Contacts of the helix formed by residues 979 - 984 (chain C) in PDB entry 3U5P
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 979 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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973C LEU 3.0 26.5 + - - -
974C TYR 3.3 2.6 + - - -
976C HIS* 2.9 22.6 + - - -
977C GLU 3.4 0.8 - - - -
978C LEU* 1.3 75.3 - - - +
980C ILE* 1.3 67.7 + - - +
981C GLU 3.1 3.1 - - - -
982C PHE* 2.8 25.1 + - - +
983C GLN* 3.1 24.2 + - - +
1003C LEU* 4.3 9.6 - - - -
1069C VAL* 4.2 9.4 - - - +
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Residues in contact with ILE 980 (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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892C VAL 5.9 2.9 - - - +
893C CYS* 6.5 0.4 - - - -
976C HIS 4.7 0.9 + - - +
977C GLU 4.6 15.0 - - - +
978C LEU 3.6 1.1 - - - -
979C SER* 1.3 74.7 + - - +
981C GLU* 1.3 61.8 + - - +
982C PHE 3.0 1.6 + - - -
983C GLN* 3.1 36.2 + - + +
984C GLU* 4.3 4.0 + - + +
12K GLY* 4.6 22.4 - - - +
15K ALA* 4.6 13.7 - - - +
16K PRO* 5.6 1.8 - - + +
17K ARG* 3.9 31.0 + - - +
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Residues in contact with GLU 981 (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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978C LEU 4.5 3.2 + - - +
979C SER 2.8 4.0 + - - -
980C ILE* 1.3 76.0 - - - +
982C PHE* 1.3 78.0 + - + +
983C GLN 3.4 0.6 + - - -
984C GLU 4.4 7.4 + - - +
986C VAL* 4.8 5.2 - - - +
987C PRO* 5.4 5.6 - - - +
1062C VAL* 3.6 19.1 - - + -
1065C ALA* 6.0 0.2 - - + -
16K PRO* 3.2 27.4 + - + +
17K ARG* 3.3 29.3 + - - +
18K ALY 3.4 45.8 + - + +
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Residues in contact with PHE 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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978C LEU 3.6 19.1 - - - -
979C SER* 2.8 20.8 + - - +
981C GLU* 1.3 88.2 - - + +
983C GLN* 1.3 60.4 + - - +
984C GLU 3.6 2.2 - - - -
986C VAL* 6.2 0.9 - - - -
1002C ASP* 3.2 10.5 - - - +
1003C LEU* 2.9 33.6 + - + +
1031C ILE* 3.8 29.4 - - + -
1032C PHE* 3.8 18.6 - + + -
1035C CYS* 3.6 26.2 - - + -
1062C VAL* 3.7 8.1 - - + -
1065C ALA* 4.2 1.8 - - + -
1066C GLY* 3.4 33.9 - - - -
1069C VAL* 4.4 5.4 - - + -
18K ALY 4.4 13.2 - - + -
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Residues in contact with GLN 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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892C VAL* 4.8 9.8 + - - +
974C TYR* 3.4 38.7 + - + -
976C HIS 5.1 0.2 + - - -
979C SER* 3.1 32.8 + - - +
980C ILE* 3.1 34.8 + - + +
981C GLU 3.4 0.2 - - - -
982C PHE* 1.3 79.5 - - - +
984C GLU* 1.3 69.3 + - + +
1002C ASP* 3.6 1.2 - - - +
1003C LEU* 3.7 19.3 - - + -
1004C SER* 2.8 34.3 + - - -
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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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974C TYR* 5.1 2.3 + - - -
980C ILE 4.3 4.2 + - - +
981C GLU 4.4 6.1 + - - +
982C PHE* 4.3 3.6 - - - -
983C GLN* 1.3 93.7 + - + +
985C PRO* 1.3 87.7 - - + +
986C VAL* 3.1 4.5 + - - +
987C PRO* 6.2 0.2 - - + -
1002C ASP* 3.7 11.3 - - - +
1004C SER* 4.0 10.4 - - - -
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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