Contacts of the helix formed by residues 792 - 799 (chain B) in PDB entry 5MJA
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 ALA 792 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790B TRP 4.0 0.4 + - - -
791B THR* 1.3 76.6 - - - +
793B PRO* 1.4 72.9 - - + +
794B GLU* 3.4 28.0 - - - +
795B ALA* 3.1 12.9 + - + +
796B ILE* 3.1 10.2 + - - +
805B SER* 3.7 22.5 + - - -
808B TRP* 3.6 26.4 - - + +
868B ARG* 3.8 2.0 - - - +
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Residues in contact with PRO 793 (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 THR 3.8 0.4 - - - +
792B ALA* 1.4 83.0 - - + +
794B GLU* 1.3 62.4 + - - +
796B ILE* 3.4 13.3 + - + +
797B ALA* 3.0 28.1 + - - +
808B TRP* 3.5 35.2 - - + -
837B ILE* 3.8 25.4 - - + -
838B GLU* 4.4 16.3 - - - +
842B ARG* 5.5 0.4 - - - +
863B LYS* 5.0 13.7 - - + +
868B ARG* 4.5 2.9 - - - +
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Residues in contact with GLU 794 (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 ALA* 3.4 14.9 - - - +
793B PRO* 1.3 74.2 - - - +
795B ALA* 1.3 60.5 + - - +
796B ILE 3.3 0.2 - - - -
797B ALA* 3.8 1.3 - - - -
798B TYR* 2.9 53.2 + - + +
800B LYS* 4.2 7.3 - - + +
802B THR* 4.8 1.0 + - - -
805B SER* 3.8 10.2 + - - -
863B LYS 4.4 2.9 - - - +
865B ARG* 3.7 26.8 - - - +
868B ARG* 2.9 44.6 + - - -
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Residues in contact with ALA 795 (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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786B ILE* 5.0 0.2 - - - +
791B THR* 3.6 24.2 - - + +
792B ALA* 3.1 5.6 + - + +
794B GLU* 1.3 77.6 - - - +
796B ILE* 1.4 60.9 + - - +
799B ARG* 2.9 31.4 + - - +
800B LYS 3.3 22.4 - - - +
801B PHE* 3.8 19.2 - - + -
805B SER* 4.2 16.6 - - - -
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Residues in contact with ILE 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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782B LEU* 5.7 0.2 - - - +
786B ILE* 3.5 21.3 - - + -
788B VAL* 3.6 29.2 - - + +
791B THR* 3.6 21.8 - - + +
792B ALA 3.1 10.1 + - - +
793B PRO* 3.7 11.9 - - + +
795B ALA* 1.4 77.3 - - - +
797B ALA* 1.3 62.9 + - - +
798B TYR 3.6 0.2 + - - -
799B ARG* 2.8 36.8 + - - +
833B VAL* 6.0 1.8 - - + -
834B ILE* 4.0 37.0 - - + -
837B ILE* 6.6 0.2 - - + -
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Residues in contact with ALA 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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782B LEU* 4.1 11.5 - - - +
793B PRO 3.0 17.7 + - - +
794B GLU* 4.3 0.7 - - - -
796B ILE* 1.3 81.0 - - - +
798B TYR* 1.4 89.3 + - + +
838B GLU* 6.1 1.1 - - - +
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Residues in contact with TYR 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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779B THR* 5.1 1.9 - - - +
780B SER 5.3 0.5 - - - +
782B LEU* 3.9 11.8 - - - +
794B GLU* 2.9 40.8 + - + +
797B ALA* 1.4 94.2 - - + +
799B ARG* 1.4 72.2 + - - +
800B LYS* 3.3 30.9 + - + +
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Residues in contact with ARG 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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779B THR* 3.7 2.8 - - - +
780B SER* 3.0 46.0 + - - +
781B SER 3.5 14.6 - - - +
782B LEU* 3.3 25.7 + - - +
783B GLY 4.9 2.2 + - - -
784B GLY 2.8 29.0 + - - +
785B LYS* 4.5 1.6 - - - +
786B ILE* 3.4 27.6 - - - +
788B VAL* 5.7 1.2 - - - +
795B ALA 2.9 18.6 + - - +
796B ILE* 2.8 42.9 + - - +
798B TYR* 1.4 78.4 - - - +
800B LYS* 1.3 55.8 + - - +
801B PHE* 3.5 14.7 - - + -
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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