Contacts of the helix formed by residues 133 - 143 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU* 4.5 8.5 - - + -
128H ALA* 2.8 29.5 + - + +
129H ILE* 4.4 1.1 - - + -
132H TYR* 1.3 77.5 - - + +
134H PRO* 1.3 66.7 - - + +
136H PHE* 3.3 6.7 + + - -
137H GLU* 2.8 32.9 + - - +
160H LEU* 4.6 6.7 - - + -
164H ILE* 3.8 29.8 - - + -
167H LEU* 3.8 26.5 - - + -
174H ILE* 3.9 26.7 - - + -
175H LEU* 3.6 23.8 - - + -
178H PHE* 3.7 25.1 - + + -
181H LEU* 3.5 20.1 - - + +
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Residues in contact with PRO 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H ALA 3.4 2.2 - - - +
129H ILE 2.9 29.8 - - - +
130H ILE* 3.7 15.3 - - - +
132H TYR 3.3 5.6 - - - +
133H PHE* 1.3 99.2 - - + +
135H VAL* 1.3 62.0 + - + +
137H GLU* 3.9 2.9 - - + +
138H LYS* 3.1 25.1 + - - +
178H PHE* 3.8 13.0 - - + -
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Residues in contact with VAL 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 3.5 47.6 - - + +
52G PHE* 4.0 17.5 - - + -
95H TYR* 5.3 0.4 - - + -
131H ARG 3.6 21.3 - - - +
132H TYR 2.9 7.1 + - - +
134H PRO* 1.3 78.1 - - + +
136H PHE* 1.3 71.2 + - + +
138H LYS* 3.4 4.7 + - - +
139H ILE* 3.0 39.3 + - + +
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Residues in contact with PHE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G PHE* 4.0 22.4 - + - -
95H TYR* 4.0 31.4 - + + -
99H THR* 3.6 24.9 - - + -
102H LEU* 6.3 0.4 - - + -
132H TYR* 3.2 38.4 - + + -
133H PHE* 3.3 6.0 + + - +
135H VAL* 1.3 80.9 - - + +
137H GLU* 1.3 66.0 + - - +
139H ILE* 3.0 19.0 + - + +
140H LEU* 3.0 21.2 + - - +
148H LEU* 3.9 23.6 - - + -
160H LEU* 3.8 28.9 - - + -
181H LEU* 3.9 18.4 - - + -
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Residues in contact with GLU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H PHE 2.8 18.2 + - - +
134H PRO* 3.9 4.3 - - + +
136H PHE* 1.3 76.8 - - - +
138H LYS* 1.3 57.4 + - - +
140H LEU* 3.4 2.2 + - - +
141H ARG* 2.8 34.6 + - + +
177H ALA 4.4 1.1 - - - +
178H PHE* 3.2 29.1 - - + +
179H PRO* 3.2 15.8 - - - +
180H PHE* 3.0 39.1 + - + +
181H LEU* 2.7 34.6 + - + +
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Residues in contact with LYS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASN* 5.8 6.5 - - - +
134H PRO 3.1 17.6 + - - +
135H VAL* 3.8 4.5 - - - +
136H PHE 3.1 0.2 - - - -
137H GLU* 1.3 80.6 - - - +
139H ILE* 1.3 66.1 + - + +
141H ARG* 3.9 7.7 - - - +
142H GLY* 2.8 19.8 + - - -
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Residues in contact with ILE 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 5.8 1.3 - - + -
95H TYR* 3.2 40.6 - - + +
135H VAL* 3.0 29.0 + - + +
136H PHE* 3.0 18.9 + - + +
138H LYS* 1.3 78.2 - - + +
140H LEU* 1.3 60.2 + - - +
142H GLY* 3.0 14.8 + - - -
143H HIS* 3.2 24.3 + - + +
148H LEU* 3.6 34.8 - - + +
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H PHE 3.0 16.1 + - - +
137H GLU 3.6 2.9 - - - +
139H ILE* 1.3 78.1 - - - +
141H ARG* 1.3 61.2 - - - +
142H GLY 3.0 1.6 - - - -
143H HIS* 3.6 13.0 + - + -
144H GLY* 2.9 31.2 + - - -
145H GLN 3.8 18.6 - - - +
147H PHE 4.3 4.7 - - - +
148H LEU* 4.2 11.9 - - + -
180H PHE* 4.2 24.2 - - + +
181H LEU* 3.8 19.3 - - + -
184H TYR* 3.7 50.5 - - + -
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Residues in contact with ARG 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H GLU* 2.8 23.1 + - + +
138H LYS* 3.9 7.2 - - - +
140H LEU* 1.3 78.0 - - - +
142H GLY* 1.3 64.3 + - - +
143H HIS 3.3 0.7 + - - -
144H GLY* 4.1 3.6 + - - -
180H PHE* 3.5 45.0 - - + -
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Residues in contact with GLY 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H LYS 2.8 15.5 + - - -
139H ILE 3.0 6.3 + - - -
140H LEU 3.0 0.4 - - - -
141H ARG* 1.3 83.6 - - - +
143H HIS* 1.3 58.3 + - - +
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Residues in contact with HIS 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H ILE* 3.2 17.8 + - + +
140H LEU* 3.6 17.9 + - + -
142H GLY* 1.3 77.1 - - - +
144H GLY* 1.3 62.3 + - - +
145H GLN* 2.7 67.4 + - + +
147H PHE 3.0 28.5 + - - -
148H LEU 3.3 19.0 + - - -
149H VAL* 5.2 1.1 - - - -
150H 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