Contacts of the helix formed by residues 133 - 143 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.5 9.0 - - + -
128D ALA* 2.8 30.4 + - + +
129D ILE* 4.4 1.1 - - + -
132D TYR* 1.3 78.1 - - + +
134D PRO* 1.3 65.4 - - + +
136D PHE* 3.3 6.0 + + - -
137D GLU* 2.8 33.1 + - - +
160D LEU* 4.6 5.8 - - + -
163D THR* 5.8 0.2 - - + -
164D ILE* 3.8 29.4 - - + -
167D LEU* 3.8 25.4 - - + -
174D ILE* 3.9 27.1 - - + -
175D LEU* 3.6 22.7 - - + -
178D PHE* 3.7 25.4 - + + -
181D LEU* 3.5 20.4 - - + +
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Residues in contact with PRO 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA 3.4 2.2 - - - +
129D ILE 2.9 30.3 - - - +
130D ILE* 3.7 15.0 - - - +
132D TYR 3.3 6.1 - - - +
133D PHE* 1.3 98.2 - - + +
135D VAL* 1.3 63.1 + - + +
137D GLU* 3.9 3.2 - - + +
138D LYS* 3.1 25.1 + - - +
178D PHE* 3.8 12.8 - - + -
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.5 48.5 - - + +
52C PHE* 4.1 15.9 - - + -
95D TYR* 5.3 0.7 - - + -
131D ARG 3.6 20.6 - - - +
132D TYR 2.9 6.7 + - - +
134D PRO* 1.3 77.3 - - + +
136D PHE* 1.3 71.6 + - + +
138D LYS* 3.4 4.9 + - - +
139D ILE* 3.0 40.3 + - + +
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PHE* 4.1 22.0 - + - -
95D TYR* 4.0 30.3 - + + -
99D THR* 3.6 24.9 - - - -
102D LEU* 6.3 0.4 - - + -
132D TYR* 3.2 37.5 - + + -
133D PHE* 3.3 7.3 + + - +
135D VAL* 1.3 82.4 - - + +
137D GLU* 1.3 66.7 + - - +
139D ILE* 3.0 19.7 + - + +
140D LEU* 3.0 20.6 + - - +
148D LEU* 3.9 24.2 - - + -
160D LEU* 3.8 27.8 - - + -
181D LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE 2.8 18.4 + - - +
134D PRO* 3.9 4.5 - - + +
136D PHE* 1.3 75.8 - - - +
138D LYS* 1.3 58.1 + - - +
140D LEU* 3.4 2.5 + - - +
141D ARG* 2.8 35.6 + - + +
177D ALA 4.4 0.5 - - - +
178D PHE* 3.2 30.4 - - + +
179D PRO* 3.2 15.8 - - - +
180D PHE* 3.0 38.6 + - + +
181D LEU* 2.7 34.8 + - + +
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Residues in contact with LYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 6.1 2.4 - - - +
134D PRO 3.1 17.1 + - - +
135D VAL* 3.8 4.9 - - - +
137D GLU* 1.3 80.4 - - - +
139D ILE* 1.3 66.3 + - + +
141D ARG* 3.8 7.1 - - - +
142D GLY* 2.8 19.2 + - - -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 5.9 0.7 - - + -
95D TYR* 3.2 41.1 - - + +
135D VAL* 3.0 26.7 + - + +
136D PHE* 3.0 19.6 + - + +
138D LYS* 1.3 77.8 - - + +
140D LEU* 1.3 58.8 + - - +
142D GLY* 3.0 14.7 + - - -
143D HIS* 3.2 25.0 + - + +
148D LEU* 3.6 35.2 - - + +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D PHE 3.0 15.8 + - - +
137D GLU 3.6 3.1 - - - +
139D ILE* 1.3 77.5 - - - +
141D ARG* 1.3 62.5 + - - +
142D GLY 3.0 0.9 - - - -
143D HIS* 3.6 13.5 + - + -
144D GLY* 2.9 31.4 + - - -
145D GLN 3.8 18.8 - - - +
147D PHE 4.3 4.0 - - - +
148D LEU* 4.2 11.2 - - + -
180D PHE* 4.2 23.0 - - + +
181D LEU* 3.8 19.5 - - + -
184D TYR* 3.7 50.5 - - + -
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLU* 2.8 22.4 + - - +
138D LYS* 3.9 7.6 - - - +
140D LEU* 1.3 78.0 - - - +
142D GLY* 1.3 65.9 + - - +
143D HIS 3.3 0.5 + - - -
144D GLY* 4.1 4.2 + - - -
180D PHE* 3.5 45.2 - - + -
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Residues in contact with GLY 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LYS 2.8 16.5 + - - -
139D ILE 3.0 5.4 + - - -
140D LEU 3.0 0.6 - - - -
141D ARG* 1.3 83.8 - - - +
143D HIS* 1.3 57.8 + - - +
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ILE* 3.2 17.2 + - + +
140D LEU* 3.6 17.4 + - + -
142D GLY* 1.3 78.1 - - - +
144D GLY* 1.3 62.0 + - - +
145D GLN* 2.7 66.7 + - + +
147D PHE 3.0 28.7 + - - -
148D LEU 3.3 18.9 + - - -
149D VAL* 5.7 0.7 - - - -
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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