Contacts of the helix formed by residues 133 - 143 (chain F) in PDB entry 1GUL
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 133 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.5 9.2 - - + -
128F ALA* 2.8 28.5 + - + +
129F ILE* 4.4 0.7 - - + -
132F TYR* 1.3 77.9 - - + +
134F PRO* 1.3 65.7 - - + +
136F PHE* 3.3 6.4 + + - -
137F GLU* 2.8 32.9 + - - +
160F LEU* 4.6 6.3 - - + -
163F THR* 5.8 0.2 - - + -
164F ILE* 3.8 28.9 - - + -
167F LEU* 3.8 27.8 - - + -
174F ILE* 3.9 26.2 - - + -
175F LEU* 3.6 22.7 - - + -
178F PHE* 3.7 25.6 - + + -
181F LEU* 3.5 19.1 - - + +
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Residues in contact with PRO 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ALA 3.4 1.8 - - - +
129F ILE 2.9 30.3 - - - +
130F ILE* 3.7 14.8 - - - +
132F TYR 3.3 6.1 - - - +
133F PHE* 1.3 99.5 - - + +
135F VAL* 1.3 62.0 + - + +
137F GLU* 3.9 3.3 - - + +
138F LYS* 3.1 24.9 + - - +
178F PHE* 3.8 13.0 - - + -
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Residues in contact with VAL 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.4 48.9 - - + +
52E PHE* 3.9 18.8 - - + -
95F TYR* 5.3 0.2 - - + -
131F ARG 3.6 21.1 - - - +
132F TYR 2.9 6.9 + - - +
134F PRO* 1.3 76.7 - - + +
136F PHE* 1.3 70.8 + - + +
138F LYS* 3.4 5.3 + - - +
139F ILE* 3.0 39.9 + - + +
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Residues in contact with PHE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E PHE* 3.9 23.6 - + - -
95F TYR* 4.0 30.7 - + + -
99F THR* 3.6 24.2 - - + -
102F LEU* 6.3 0.7 - - + -
132F TYR* 3.2 39.3 - + + -
133F PHE* 3.3 6.4 + + - +
135F VAL* 1.3 80.4 - - + +
137F GLU* 1.3 66.8 + - - +
139F ILE* 3.0 19.2 + - + +
140F LEU* 3.0 20.7 + - - +
148F LEU* 3.9 23.6 - - + -
160F LEU* 3.8 27.8 - - + -
181F LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE 2.8 18.9 + - - +
134F PRO* 3.9 4.3 - - + +
136F PHE* 1.3 77.5 - - - +
138F LYS* 1.3 58.1 + - - +
140F LEU* 3.4 2.1 + - - +
141F ARG* 2.8 35.2 + - + +
177F ALA 4.4 1.0 - - - +
178F PHE* 3.2 29.0 - - + +
179F PRO* 3.2 15.8 - - - +
180F PHE* 3.0 40.6 + - + +
181F LEU* 2.7 33.9 + - + +
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Residues in contact with LYS 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ASN* 5.6 9.3 - - - +
134F PRO 3.1 17.1 + - - +
135F VAL* 3.8 5.6 - - - +
136F PHE 3.1 0.2 - - - -
137F GLU* 1.3 81.2 - - - +
139F ILE* 1.3 66.3 + - + +
141F ARG* 3.9 6.4 - - - +
142F GLY* 2.8 19.4 + - - -
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 5.7 1.1 - - + -
95F TYR* 3.2 40.8 - - + +
135F VAL* 3.0 26.1 + - + +
136F PHE* 3.0 18.7 + - + +
138F LYS* 1.3 78.7 - - + +
140F LEU* 1.3 59.3 + - - +
142F GLY* 3.0 14.2 + - - -
143F HIS* 3.2 24.6 + - + +
148F LEU* 3.6 35.0 - - + +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F PHE 3.0 15.9 + - - +
137F GLU 3.6 3.4 - - - +
139F ILE* 1.3 78.7 - - - +
141F ARG* 1.3 61.0 + - - +
142F GLY 3.0 1.6 - - - -
143F HIS* 3.6 13.9 + - + -
144F GLY* 2.9 31.2 + - - -
145F GLN 3.8 19.0 - - - +
147F PHE 4.3 3.8 - - - +
148F LEU* 4.2 11.7 - - + -
180F PHE* 4.2 24.0 - - + +
181F LEU* 3.8 19.7 - - + -
184F TYR* 3.7 49.8 - - + -
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Residues in contact with ARG 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F GLU* 2.8 22.6 + - - +
138F LYS* 3.9 7.4 - - - +
140F LEU* 1.3 77.8 - - - +
142F GLY* 1.3 65.3 + - - +
143F HIS 3.3 0.5 + - - -
144F GLY* 4.1 3.8 + - - -
180F PHE* 3.5 44.4 - - + -
46H ASP* 3.0 42.2 + - - -
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Residues in contact with GLY 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F LYS* 2.8 16.7 + - - -
139F ILE 3.0 5.6 + - - -
140F LEU 3.0 0.4 - - - -
141F ARG* 1.3 83.8 - - - +
143F HIS* 1.3 57.9 + - - +
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Residues in contact with HIS 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F ILE* 3.2 17.4 + - + +
140F LEU* 3.6 17.9 + - + -
142F GLY* 1.3 76.8 - - - +
144F GLY* 1.3 60.7 + - - +
145F GLN* 2.7 65.8 + - + +
147F PHE 3.0 28.9 + - - -
148F LEU 3.3 18.5 + - - -
149F VAL* 5.7 0.9 - - - -
150F GLY 6.2 0.4 - - - -
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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