Contacts of the helix formed by residues 157 - 165 (chain B) in PDB entry 1S5E
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 PRO 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B PRO* 5.8 1.8 - - + -
95B PHE* 4.6 1.3 - - - -
155B ILE 3.5 5.3 - - - +
156B ALA* 1.3 88.1 - - - +
158B ALA* 1.3 66.2 + - - +
159B ALA* 4.2 8.5 - - + +
160B ASP* 3.0 44.4 + - - +
161B GLY 3.9 1.7 + - - -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 5.6 0.2 - - - -
99B ASP* 3.9 30.0 + - + +
100B VAL* 4.1 10.0 - - + +
156B ALA 3.7 1.7 + - - -
157B PRO* 1.3 71.6 - - - +
159B ALA* 1.3 56.9 + - - +
161B GLY* 2.8 19.4 + - - -
162B TYR* 3.2 43.5 + - + +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PRO* 3.1 8.5 + - + +
158B ALA* 1.3 78.3 - - - +
160B ASP* 1.3 63.8 + - - +
161B GLY 3.2 0.2 - - - -
162B TYR* 3.5 24.1 + - + -
163B GLY 5.0 0.5 + - - -
182B HIS* 3.9 27.1 + - + +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PRO* 5.9 2.1 - - - +
95B PHE* 3.8 12.0 - - + -
156B ALA* 4.4 4.9 - - + +
157B PRO* 3.0 37.0 + - - +
159B ALA* 1.3 80.0 - - - +
161B GLY* 1.3 59.8 + - - +
162B TYR 3.7 0.2 - - - -
163B GLY* 4.9 2.1 + - - -
164B LEU* 3.8 18.2 - - - +
210B PHE* 4.9 10.7 - - + -
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 5.4 0.3 - - - +
95B PHE* 3.4 24.8 - - - -
100B VAL* 3.3 16.8 - - - +
158B ALA 2.8 10.7 + - - -
160B ASP* 1.3 78.5 - - - +
162B TYR* 1.3 64.0 + - - -
163B GLY 3.2 2.9 - - - -
164B LEU* 2.8 18.2 + - - +
165B ALA 3.1 9.2 + - - -
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP 3.5 22.2 + - - -
100B VAL* 3.9 17.3 - - - -
158B ALA* 3.2 26.0 + - + +
159B ALA* 3.5 30.2 + - + -
160B ASP 3.7 1.0 - - - -
161B GLY* 1.3 75.1 - - - +
163B GLY* 1.3 58.2 + - - +
165B ALA* 3.2 23.0 + - - +
174B TRP* 3.7 6.8 - - - -
178B PRO* 3.6 35.2 - - + +
179B TRP* 3.7 20.4 - + + -
182B HIS* 3.8 35.7 - + + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ALA 5.0 0.4 + - - -
160B ASP 4.9 2.9 + - - -
161B GLY 3.2 0.8 - - - -
162B TYR* 1.3 77.9 - - - +
164B LEU* 1.3 61.0 + - - +
165B ALA 3.5 0.4 - - - -
174B TRP* 4.3 2.7 - - - -
182B HIS* 3.4 31.7 - - - +
184B PRO* 3.5 24.8 - - - +
203B THR* 4.8 2.3 + - - -
206B LEU* 4.1 11.6 - - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ILE* 6.0 0.7 - - + -
40B ASN* 5.3 0.3 - - - -
41B LEU* 3.7 16.9 + - + +
59B TYR* 4.1 10.0 + - - +
95B PHE* 4.3 7.4 - - + -
100B VAL* 5.3 0.2 - - - -
116B LEU* 4.0 16.4 - - + -
160B ASP 3.8 18.8 - - - +
161B GLY* 2.8 10.1 + - - +
163B GLY* 1.3 78.0 - - - +
165B ALA* 1.3 65.4 - - - +
166B GLY* 3.0 7.0 + - - -
203B THR* 4.3 11.6 - - + +
206B LEU* 3.7 19.3 - - + +
207B GLY* 3.5 33.0 - - - +
210B PHE* 4.0 24.7 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.7 2.4 - - - +
42B TYR* 2.9 32.4 + - - +
100B VAL* 4.2 6.5 - - + -
101B LEU* 3.8 15.6 - - + +
161B GLY 3.1 6.9 + - - +
162B TYR 3.2 16.0 + - - +
163B GLY 3.5 0.8 - - - -
164B LEU* 1.3 78.8 - - - +
166B GLY* 1.3 58.0 + - - +
167B PHE* 3.4 32.3 - - + -
174B TRP* 4.3 2.0 - - + -
179B TRP* 4.1 7.0 - - + +
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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