Contacts of the helix formed by residues 979 - 984 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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973F LEU 2.9 27.7 + - - -
974F TYR* 3.3 1.9 + - - -
976F HIS* 2.8 23.3 + - - -
977F GLU 3.4 1.0 - - - -
978F LEU* 1.3 75.7 - - - +
980F ILE* 1.3 67.5 + - - +
981F GLU 3.1 3.4 - - - -
982F PHE* 2.9 22.1 + - - +
983F GLN* 3.2 23.9 + - - +
1003F LEU* 4.4 8.3 - - - -
1069F VAL* 4.2 11.0 - - - -
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Residues in contact with ILE 980 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892F VAL 5.8 4.5 - - - +
893F CYS* 5.9 4.5 - - - +
976F HIS 4.7 1.1 + - - +
977F GLU 4.6 6.7 - - - +
978F LEU 3.6 0.6 - - - -
979F SER* 1.3 75.8 + - - +
981F GLU* 1.3 60.8 + - - +
982F PHE 3.1 1.4 + - - -
983F GLN* 3.1 35.7 + - + +
984F GLU* 4.4 4.0 + - - +
12N GLY* 5.5 13.0 - - - -
15N ALA* 4.1 24.5 - - - +
17N ARG* 4.0 30.8 + - - +
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Residues in contact with GLU 981 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978F LEU 4.5 3.0 + - - +
979F SER 2.9 2.0 + - - -
980F ILE* 1.3 78.4 - - - +
982F PHE* 1.3 74.0 + - + +
984F GLU 4.4 8.3 - - - +
986F VAL* 5.1 3.1 - - - +
987F PRO* 5.4 6.6 - - - +
1062F VAL* 3.7 19.7 - - + -
1065F ALA* 6.0 0.9 - - + -
15N ALA 5.7 0.8 - - - +
16N PRO* 3.2 27.5 + - + +
17N ARG* 2.5 29.9 - - - +
18N ALY 3.2 55.3 + - - +
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Residues in contact with PHE 982 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978F LEU 3.8 15.0 - - - -
979F SER* 2.9 21.6 + - - +
981F GLU* 1.3 85.7 - - + +
983F GLN* 1.3 61.1 + - - +
984F GLU 3.6 2.0 - - - -
1002F ASP* 3.3 9.1 - - - +
1003F LEU* 2.9 34.5 + - + -
1031F ILE* 3.8 28.5 - - + -
1032F PHE* 3.9 16.2 - + + -
1035F CYS* 3.5 27.6 - - + -
1062F VAL* 3.7 14.4 - - + -
1065F ALA* 4.2 4.9 - - + -
1066F GLY* 3.4 36.3 - - - -
1069F VAL* 4.6 3.6 - - + -
18N ALY 4.4 12.8 - - + -
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Residues in contact with GLN 983 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892F VAL* 4.7 9.6 + - - +
974F TYR* 3.3 41.6 + - + -
976F HIS 5.0 0.4 + - - -
979F SER* 3.2 30.5 + - - +
980F ILE* 3.1 35.1 + - + +
982F PHE* 1.3 80.1 - - - +
984F GLU* 1.3 70.0 + - + +
1002F ASP* 3.7 0.9 - - - +
1003F LEU* 3.7 17.9 - - + -
1004F SER* 2.8 34.5 + - - -
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Residues in contact with GLU 984 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974F TYR* 4.8 3.1 + - - -
980F ILE 4.4 4.5 + - - +
981F GLU 4.4 9.2 + - - +
982F PHE* 4.4 1.2 - - - +
983F GLN* 1.3 93.2 - - + +
985F PRO* 1.3 86.3 - - + +
986F VAL* 3.2 4.2 + - - +
1002F ASP* 3.5 12.0 - - - +
1004F SER* 3.9 14.2 - - - -
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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