Contacts of the helix formed by residues 795 - 802 (chain B) in PDB entry 3P8C
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 795 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731B GLN* 3.2 38.9 + - + +
791B TRP* 2.9 48.5 + - + +
794B GLU* 1.3 81.9 - - - +
796B LEU* 1.3 64.7 + - - +
797B LEU 3.7 0.2 - - - -
798B ARG* 3.7 1.7 + - - +
799B GLN* 3.1 30.9 + - + +
825B PHE* 3.4 27.6 - - + -
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Residues in contact with LEU 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791B TRP* 3.2 36.4 + - + -
792B TYR* 3.5 24.5 - - + +
795B THR* 1.3 77.1 - - - +
797B LEU* 1.3 75.3 + - + +
799B GLN* 3.1 14.9 + - - +
800B VAL* 3.2 27.4 + - + +
805B ILE* 3.7 6.6 - - + +
814B PHE* 4.2 22.4 - - + -
825B PHE* 4.0 19.1 - - + -
827B ALA* 4.2 13.9 - - + +
830B TYR* 4.1 10.3 - - + -
831B SER* 4.4 6.1 - - - -
916B PHE* 5.0 4.7 - - + -
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Residues in contact with LEU 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792B TYR 2.8 24.7 + - - +
793B LEU* 4.0 17.9 - - + +
796B LEU* 1.3 80.4 - - + +
798B ARG* 1.3 61.4 + - - +
800B VAL* 3.4 7.3 + - - +
801B SER* 3.3 22.5 + - - -
814B PHE* 4.2 11.4 - - + -
855B LEU* 3.6 31.0 - - + -
912B VAL* 4.0 26.9 - - + +
913B ILE* 4.6 13.5 - - + -
916B PHE* 3.9 31.9 - - + -
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Residues in contact with ARG 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B GLN* 3.1 35.0 + - - +
793B LEU 3.3 12.0 + - - +
794B GLU* 2.7 38.7 + - - +
795B THR* 4.0 1.1 - - - +
796B LEU 3.2 0.6 - - - -
797B LEU* 1.3 76.5 - - - +
799B GLN* 1.3 79.2 + - - +
801B SER* 3.4 8.1 + - - -
802B ASN* 3.1 53.2 + - - +
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Residues in contact with GLN 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B GLN* 4.6 4.6 + - - +
795B THR* 3.1 18.1 + - + +
796B LEU 3.1 5.4 + - - +
798B ARG* 1.3 108.3 - - - +
800B VAL* 1.3 61.6 + - - +
802B ASN* 3.5 14.1 + - - +
803B GLY 3.2 4.0 + - - -
804B HIS* 3.0 50.4 + - + +
805B ILE* 3.6 19.0 + - + -
823B LEU* 3.5 26.1 - - + +
825B PHE* 4.6 4.9 - - + -
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Residues in contact with VAL 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B LEU* 3.2 17.6 + - + +
797B LEU* 3.5 14.8 - - + +
798B ARG 3.3 0.4 - - - -
799B GLN* 1.3 76.8 - - - +
801B SER* 1.3 62.1 + - - +
803B GLY* 3.1 14.6 + - - -
805B ILE* 3.3 38.8 - - + +
814B PHE* 3.8 24.5 - - + -
912B VAL* 3.6 27.4 - - + -
1028B ASN* 3.5 19.4 + - - +
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Residues in contact with SER 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B LEU 3.3 10.8 + - - -
798B ARG* 3.5 13.3 - - - -
800B VAL* 1.3 77.9 - - - +
802B ASN* 1.3 65.4 + - - +
803B GLY* 3.2 2.0 + - - -
905B LYS* 5.5 7.2 - - - -
909B ILE* 4.0 36.7 - - - +
912B VAL* 5.8 2.1 - - - +
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Residues in contact with ASN 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B ARG* 3.1 42.4 + - - +
799B GLN* 3.5 28.0 + - - +
800B VAL 3.2 0.8 - - - -
801B SER* 1.3 79.9 - - - +
803B GLY* 1.3 57.3 + - - +
804B HIS* 3.6 19.8 + - + +
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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