Contacts of the helix formed by residues 89 - 95 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C THR* 3.9 18.6 + - - +
85C ASP 3.4 18.1 + - - +
86C LEU* 2.8 18.4 + - - +
88C LYS* 1.3 86.2 - - + +
90C MET* 1.3 62.2 + - - +
115C QPA 4.6 2.9 - - - -
397C ARG* 3.8 19.4 + - - -
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Residues in contact with MET 90 (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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26C LEU* 3.9 9.9 - - - -
30C PHE* 4.1 10.8 - - + -
49C ASP* 3.6 38.4 - - - +
52C THR* 4.0 26.2 - - + +
53C SER* 3.5 21.3 - - - +
56C LEU* 5.9 0.2 - - + -
86C LEU 3.2 3.4 + - - -
87C VAL 3.0 7.2 + - - +
88C LYS 3.3 0.6 - - - -
89C THR* 1.3 82.7 - - - +
91C ARG* 1.3 60.1 + - - +
92C ALA* 2.8 20.4 + - + +
93C SER* 2.9 49.5 + - - +
115C QPA 3.9 3.6 - - - +
397C ARG* 4.0 15.0 - - - +
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Residues in contact with ARG 91 (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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87C VAL* 3.4 12.1 + - - +
90C MET* 1.3 69.8 - - - +
92C ALA* 1.3 62.7 + - - +
93C SER* 3.0 3.1 + - - -
94C ILE* 3.3 22.7 + - - +
112C PRO* 3.5 34.6 + - + +
113C GLY 2.8 31.3 + - - +
114C GLY 4.1 3.0 + - - -
115C QPA 2.9 56.9 + - - +
120C ARG* 3.0 67.7 + - - +
122C VAL* 5.2 1.6 - - - +
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Residues in contact with ALA 92 (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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26C LEU* 4.2 13.7 - - + -
30C PHE* 4.1 4.4 - - + -
90C MET* 2.8 20.6 + - + +
91C ARG* 1.3 71.5 - - - +
93C SER* 1.3 51.1 + - - +
94C ILE* 2.9 11.1 - - - +
95C TRP* 2.7 47.5 + - + +
115C QPA 5.5 0.2 + - - -
501C EPZ 3.9 27.6 - - + -
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Residues in contact with SER 93 (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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30C PHE* 4.1 11.6 - - - -
52C THR* 5.0 0.5 - - - +
56C LEU* 3.8 19.1 - - - +
82C ALA* 4.8 0.9 - - - -
86C LEU* 4.3 7.8 + - - +
87C VAL* 3.9 31.1 + - - -
90C MET* 2.9 28.8 + - - +
92C ALA* 1.3 70.4 - - - +
94C ILE* 1.3 53.8 + - - +
95C TRP* 2.7 17.1 + - - -
96C ALA* 2.8 22.9 + - - +
109C VAL* 4.3 4.4 - - - +
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Residues in contact with ILE 94 (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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87C VAL* 5.2 1.4 - - - +
91C ARG 3.3 18.6 + - - +
92C ALA* 2.8 7.1 + - - +
93C SER* 1.3 75.9 - - - +
95C TRP* 1.3 69.1 + - + +
96C ALA 3.1 1.8 + - - -
97C LEU* 3.1 31.2 + - + +
98C GLY 4.7 0.3 + - - -
109C VAL* 3.7 27.5 - - + +
110C SER 4.5 0.9 - - - +
112C PRO* 4.4 22.4 - - + -
122C VAL* 4.6 19.5 - - + -
125C HIS* 4.2 35.9 - - + +
143C VAL* 4.8 8.1 - - + -
168C THR* 5.0 2.8 + - - -
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Residues in contact with TRP 95 (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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23C ASN 4.9 0.2 - - - -
26C LEU* 4.2 4.9 - - + -
27C PRO* 3.4 44.0 - - + -
30C PHE* 3.8 27.4 - + + +
92C ALA* 2.7 22.7 + - + +
93C SER 2.7 2.0 + - - -
94C ILE* 1.3 79.1 - - + +
96C ALA* 1.3 61.4 + - - -
97C LEU* 3.2 0.4 - - - -
98C GLY 4.0 1.6 + - - -
99C PRO* 3.1 22.2 - - - +
125C HIS* 4.2 6.0 - + - -
163C VAL* 4.6 6.5 - - + -
164C GLY* 3.1 38.5 + - - -
167C VAL* 3.7 32.9 - - + +
168C THR* 3.5 20.4 - - - -
501C EPZ 3.6 39.0 - - + -
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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