Contacts of the helix formed by residues 935 - 946 (chain B) in PDB entry 4XUF
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 SER 935 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803B GLU* 4.4 9.9 - - - -
868B LYS* 5.8 4.9 - - - -
871B VAL* 5.0 1.8 - - - -
933B ARG 3.9 0.8 + - - -
934B PRO* 1.3 73.8 - - - +
936B PHE* 1.3 68.2 + - - +
937B PRO* 3.7 14.8 - - - +
938B ASN* 2.3 57.2 + - - +
939B LEU* 3.2 7.7 - - - +
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Residues in contact with PHE 936 (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 ALA* 4.4 12.1 - - + +
799B MET* 2.6 48.9 - - + -
800B GLU* 4.1 13.0 - - - +
803B GLU* 2.9 21.6 + - - +
812B LEU* 5.0 0.4 - - + -
867B ILE* 3.2 37.2 - - + -
870B ASP* 3.7 24.7 - - + -
871B VAL* 4.1 9.9 - - + +
874B TYR* 4.4 25.6 - + + -
934B PRO 3.9 0.8 + - - -
935B SER* 1.3 69.6 - - - +
937B PRO* 1.3 66.2 - - + +
939B LEU* 2.5 42.1 + - + +
940B THR* 3.2 7.3 + - - -
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Residues in contact with PRO 937 (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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800B GLU* 3.9 32.6 - - + +
803B GLU* 3.3 16.8 - - - +
935B SER* 3.7 13.2 - - - +
936B PHE* 1.3 94.4 - - + +
938B ASN* 1.3 64.2 - - - +
940B THR* 3.2 16.3 + - - +
941B SER* 3.4 11.6 + - - -
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Residues in contact with ASN 938 (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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934B PRO* 4.4 8.2 - - + +
935B SER* 2.3 47.5 + - - +
936B PHE 2.8 1.6 + - - -
937B PRO* 1.3 76.5 - - - +
939B LEU* 1.3 56.1 + - - +
941B SER* 2.7 23.5 + - - -
942B PHE* 2.9 42.6 + - + -
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Residues in contact with LEU 939 (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 ALA* 3.9 17.7 - - + +
871B VAL* 4.9 3.1 - - + -
874B TYR* 4.1 21.8 - - + -
921B ILE* 3.6 30.7 - - + -
925B CYS* 4.4 9.0 - - - -
934B PRO* 3.9 26.0 - - + +
935B SER 3.2 30.0 + - - +
936B PHE* 2.5 21.9 + - + +
938B ASN* 1.3 74.7 - - - +
940B THR* 1.3 59.2 + - - +
942B PHE* 4.3 10.5 - - + -
943B LEU* 3.1 42.9 + - + +
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Residues in contact with THR 940 (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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793B TYR* 3.2 31.9 - - + +
796B ALA* 3.6 26.0 + - - -
797B LYS* 3.4 34.9 - - + +
800B GLU* 4.4 14.5 + - - +
936B PHE 3.2 6.8 + - - -
937B PRO* 3.2 11.3 + - - +
939B LEU* 1.3 77.6 - - - +
941B SER* 1.3 59.6 + - - +
944B GLY* 3.3 8.5 + - - -
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Residues in contact with SER 941 (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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937B PRO 3.4 4.8 + - - -
938B ASN* 2.7 28.6 + - - +
940B THR* 1.3 78.7 - - - +
942B PHE* 1.3 73.1 + - - +
944B GLY* 3.5 1.3 + - - -
945B CYS* 3.5 26.3 + - - -
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Residues in contact with PHE 942 (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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921B ILE* 3.9 32.5 - - + -
924B SER* 5.9 1.1 - - - -
934B PRO* 4.7 13.9 - - + -
938B ASN* 2.9 42.8 + - + +
939B LEU* 3.4 12.8 + - + +
941B SER* 1.3 85.6 + - - +
943B LEU* 1.3 62.5 + - + +
945B CYS* 3.4 17.0 + - - +
946B GLN* 4.0 10.5 + - - +
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Residues in contact with LEU 943 (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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789B LEU* 4.1 15.7 - - + +
792B ALA* 3.6 20.0 - - + -
793B TYR* 3.5 43.3 - - + +
796B ALA* 5.5 0.2 - - + -
874B TYR* 3.9 6.5 - - + +
878B LEU* 5.1 2.7 - - + -
918B ILE* 4.7 8.1 - - + -
921B ILE* 3.9 24.7 - - + -
939B LEU* 3.1 40.2 + - + +
942B PHE* 1.3 77.9 - - - +
944B GLY* 1.3 63.8 + - - +
945B CYS 3.2 0.2 - - - -
946B GLN* 3.3 34.4 + - - +
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Residues in contact with GLY 944 (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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793B TYR* 4.1 12.3 - - - -
940B THR 3.3 19.2 + - - -
941B SER* 3.5 2.9 + - - -
942B PHE 3.2 1.0 - - - -
943B LEU* 1.3 77.9 - - - +
945B CYS* 1.3 61.1 + - - +
946B GLN 3.4 4.7 + - - -
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Residues in contact with CYS 945 (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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941B SER* 3.5 14.7 + - - -
942B PHE* 3.4 11.8 + - - +
943B LEU 3.2 0.6 - - - -
944B GLY* 1.3 78.0 - - - +
946B GLN* 1.3 62.8 + - + +
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Residues in contact with GLN 946 (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 GLU* 6.2 0.6 - - - +
789B LEU* 3.6 43.6 - - + +
915B THR* 5.2 3.2 - - - +
917B GLU* 3.4 38.1 + - + +
918B ILE* 4.1 10.4 - - - +
921B ILE* 5.1 5.9 - - - +
942B PHE 4.1 13.6 + - - +
943B LEU* 3.3 21.4 + - - +
944B GLY 3.2 4.6 - - - -
945B CYS* 1.3 84.4 - - + +
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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