Contacts of the helix formed by residues 981 - 989 (chain C) in PDB entry 5UHE
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 GLN 981 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596C PHE* 5.9 1.8 - - - -
598C GLU* 4.3 14.8 + - - +
599C HIS* 5.8 2.0 + - - -
977C PHE 6.1 0.2 - - - -
978C ASP* 4.3 7.3 + - - +
979C GLY 3.7 15.9 + - - +
980C ALA* 1.3 79.0 + - - +
982C GLU* 1.3 80.3 + - - +
983C ALA* 3.0 12.9 + - + +
984C GLU* 2.7 24.2 + - - +
985C LEU* 3.0 24.7 + - - +
842D GLU 4.1 9.0 - - - +
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Residues in contact with GLU 982 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C HIS* 4.8 6.4 + - + -
932C LEU* 5.8 5.4 - - + -
981C GLN* 1.3 93.2 - - - +
983C ALA* 1.3 63.6 + - + +
985C LEU* 4.0 8.7 - - - -
986C GLN* 3.3 23.2 + - - +
733D MET* 3.8 14.9 - - + +
841D ARG* 3.3 42.5 + - + +
842D GLU* 3.2 39.5 - - - +
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Residues in contact with ALA 983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955C TRP* 4.3 20.8 - - + +
981C GLN* 3.0 7.8 - - + +
982C GLU* 1.3 81.8 - - + +
984C GLU* 1.3 68.7 + - + +
986C GLN* 3.1 8.7 + - - +
987C GLY* 3.1 19.8 + - - -
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Residues in contact with GLU 984 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 4.6 14.7 - - + +
955C TRP* 3.5 32.5 - - + +
958C ARG* 4.1 10.9 - - - +
959C LEU* 3.8 40.2 + - + +
960C PRO* 5.2 0.9 - - - +
979C GLY 4.2 1.4 - - - +
980C ALA* 3.5 8.2 - - + -
981C GLN* 2.7 45.4 + - + +
983C ALA* 1.3 79.8 - - + +
985C LEU* 1.3 52.7 + - - +
987C GLY 3.3 0.9 + - - -
988C LEU* 2.7 42.7 + - + +
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Residues in contact with LEU 985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C PHE* 4.6 9.9 - - + -
932C LEU* 3.9 36.1 - - + +
935C HIS* 3.9 24.2 - - + -
936C LEU* 3.6 42.2 - - + +
939C CYS* 4.9 2.2 - - - -
980C ALA* 4.9 6.9 - - + +
981C GLN 3.0 16.2 + - - +
982C GLU* 3.9 8.3 - - - +
983C ALA 3.1 0.2 - - - -
984C GLU* 1.3 77.4 - - - +
986C GLN* 1.3 62.8 + - - +
988C LEU* 3.2 10.0 + - + +
989C LEU* 3.1 28.5 + - + +
733D MET* 4.3 10.5 - - - -
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Residues in contact with GLN 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982C GLU 3.3 14.7 + - - +
983C ALA* 3.1 6.1 + - - +
985C LEU* 1.3 77.3 - - - +
987C GLY* 1.3 63.9 + - - +
989C LEU* 3.4 17.4 + - - +
990C SER* 3.7 9.5 + - - -
1004C ALA* 4.3 12.7 - - + +
733D MET* 3.8 23.8 - - + +
841D ARG* 5.0 7.3 + - - -
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Residues in contact with GLY 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955C TRP* 3.5 33.8 - - - -
983C ALA 3.1 10.5 + - - -
984C GLU 3.6 3.1 - - - -
986C GLN* 1.3 79.2 - - - +
988C LEU* 1.3 60.6 + - - +
990C SER* 3.1 18.3 + - - -
991C CYS* 3.4 13.9 + - - -
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Residues in contact with LEU 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.9 33.7 - - + -
936C LEU* 4.7 8.3 - - + -
939C CYS* 3.8 16.0 - - + -
944C TRP* 3.5 52.6 - - + +
946C VAL* 4.7 1.1 - - + -
955C TRP* 4.1 16.4 - - + -
959C LEU* 4.6 9.2 - - + -
984C GLU* 2.7 29.6 + - + +
985C LEU* 3.2 10.3 + - + +
987C GLY* 1.3 74.3 - - - +
989C LEU* 1.3 61.4 + - - +
991C CYS* 3.2 16.5 + - - +
992C THR* 3.5 12.1 + - - +
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Residues in contact with LEU 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935C HIS* 4.2 29.6 - - + +
938C TRP* 5.3 2.2 - - + -
939C CYS* 3.8 18.4 - - - -
985C LEU* 3.1 20.1 + - + +
986C GLN* 3.5 15.7 - - - +
987C GLY 3.1 0.6 - - - -
988C LEU* 1.3 77.3 - - - +
990C SER* 1.3 57.4 + - - +
992C THR* 3.1 20.8 + - + +
1002C VAL* 4.8 8.1 - - + -
1003C ASP 3.0 22.0 - - - +
1004C ALA* 3.6 25.8 - - - +
1005C ASP 4.3 0.9 - - - -
1006C GLY* 3.9 23.3 - - - +
733D MET* 4.2 14.1 - - + -
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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