Contacts of the helix formed by residues 150 - 155 (chain A) in PDB entry 4I5L
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 LEU 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.9 21.3 - - + +
112A LEU* 3.6 31.9 - - + -
113A ARG* 4.3 4.5 - - + -
128A PHE* 4.0 15.8 - - + -
131A LEU* 3.7 30.1 - - + -
132A VAL* 4.5 11.9 - - + -
135A LEU* 3.8 17.0 - - + -
146A SER 4.0 12.6 - - - +
147A ALA* 2.9 12.9 + - - +
149A GLY* 1.3 82.1 - - - +
151A PHE* 1.3 64.6 + - - +
152A SER 3.5 1.8 - - - -
153A VAL* 3.4 18.7 - - - +
154A CYS* 3.5 12.7 - - - -
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.7 17.3 - - + -
136A ALA* 4.7 2.0 - - + -
147A ALA* 3.3 23.8 - - + -
148A CYS* 3.8 10.9 + - - +
149A GLY 3.7 1.0 - - - -
150A LEU* 1.3 77.6 - - - +
152A SER* 1.3 66.6 + - - +
154A CYS* 3.3 7.6 + - - -
155A TYR* 3.1 26.9 + - - +
166A LEU* 3.2 51.0 - - + +
169A TYR* 3.8 15.5 - - + -
170A PHE* 3.7 25.4 - + + -
173A LEU* 3.6 32.1 - - + -
192A PHE* 3.8 20.4 - + + -
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.6 10.9 + - - -
148A CYS 5.4 0.2 + - - -
149A GLY 5.1 1.0 + - - -
150A LEU 3.5 0.6 - - - -
151A PHE* 1.3 79.2 - - - +
153A VAL* 1.3 63.7 + - - +
156A PRO* 3.4 18.0 - - - +
191A GLU* 3.6 54.1 + - - +
192A PHE* 4.1 5.3 - - - +
195A VAL* 3.6 23.0 - - - +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.7 48.0 - - + +
116A SER* 3.3 35.4 + - - +
117A HIS* 4.0 22.1 - - + +
124A LEU* 4.8 5.0 - - - +
128A PHE* 4.0 11.7 - - + -
150A LEU* 3.4 19.7 - - - +
152A SER* 1.3 81.2 + - - +
154A CYS* 1.3 58.5 + - - +
156A PRO* 4.1 5.8 - - - +
157A ARG* 4.8 9.7 + - - -
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Residues in contact with CYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.9 18.5 - - + +
128A PHE* 3.8 28.3 - - + -
129A VAL* 4.1 14.8 - - + -
132A VAL* 4.6 4.5 - - - -
150A LEU 3.5 17.7 - - - -
151A PHE* 3.8 5.4 - - - -
153A VAL* 1.3 81.4 - - - +
155A TYR* 1.3 69.0 + - - +
156A PRO* 3.6 1.2 - - - -
157A ARG 3.6 5.4 + - - -
158A VAL* 3.5 19.2 - - - +
166A LEU* 4.0 24.7 - - - -
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE 3.1 17.8 + - - +
154A CYS* 1.3 76.4 - - - +
156A PRO* 1.4 72.9 - - + +
157A ARG 3.0 1.2 + - - -
158A VAL* 3.5 7.3 - - - +
163A LYS* 3.1 69.5 - - + +
166A LEU* 4.0 18.4 - - + -
167A ARG* 2.8 29.9 + - + -
192A PHE* 4.0 9.4 - + + -
195A VAL* 3.6 29.8 - - + -
196A LEU* 3.4 29.9 - - + +
197A GLU* 2.7 29.5 + - - -
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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