Contacts of the helix formed by residues 133 - 143 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.5 8.3 - - + -
128B ALA* 2.8 30.2 + - + +
129B ILE* 4.4 0.9 - - + -
132B TYR* 1.3 78.0 - - + +
134B PRO* 1.3 66.0 - - + +
136B PHE* 3.3 6.4 + + - -
137B GLU* 2.8 32.6 + - - +
160B LEU* 4.6 6.7 - - + -
163B THR* 5.8 0.2 - - + -
164B ILE* 3.8 28.9 - - + -
167B LEU* 3.8 26.7 - - + -
174B ILE* 3.9 27.4 - - + -
175B LEU* 3.6 22.9 - - + -
178B PHE* 3.7 25.6 - + + -
181B LEU* 3.5 20.4 - - + +
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Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA 3.4 2.0 - - - +
129B ILE 2.9 30.3 - - - +
130B ILE* 3.7 14.6 - - - +
132B TYR 3.3 5.4 - - - +
133B PHE* 1.3 99.5 - - + +
135B VAL* 1.3 62.6 + - + +
137B GLU* 3.9 2.9 - - + +
138B LYS* 3.1 24.9 + - - +
178B PHE* 3.8 13.2 - - + -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.4 48.5 - - + +
52A PHE* 4.1 16.4 - - + -
95B TYR* 5.3 0.2 - - + -
131B ARG 3.6 20.9 - - - +
132B TYR 2.9 6.6 + - - +
134B PRO* 1.3 76.2 - - + +
136B PHE* 1.3 71.9 + - + +
138B LYS* 3.4 4.9 + - - +
139B ILE* 3.0 38.9 + - + +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 4.0 22.9 - + - -
95B TYR* 4.0 29.6 - + + -
99B THR* 3.6 25.1 - - + -
102B LEU* 6.3 0.2 - - + -
132B TYR* 3.2 39.3 - + + -
133B PHE* 3.3 6.3 + + - +
135B VAL* 1.3 81.1 - - + +
137B GLU* 1.3 68.2 + - - +
139B ILE* 3.0 18.6 + - + +
140B LEU* 3.0 20.9 + - - +
148B LEU* 3.9 23.3 - - + -
160B LEU* 3.8 28.5 - - + -
181B LEU* 3.9 18.6 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE 2.8 18.4 + - - +
134B PRO* 3.9 4.7 - - + +
136B PHE* 1.3 76.4 - - - +
138B LYS* 1.3 57.8 + - - +
140B LEU* 3.6 2.2 - - - +
141B ARG* 2.8 35.3 + - + +
177B ALA 4.4 0.7 - - - +
178B PHE* 3.2 29.7 - - + +
179B PRO* 3.2 15.9 - - - +
180B PHE* 3.0 39.2 + - + +
181B LEU* 2.7 34.6 + - + +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 5.9 5.5 - - - +
134B PRO 3.1 17.6 + - - +
135B VAL* 3.8 5.2 - - - +
136B PHE 3.1 0.2 - - - -
137B GLU* 1.3 81.9 - - - +
139B ILE* 1.3 65.6 + - + +
141B ARG* 3.8 6.8 - - - +
142B GLY* 2.8 19.3 + - - -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 5.8 0.9 - - + -
95B TYR* 3.2 39.9 - - + +
135B VAL* 3.0 26.1 + - + +
136B PHE* 3.0 19.5 + - + +
138B LYS* 1.3 79.1 - - + +
140B LEU* 1.3 59.8 + - - +
142B GLY* 3.0 15.1 + - - -
143B HIS* 3.2 23.8 + - + +
148B LEU* 3.6 33.9 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE 3.0 16.5 + - - +
137B GLU 3.6 2.9 - - - +
139B ILE* 1.3 77.9 - - - +
141B ARG* 1.3 60.5 - - - +
142B GLY 3.0 1.8 - - - -
143B HIS* 3.6 13.3 + - + -
144B GLY* 2.9 31.7 + - - -
145B GLN 3.8 18.3 - - - +
147B PHE 4.3 4.3 - - - +
148B LEU* 4.2 11.9 - - + -
180B PHE* 4.2 23.1 - - + +
181B LEU* 3.8 19.7 - - + -
184B TYR* 3.7 50.3 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU* 2.8 22.6 + - - +
138B LYS* 3.9 7.9 - - - +
140B LEU* 1.3 77.8 - - - +
142B GLY* 1.3 64.8 + - - +
143B HIS 3.3 0.5 + - - -
144B GLY* 4.1 3.5 + - - -
180B PHE* 3.5 44.8 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS 2.8 15.7 + - - -
139B ILE 3.0 5.1 + - - -
140B LEU 3.0 0.4 - - - -
141B ARG* 1.3 85.3 - - - +
143B HIS* 1.3 57.6 + - - +
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Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 3.2 17.1 + - + +
140B LEU* 3.6 18.1 + - + -
142B GLY* 1.3 77.0 - - - +
144B GLY* 1.3 61.6 + - - +
145B GLN* 2.7 66.4 + - + +
147B PHE 3.0 28.5 + - - -
148B LEU 3.3 18.6 + - - -
149B VAL* 5.2 0.9 - - - -
150B 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