Contacts of the helix formed by residues 91 - 95 (chain E) 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 ARG 91 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E VAL* 3.3 12.3 + - - +
90E MET* 1.3 68.9 - - - +
92E ALA* 1.3 62.6 + - - +
93E SER 3.1 1.6 + - - -
94E ILE* 3.2 23.1 + - - +
112E PRO* 3.5 33.8 + - + +
113E GLY 2.8 32.7 + - - +
114E GLY 4.0 2.4 + - - -
115E QPA 2.9 56.9 + - - +
120E ARG* 3.0 68.3 + - - +
122E VAL* 5.3 1.8 - - - +
501E EPZ 6.0 0.2 - - - +
336H PRO* 5.9 0.6 - - - +
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.1 21.5 - - + -
30E PHE* 4.2 3.9 - - + -
90E MET* 2.7 21.9 + - + +
91E ARG* 1.3 70.9 - - - +
93E SER* 1.3 51.3 + - - +
94E ILE* 2.9 11.2 - - - +
95E TRP* 2.8 47.1 + - + +
115E QPA 5.5 0.2 + - - -
501E EPZ 4.1 20.4 - - + -
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E PHE* 4.1 11.6 - - - -
52E THR* 5.0 0.3 - - - +
56E LEU* 3.8 19.5 - - - +
82E ALA* 4.8 0.9 - - - -
86E LEU* 4.2 8.5 + - - +
87E VAL* 4.0 30.0 + - - -
90E MET* 2.9 29.2 + - - +
92E ALA* 1.3 76.6 - - - +
94E ILE* 1.3 54.8 + - - +
95E TRP 2.7 11.8 + - - -
96E ALA* 2.7 22.3 + - - +
109E VAL* 4.3 3.9 - - - +
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E VAL* 5.2 1.6 - - - +
91E ARG 3.2 19.3 + - - +
92E ALA* 2.8 6.3 + - - +
93E SER* 1.3 76.1 - - - +
95E TRP* 1.3 65.1 + - + +
96E ALA 3.0 5.6 + - - -
97E LEU* 3.1 30.8 + - + +
98E GLY 4.7 0.5 + - - -
109E VAL* 3.8 27.5 - - + +
110E SER 4.5 1.1 - - - +
112E PRO* 4.4 22.7 - - + -
122E VAL* 4.6 19.5 - - + -
125E HIS* 4.3 35.0 - - + +
143E VAL* 4.8 7.0 - - + -
168E THR* 5.0 2.6 + - - -
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Residues in contact with TRP 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ASN 4.9 0.2 - - - -
26E LEU* 4.2 6.5 - - + -
27E PRO* 3.4 43.1 - - + -
30E PHE* 3.8 29.6 - + + +
92E ALA* 2.8 22.9 + - + +
93E SER 2.7 5.5 + - - -
94E ILE* 1.3 75.3 - - + +
96E ALA* 1.3 62.6 + - - -
97E LEU* 3.2 0.7 - - - -
98E GLY 4.6 0.9 - - - -
99E PRO* 3.1 22.5 - - - +
125E HIS* 4.2 5.2 - + - -
163E VAL* 4.5 5.6 - - + -
164E GLY* 3.0 39.4 + - - -
167E VAL* 3.6 31.1 - - + +
168E THR* 3.5 20.6 - - - -
501E EPZ 3.6 40.2 - - + -
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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