Contacts of the helix formed by residues 141 - 152 (chain O) in PDB entry 3L73
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 GLN 141 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68O LEU* 3.9 24.5 - - + -
137O VAL* 3.2 26.0 + - - +
138O THR* 4.1 8.7 + - - +
140O LEU* 1.3 76.7 - - - +
142O PRO* 1.3 64.2 - - + +
143O GLN 2.7 6.6 + - - -
144O LEU* 2.8 23.0 + - + +
183O ILE* 3.7 6.6 - - - +
184O GLY* 2.8 51.4 + - - +
186O ILE* 2.9 47.2 + - - +
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Residues in contact with PRO 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O THR 3.3 12.6 - - - +
139O ASP* 3.1 20.4 - - - +
140O LEU 3.1 2.7 - - - -
141O GLN* 1.3 90.9 - - + +
143O GLN* 1.3 60.1 + - + +
144O LEU 3.3 0.2 - - - -
145O LYS* 3.3 22.8 - - + +
146O VAL* 3.9 6.6 + - - +
183O ILE* 4.7 7.9 - - + -
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Residues in contact with GLN 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N ARG* 3.3 23.3 + - - +
283N THR* 4.5 10.5 + - - +
284N PHE 4.9 4.4 + - - -
285N GLY* 5.6 3.2 - - - -
71O LEU* 3.9 19.5 - - + -
139O ASP 5.7 0.2 - - - +
140O LEU* 2.7 30.7 + - + +
141O GLN 2.7 4.8 + - - -
142O PRO* 1.3 74.0 - - + +
144O LEU* 1.3 63.2 + - - +
145O LYS 3.0 2.2 - - - -
146O VAL* 2.9 29.7 + - - +
147O ASP* 2.8 27.9 + - + +
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Residues in contact with LEU 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O HIS* 3.6 31.7 - - + +
68O LEU* 3.8 23.6 - - + -
71O LEU* 3.3 26.2 - - + -
141O GLN* 2.8 21.0 + - - +
143O GLN* 1.3 76.5 - - - +
145O LYS* 1.3 63.5 + - - +
147O ASP* 4.5 0.7 - - - -
148O LYS* 3.0 29.3 + - - +
178O CYS* 4.0 14.1 - - - -
183O ILE* 3.2 32.3 - - + +
186O ILE* 4.0 17.9 - - + -
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Residues in contact with LYS 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141O GLN 4.1 0.2 + - - -
142O PRO* 3.3 16.8 + - + +
143O GLN 3.0 0.2 - - - -
144O LEU* 1.3 79.6 - - - +
146O VAL* 1.3 57.6 + - + +
148O LYS* 3.9 4.7 - - - +
149O ALA* 3.2 25.6 + - - +
183O ILE* 4.2 20.7 - - + +
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Residues in contact with VAL 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N ARG* 4.1 49.1 - - + +
283N THR* 5.2 3.1 - - + -
142O PRO 4.5 7.2 - - - +
143O GLN* 2.9 28.6 + - - +
145O LYS* 1.3 74.4 - - + +
147O ASP* 1.3 61.1 + - - +
148O LYS 3.1 1.6 - - - -
149O ALA* 2.6 32.8 + - - +
150O VAL* 3.2 17.0 + - + +
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Residues in contact with ASP 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283N THR* 5.0 5.0 - - - +
67O HIS* 3.0 23.5 + - - +
70O ARG* 4.2 2.8 + - - -
71O LEU* 3.8 24.9 - - + +
143O GLN* 2.8 22.5 + - + +
144O LEU 4.1 1.8 - - - +
146O VAL* 1.3 77.3 - - - +
148O LYS* 1.3 62.4 + - - +
150O VAL* 3.4 22.2 - - - +
151O ALA* 3.4 7.6 + - - +
177O TYR* 4.0 11.2 - - - -
68V ILE* 3.6 22.8 - - - +
74V ALA* 3.8 14.7 - - - +
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Residues in contact with LYS 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O HIS* 4.4 7.6 - - + -
144O LEU 3.0 19.0 + - - +
145O LYS* 3.9 4.5 - - - +
147O ASP* 1.3 79.8 + - - +
149O ALA* 1.3 61.6 + - - +
151O ALA* 3.4 1.0 + - - +
152O PHE* 3.1 59.6 + - + +
177O TYR* 3.7 24.6 + - + -
178O CYS 2.9 30.5 + - - +
179O PRO* 3.6 10.9 - - - +
180O ASP* 3.1 26.2 + - - +
183O ILE* 5.5 3.1 - - + -
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Residues in contact with ALA 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145O LYS 3.2 14.7 + - - +
146O VAL* 2.6 21.2 + - - +
148O LYS* 1.3 70.3 - - - +
150O VAL* 1.3 63.5 + - + +
152O PHE* 3.7 6.7 + - - +
153O GLN* 3.2 19.6 + - - +
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Residues in contact with VAL 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N ARG* 5.3 9.6 - - + +
283N THR* 4.6 15.7 - - + -
146O VAL* 3.2 18.4 + - + +
147O ASP 3.4 11.7 - - - +
149O ALA* 1.3 75.2 - - + +
151O ALA* 1.3 71.4 + - + +
153O GLN* 2.8 42.7 + - - +
154O SER* 4.6 1.6 + - - -
74V ALA* 4.2 25.8 - - + +
76V VAL* 5.7 0.3 - - - +
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Residues in contact with ALA 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147O ASP 3.4 8.0 + - - +
148O LYS 3.6 8.3 - - - +
149O ALA 3.3 0.2 - - - -
150O VAL* 1.3 85.7 - - + +
152O PHE* 1.3 58.7 + - + +
153O GLN 2.8 6.8 + - - -
154O SER* 3.3 12.1 + - - -
157O VAL* 3.0 19.4 - - + +
177O TYR* 3.6 40.6 - - + +
75V SER 6.0 0.2 - - - +
76V VAL* 4.7 15.2 - - + +
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Residues in contact with PHE 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O LYS* 3.1 48.7 + - + +
149O ALA* 4.0 7.9 - - - +
150O VAL 3.3 0.6 - - - -
151O ALA* 1.3 78.4 - - + +
153O GLN* 1.3 61.8 + - - +
154O SER 3.2 5.2 - - - +
155O PRO* 4.8 1.7 - - - +
157O VAL* 3.4 12.8 - - + -
158O GLY* 4.5 17.7 - - - -
161O GLU* 4.0 24.9 - - + -
162O ASN* 6.1 1.3 - - - -
177O TYR* 3.8 24.9 - + - -
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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