 - - - +
820C ARG* 1.3 70.2 + - - +
821C ALA 2.9 2.0 - - - -
822C GLY* 2.8 16.0 + - - +
823C LEU 4.5 3.1 + - - +
1317D LYS* 4.0 7.1 + - - -
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Residues in contact with ARG 820 (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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815C LYS* 3.6 36.7 + - + +
816C THR 3.1 17.4 + - - +
817C ARG* 3.3 20.5 + - - +
819C SER* 1.3 82.5 + - - +
821C ALA* 1.3 58.3 + - - +
1317D LYS* 3.3 21.8 - - - +
1318D TYR* 3.5 29.0 - - + -
1321D ALA* 3.3 38.5 + - + +
1322D LYS* 4.1 28.8 - - - +
32I T 2.7 44.5 + - - -
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Residues in contact with ALA 821 (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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817C ARG 2.9 15.2 + - - +
818C SER 3.8 0.7 - - - +
819C SER 2.9 0.6 - - - -
820C ARG* 1.3 79.0 - - - +
822C GLY* 1.3 61.6 + - - +
823C LEU* 3.6 27.5 - - + +
827C VAL* 4.7 0.7 - - + -
849C VAL* 4.0 12.8 - - + -
1314D ALA* 4.0 14.5 - - + +
1317D LYS* 3.6 14.6 - - - +
1318D TYR* 3.8 23.3 - - + +
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Residues in contact with GLY 822 (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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818C SER 2.9 0.4 + - - -
819C SER* 2.8 17.2 + - - -
821C ALA* 1.3 78.9 - - - +
823C LEU* 1.3 71.8 + - - +
824C GLN* 5.3 2.2 + - - -
856C GLU* 4.8 1.4 - - - +
1317D LYS* 3.9 15.0 - - - +
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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