Contacts of the helix formed by residues 149 - 157 (chain A) in PDB entry 2Z7S
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ASP* 1.3 70.5 - - - +
150A PHE* 1.3 60.9 + - - +
152A ARG* 3.8 5.3 - - - +
153A LEU* 2.8 32.1 + - + +
159A PHE* 4.1 12.9 - - + -
167A TYR* 3.8 43.1 - - + +
190A PRO* 3.3 17.7 + - + +
193A ILE* 2.8 47.6 + - + +
195A LEU* 4.2 18.8 - - + +
251A LEU* 4.8 1.3 - - + -
255A MET* 3.9 26.5 - - + -
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Residues in contact with PHE 150 (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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148A ASP* 2.7 18.6 + - - +
149A LEU* 1.3 72.2 - - - +
151A THR* 1.3 63.5 + - - -
153A LEU* 3.2 6.7 + - + +
154A SER* 2.9 41.0 + - - -
190A PRO* 3.3 16.4 + - + +
191A GLU* 3.6 48.9 - - + +
254A GLU* 5.1 9.9 - - - -
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Residues in contact with THR 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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147A GLY* 5.9 1.1 - - - -
148A ASP* 2.6 38.8 + - - -
150A PHE* 1.3 80.0 - - - +
152A ARG* 1.3 62.5 + - - +
154A SER* 2.6 23.9 + - - +
155A LYS* 3.2 30.3 + - + +
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Residues in contact with ARG 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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148A ASP 3.3 10.3 + - - +
149A LEU* 3.9 9.9 - - + +
150A PHE 3.3 0.4 - - - -
151A THR* 1.3 80.4 - - - +
153A LEU* 1.3 58.2 + - - +
155A LYS* 3.3 7.8 + - + +
156A GLU* 2.6 70.1 + - - +
159A PHE* 3.5 21.4 - - + -
163A ASP* 2.9 26.4 + - - -
167A TYR* 2.7 43.9 + - - -
195A LEU* 4.8 6.3 - - + -
337A PRO 5.6 0.2 - - - -
338A PHE* 3.5 47.6 - - + +
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Residues in contact with LEU 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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149A LEU* 2.8 17.6 + - + +
150A PHE* 3.2 8.0 + - + +
152A ARG* 1.3 77.7 - - - +
154A SER* 1.3 53.9 + - - +
157A VAL* 2.4 40.4 + - - +
158A MET* 3.5 28.7 - - - +
159A PHE* 3.7 23.5 - - + -
190A PRO* 4.7 10.1 - - + -
254A GLU* 3.7 48.0 - - + +
255A MET* 4.1 17.0 - - + -
258A GLY* 4.9 1.6 - - - +
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Residues in contact with SER 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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150A PHE* 2.9 29.2 + - - -
151A THR* 2.6 25.5 + - - +
153A LEU* 1.3 75.8 - - - +
155A LYS* 1.3 68.1 + - - +
157A VAL* 3.3 19.8 - - - +
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Residues in contact with LYS 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 THR* 3.2 30.1 + - + +
152A ARG* 3.8 8.7 - - + +
154A SER* 1.3 87.0 + - - +
156A GLU* 1.3 64.8 + - + +
157A VAL* 4.6 2.9 - - - +
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Residues in contact with GLU 156 (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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152A ARG* 2.6 66.1 + - + +
155A LYS* 1.3 81.7 - - + +
157A VAL* 1.3 58.8 + - - +
158A MET* 2.7 33.0 + - - +
159A PHE* 4.2 7.6 - - + -
338A PHE* 3.9 11.9 - - - -
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Residues in contact with VAL 157 (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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153A LEU* 2.4 28.7 + - - -
154A SER* 3.3 18.8 - - - +
155A LYS 4.6 3.1 - - - +
156A GLU* 1.3 71.3 - - - +
158A MET* 1.3 68.9 + - + +
257A THR 5.5 0.2 - - - +
258A GLY* 3.0 22.8 - - - +
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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