Contacts of the helix formed by residues 836 - 841 (chain J) in PDB entry 4XLR
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 VAL 836 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812J ALA* 4.7 5.4 - - + +
813J LEU* 4.8 12.6 - - + -
816J TYR* 3.6 39.0 - - + -
821J VAL* 3.6 21.3 - - + -
822J ALA 3.2 24.9 - - - +
823J LEU* 3.6 7.6 - - + +
825J ALA 3.8 1.5 + - - +
827J ILE* 3.6 18.8 - - + -
834J THR 3.9 0.2 + - - -
835J SER* 1.3 75.3 + - - +
837J GLY* 1.3 57.2 + - - +
839J LEU* 3.5 7.5 + - + +
840J LYS* 2.9 34.7 + - + +
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Residues in contact with GLY 837 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823J LEU* 3.3 25.8 + - - -
835J SER* 3.1 1.8 + - - -
836J VAL* 1.3 75.8 - - - +
838J ARG* 1.3 58.8 + - - +
839J LEU 3.0 2.9 - - - -
841J PHE* 2.7 43.9 + - - +
862J ASP* 6.0 0.9 - - - -
863J VAL 3.0 16.1 - - - +
864J VAL* 4.0 1.5 - - - -
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Residues in contact with ARG 838 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826J PRO* 5.4 9.3 - - - +
833J GLU* 4.3 16.5 + - - -
834J THR* 3.2 27.8 - - - +
835J SER* 3.3 24.7 + - - +
837J GLY* 1.3 75.0 - - - +
839J LEU* 1.3 61.9 + - + +
841J PHE 3.7 3.8 - - - +
842J VAL* 3.8 5.4 - - - +
863J VAL* 2.8 47.9 + - + +
864J VAL* 3.9 3.1 - - - +
865J THR* 2.5 30.7 + - - +
874J GLU* 2.9 38.0 + - + +
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Residues in contact with LEU 839 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982D PHE* 5.6 4.7 - - + -
65H PHE* 4.9 18.6 - - + -
809J PRO* 4.5 17.9 - - + +
812J ALA* 5.4 1.6 - - + -
813J LEU* 5.2 10.3 - - + -
827J ILE* 5.4 2.9 - - + -
829J VAL* 3.6 32.8 - - + -
834J THR* 3.7 23.3 - - + +
835J SER 3.6 12.8 - - - +
836J VAL* 3.5 10.2 + - + +
837J GLY 3.0 0.6 - - - -
838J ARG* 1.3 80.5 - - + +
840J LYS* 1.3 68.1 + - - +
842J VAL* 3.2 19.4 - - - +
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Residues in contact with LYS 840 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H PRO* 5.7 8.3 - - + +
153H ALA* 6.1 0.7 - - - +
154H GLU* 3.3 40.2 + - - +
168H ASP* 5.0 7.4 - - - +
813J LEU* 4.4 19.8 - - + +
816J TYR* 4.2 34.2 - - + -
817J GLU* 5.1 2.2 + - - -
823J LEU* 4.7 3.1 - - + -
836J VAL* 2.9 22.4 + - + +
839J LEU* 1.3 75.1 - - - +
841J PHE* 1.3 92.5 + - + +
842J VAL* 3.8 2.4 + - - +
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Residues in contact with PHE 841 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H TYR* 6.6 0.2 - + - -
152H PRO* 5.6 10.5 - - + -
816J TYR* 5.5 0.4 - - - -
823J LEU* 4.3 10.3 - - + -
837J GLY* 2.7 32.0 + - - +
838J ARG 3.7 1.2 - - - +
840J LYS* 1.3 110.2 - - + +
842J VAL* 1.3 64.7 + - - +
843J PHE* 3.5 34.8 - + + -
852J ALA* 5.5 3.6 - - + -
857J LEU* 3.5 26.9 - - + -
858J LEU* 3.6 40.4 - - + -
864J VAL* 3.6 8.1 - - + -
865J THR 3.4 18.2 + - - -
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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