Contacts of the helix formed by residues 882 - 889 (chain i) in PDB entry 5JPQ
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 882 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873i ALA 2.7 26.0 - - - +
874i VAL* 2.7 24.7 - - - +
875i LYS 2.5 16.8 - - - +
876i LEU 3.0 1.4 - - - +
881i GLN* 1.4 62.6 - - - +
883i ILE* 1.3 50.7 - - - +
885i LEU 2.6 21.5 + - - -
886i ALA* 2.8 29.7 - - + +
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Residues in contact with ILE 883 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874i VAL 3.9 0.2 + - - -
875i LYS* 2.7 12.9 + - + +
879i LEU 2.5 16.6 - - - +
880i GLN 2.9 9.6 - - - +
881i GLN 2.6 36.2 + - - +
882i ALA* 1.3 65.4 - - - +
884i LEU* 1.3 67.8 + - - +
911i ILE* 4.6 9.9 - - + +
912i PHE* 4.5 15.9 - - - +
915i ILE* 4.5 8.3 - - + -
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Residues in contact with LEU 884 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875i LYS 2.7 5.8 + - - +
876i LEU* 3.4 3.1 - - - -
877i SER 2.9 19.1 - - - +
878i GLY* 2.6 50.4 - - - +
879i LEU* 2.7 23.3 + - - +
882i ALA 2.6 6.3 + - - -
883i ILE* 1.3 78.2 - - - +
885i LEU* 1.3 58.4 + - - +
888i GLY 3.0 0.7 + - - -
912i PHE 5.2 3.1 - - - +
915i ILE* 4.7 10.1 - - + -
916i MET 5.9 0.9 - - - +
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Residues in contact with LEU 885 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873i ALA* 2.8 38.8 - - - +
876i LEU 2.6 5.3 + - - -
877i SER* 2.9 24.0 - - - -
878i GLY 4.1 0.2 - - - +
882i ALA 2.6 7.9 + - - -
884i LEU* 1.3 69.2 - - - +
886i ALA* 1.3 59.8 + - - -
889i LEU* 2.6 40.0 + - + +
890i GLN 3.1 4.5 + - - -
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Residues in contact with ALA 886 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873i ALA 4.7 0.2 - - - -
881i GLN* 2.9 11.0 - - + -
882i ALA* 2.8 42.0 + - + +
885i LEU* 1.3 76.1 - - - +
887i LEU* 1.3 57.0 + - - +
890i GLN* 2.7 32.7 - - + +
891i ARG 2.9 1.7 + - - -
892i LYS* 2.8 19.5 + - + -
897i LEU* 5.2 0.9 - - + -
798j PRO* 5.9 2.5 - - + -
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Residues in contact with LEU 887 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879i LEU* 2.9 23.8 - - + -
880i GLN* 3.3 18.2 - - + +
881i GLN* 2.8 16.7 - - + +
884i LEU 3.5 2.0 + - - -
885i LEU 3.1 0.2 - - - -
886i ALA* 1.3 78.1 - - - +
888i GLY* 1.4 57.3 + - - +
891i ARG* 2.9 23.7 + - - -
892i LYS 3.9 13.9 - - - +
893i ASP 6.2 0.2 - - - -
894i ILE* 6.5 0.2 - - - -
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Residues in contact with GLY 888 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855i LEU* 6.2 1.6 - - - -
856i ASP 4.9 9.0 - - - +
857i LEU* 4.5 14.6 - - - +
862i ALA* 6.4 0.4 - - - -
878i GLY 3.1 19.1 - - - -
879i LEU* 3.0 5.9 - - - +
884i LEU 3.0 10.3 + - - -
887i LEU* 1.4 78.5 - - - +
889i LEU* 1.4 60.8 + - - +
891i ARG* 4.5 1.2 + - - +
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Residues in contact with LEU 889 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877i SER* 5.7 1.1 - - - -
885i LEU* 2.6 29.1 + - + +
888i GLY* 1.4 75.5 - - - +
890i GLN* 1.4 60.8 + - + +
891i ARG* 3.4 2.1 + - - +
787j LEU* 4.9 12.3 - - + +
790j LEU* 3.8 16.1 - - + +
791j SER* 4.5 9.2 + - - -
798j PRO* 6.3 0.9 - - + -
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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