Contacts of the helix formed by residues 89 - 95 (chain F) in PDB entry 3SWD
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 THR 89 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F THR* 3.9 18.8 + - - +
85F ASP 3.3 17.8 + - - +
86F LEU* 2.9 14.8 + - - +
88F LYS* 1.3 90.1 - - + +
90F MET* 1.3 62.0 + - - +
115F QPA 4.5 3.5 + - - -
397F ARG* 3.9 19.4 + - - -
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Residues in contact with MET 90 (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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26F LEU* 4.0 9.0 - - + -
30F PHE* 4.1 11.0 - - + -
49F ASP* 3.6 36.8 - - - +
52F THR* 4.0 26.2 - - + +
53F SER* 3.6 21.5 - - - +
56F LEU* 5.9 0.2 - - + -
86F LEU 3.2 3.4 + - - +
87F VAL 3.0 8.0 + - - +
88F LYS 3.3 0.6 + - - -
89F THR* 1.3 82.7 - - - +
91F ARG* 1.3 53.0 + - - +
92F ALA* 2.8 27.0 + - + +
93F SER* 2.9 47.2 + - - +
115F QPA 3.8 3.8 - - - +
397F ARG* 4.0 16.4 - - - +
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Residues in contact with ARG 91 (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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87F VAL* 3.3 12.7 + - - +
90F MET* 1.3 69.1 - - - +
92F ALA* 1.3 61.1 + - - +
93F SER* 3.1 1.8 + - - -
94F ILE* 3.3 23.3 + - - +
112F PRO* 3.5 32.8 + - + +
113F GLY 2.8 33.3 + - - +
114F GLY 4.1 2.8 + - - -
115F QPA 2.9 58.0 + - - +
120F ARG* 3.0 67.0 + - - +
122F VAL* 5.3 1.6 - - - +
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Residues in contact with ALA 92 (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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26F LEU* 4.1 13.7 - - + -
30F PHE* 4.1 3.3 - - + -
90F MET* 2.8 21.7 + - + +
91F ARG* 1.3 71.1 - - - +
93F SER* 1.3 51.8 + - - +
94F ILE* 2.9 11.4 - - - +
95F TRP* 2.7 47.4 + - + +
115F QPA 5.5 0.2 + - - -
501F EPZ 4.0 27.4 - - + -
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Residues in contact with SER 93 (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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30F PHE* 4.0 11.8 - - - -
52F THR* 5.0 0.3 - - - +
56F LEU* 3.7 19.9 - - - +
82F ALA* 4.8 0.4 - - - -
86F LEU* 4.2 7.7 + - - +
87F VAL* 3.9 31.4 + - - -
90F MET* 2.9 28.3 + - - +
92F ALA* 1.3 77.7 - - - +
94F ILE* 1.3 62.4 + - - +
95F TRP 2.8 2.2 + - - -
96F ALA* 2.8 23.8 + - - +
109F VAL* 4.3 4.4 - - - +
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Residues in contact with ILE 94 (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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87F VAL* 5.2 1.8 - - - +
91F ARG 3.3 20.1 + - - +
92F ALA* 2.8 6.9 + - - +
93F SER* 1.3 76.6 - - - +
95F TRP* 1.3 64.5 + - + +
96F ALA 3.0 5.6 + - - -
97F LEU* 3.1 30.4 + - + +
98F GLY 4.7 0.5 + - - -
109F VAL* 3.8 26.2 - - + +
110F SER 4.5 0.9 - - - +
112F PRO* 4.4 23.6 - - + -
122F VAL* 4.6 20.0 - - + -
125F HIS* 4.3 34.3 - - + +
143F VAL* 4.9 7.6 - - + -
168F THR* 5.0 2.4 + - - -
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Residues in contact with TRP 95 (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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23F ASN 5.0 0.2 - - - -
26F LEU* 4.1 5.2 - - + -
27F PRO* 3.5 45.8 - - + -
30F PHE* 3.8 28.8 - + + +
92F ALA* 2.7 24.8 + - + +
93F SER 2.8 0.8 + - - -
94F ILE* 1.3 79.6 - - + +
96F ALA* 1.3 62.1 + - - +
97F LEU* 3.3 0.9 - - - -
98F GLY 4.0 0.8 + - - -
99F PRO* 3.0 22.3 - - - +
125F HIS* 4.2 5.3 - + - -
163F VAL* 4.6 5.4 - - + -
164F GLY* 3.1 38.7 + - - -
167F VAL* 3.6 28.0 - - + +
168F THR* 3.5 21.3 + - - -
501F EPZ 3.7 42.0 - - + -
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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