Contacts of the helix formed by residues 141 - 151 (chain C) in PDB entry 3A13
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 PHE 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C ALA* 1.3 91.7 - - + +
142C GLY* 1.3 63.8 + - - +
144C GLU* 4.2 0.9 + - - +
145C GLY* 2.8 40.9 + - - -
146C VAL* 4.2 3.1 - - + -
149C MET* 3.6 29.8 - - + -
272C ALA* 5.7 1.6 - - - -
275C GLY* 3.5 27.4 - - - -
276C LEU 3.7 8.7 - - - -
277C ALA* 3.7 35.2 - - + -
311C ASP* 2.8 14.7 + - - +
360C LYS* 3.9 14.2 + - - +
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Residues in contact with GLY 142 (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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139C PRO* 3.5 14.7 - - - +
141C PHE* 1.3 76.7 - - - +
143C ILE* 1.3 67.5 + - - -
144C GLU 3.4 0.4 - - - -
146C VAL* 3.0 22.0 + - - +
311C ASP* 2.7 24.5 + - - -
360C LYS* 4.5 5.2 - - - -
361C ALA 3.0 15.3 - - - -
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Residues in contact with ILE 143 (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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142C GLY* 1.3 70.3 - - - -
144C GLU* 1.3 67.1 + - - +
146C VAL* 3.0 2.8 + - - +
147C ARG* 2.8 49.0 + - - +
338C ARG* 3.7 26.7 - - + -
361C ALA* 2.8 23.9 + - + +
362C ALA* 3.6 24.2 - - - +
363C PHE* 3.7 34.3 - - + -
385C ASP* 4.1 21.1 - - + +
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Residues in contact with GLU 144 (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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141C PHE 4.8 1.3 - - - +
142C GLY 3.4 0.4 - - - -
143C ILE* 1.3 81.0 - - - +
145C GLY* 1.3 58.3 + - - +
147C ARG* 3.9 5.7 - - - +
148C LYS* 3.0 30.7 + - - +
360C LYS* 6.0 4.5 - - + +
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Residues in contact with GLY 145 (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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141C PHE* 2.8 48.8 + - - -
144C GLU* 1.3 75.3 - - - +
146C VAL* 1.3 58.0 + - - +
148C LYS* 3.6 5.8 + - - +
149C MET* 3.1 25.6 + - - +
360C LYS* 5.9 0.9 - - - -
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Residues in contact with VAL 146 (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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141C PHE* 4.2 12.6 - - + -
142C GLY 3.0 19.1 + - - +
143C ILE 3.0 4.0 + - - +
145C GLY* 1.3 73.6 - - - +
147C ARG* 1.3 68.0 + - - +
148C LYS 3.1 1.3 - - - -
149C MET* 3.2 7.0 + - + +
150C LEU* 3.0 42.7 + - + +
157C ILE* 5.2 2.7 - - + -
251C HIS* 4.3 11.0 - - + +
277C ALA* 4.3 6.5 - - + -
311C ASP* 4.7 2.9 - - + -
312C GLN* 3.4 35.2 - - + +
363C PHE* 3.9 20.0 - - + -
387C VAL* 6.0 0.2 - - + -
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Residues in contact with ARG 147 (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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143C ILE* 2.8 25.7 + - - +
144C GLU* 3.9 5.6 - - - +
146C VAL* 1.3 76.0 - - - +
148C LYS* 1.3 56.6 + - - +
150C LEU* 4.9 2.2 - - - -
151C GLU* 2.9 24.6 + - - -
152C ILE* 2.9 39.6 + - - +
153C LYS* 3.4 27.3 + - - +
154C ASP 3.4 4.6 + - - -
155C ARG 3.0 28.9 + - - -
156C PRO* 4.4 0.6 - - - +
157C ILE* 4.2 7.1 - - + +
363C PHE* 4.0 22.6 - - + -
384C THR 3.1 15.6 + - - -
385C ASP* 2.7 35.5 + - - +
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Residues in contact with LYS 148 (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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144C GLU 3.0 19.9 + - - +
145C GLY* 3.7 7.4 - - - +
147C ARG* 1.3 75.6 - - - +
149C MET* 1.3 65.8 + - - +
151C GLU* 3.3 20.5 + - - +
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Residues in contact with MET 149 (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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141C PHE* 3.6 38.4 - - + -
145C GLY 3.1 11.7 + - - +
146C VAL* 3.2 12.3 + - - +
148C LYS* 1.3 77.1 - - - +
150C LEU* 1.3 75.5 + - + +
151C GLU* 4.5 0.2 - - - +
223C LYS* 3.5 22.2 - - - +
250C LYS* 3.5 45.0 + - + +
251C HIS* 3.6 18.2 - - + -
275C GLY 5.6 0.4 - - - +
277C ALA* 3.8 18.8 - - + -
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Residues in contact with LEU 150 (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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146C VAL* 3.0 31.9 + - + +
147C ARG* 4.3 1.8 - - - +
149C MET* 1.3 90.2 - - + +
151C GLU* 1.3 69.2 + - - +
152C ILE* 3.2 24.4 - - + +
157C ILE* 3.8 31.6 - - + -
186C ASP* 4.8 4.9 - - + +
223C LYS* 3.4 28.1 + - + +
224C LYS* 4.1 19.3 - - - +
225C THR* 4.1 29.4 - - + -
227C PHE* 6.1 1.1 - - + -
250C LYS* 4.9 1.6 - - - +
251C HIS* 5.1 1.3 - - + -
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Residues in contact with GLU 151 (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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147C ARG 2.9 10.9 + - - -
148C LYS* 3.3 14.8 + - - +
149C MET 4.5 0.6 - - - +
150C LEU* 1.3 79.8 - - - +
152C ILE* 1.3 59.2 + - - +
153C LYS 4.1 1.0 + - - -
221C GLY 5.2 5.2 - - - +
223C LYS* 3.4 33.1 + - + +
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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