Contacts of the helix formed by residues 148 - 156 (chain A) in PDB entry 1YSD
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TYR* 6.0 1.2 - - - -
29A GLY* 2.9 35.4 + - - -
54A PHE* 3.4 27.7 - - - -
144A PHE* 2.8 48.1 + - + +
145A ILE 4.4 0.2 - - - -
147A GLU* 1.3 93.3 + - + +
149A PRO* 1.3 65.0 - - - +
150A GLN* 3.3 2.5 - - - -
151A ASP* 2.6 45.4 + - + +
152A TRP* 3.2 10.4 + - - +
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.1 26.6 - - + +
146A ASP 3.8 6.5 - - - +
147A GLU 3.4 8.3 - - - +
148A ARG* 1.3 87.9 - - - +
150A GLN* 1.3 66.0 + - + +
152A TRP* 3.2 8.5 + - + +
153A PHE* 2.9 40.5 + - + -
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG 3.3 1.0 - - - -
149A PRO* 1.3 87.0 - - + +
151A ASP* 1.3 62.0 + - - +
153A PHE* 3.4 26.6 + - - +
154A GLU* 3.0 26.9 + - - +
158A GLU* 5.4 2.6 - - - +
275B GLU* 4.7 10.4 - - - +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.8 0.5 - - - +
53A ARG* 4.8 0.3 - - - -
54A PHE* 3.2 36.3 - - + -
144A PHE* 3.8 14.1 - - + -
148A ARG* 2.6 45.9 + - - +
150A GLN* 1.3 76.5 - - - +
152A TRP* 1.3 67.9 + - - +
154A GLU* 3.4 8.9 + - - +
155A ASP* 3.3 17.7 + - - +
273B ARG* 4.6 4.2 + - - -
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Residues in contact with TRP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.5 3.8 - - + -
33A ILE* 3.9 15.9 - - + -
88A LEU* 3.8 19.1 - - + -
113A ASN 4.5 5.5 + - - -
114A PHE* 3.7 34.8 - + + -
141A MET* 3.4 23.8 - - + -
144A PHE* 3.9 12.5 - - + -
145A ILE* 3.7 39.2 - - + +
148A ARG 3.2 11.0 + - - +
149A PRO* 3.2 9.3 + - + +
151A ASP* 1.3 77.8 - - - +
153A PHE* 1.3 83.5 + + - +
155A ASP* 3.0 28.0 + - + +
156A ILE* 3.5 32.2 + - + +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 5.9 1.8 - - + -
149A PRO* 2.9 25.7 + - + +
150A GLN* 3.6 31.0 - - - +
152A TRP* 1.3 97.5 - + - +
154A GLU* 1.3 60.6 + - - +
156A ILE* 3.0 16.7 + - + +
158A GLU* 2.8 62.1 + - + +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ARG* 2.7 32.8 + - - +
54A PHE* 5.2 0.7 - - - -
150A GLN 3.0 14.0 + - - +
151A ASP* 3.6 13.9 - - - +
152A TRP 3.2 0.4 - - - -
153A PHE* 1.3 75.2 - - - +
155A ASP* 1.3 62.7 + - - +
157A GLY* 3.1 13.6 + - - +
158A GLU 4.2 5.8 + - - -
273B ARG* 2.7 50.6 + - - +
274B LEU 3.6 24.7 - - - +
275B GLU* 4.8 13.1 - - - +
276B GLY 5.2 2.5 - - - +
301B TYR* 4.3 4.0 - - - -
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.2 12.0 - - + +
33A ILE* 4.2 5.5 - - - +
51A ASN* 2.8 33.0 + - - -
53A ARG* 2.8 32.9 + - - +
62A HIS* 2.7 50.2 + - - -
151A ASP 3.3 7.4 + - - +
152A TRP* 3.0 32.8 + - + +
154A GLU* 1.3 78.6 - - - +
156A ILE* 1.3 58.1 + - - +
157A GLY 3.5 0.4 + - - -
300B MET* 4.1 3.5 - - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 4.9 7.0 - - + -
91A CYS* 5.2 3.1 - - + -
114A PHE* 3.9 32.3 - - + -
152A TRP* 3.7 52.5 - - + +
153A PHE* 3.0 16.1 + - + +
155A ASP* 1.3 82.1 - - - +
157A GLY* 1.3 62.2 + - - +
158A GLU* 3.2 28.1 + - + +
300B MET* 3.8 26.2 - - + +
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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