Contacts of the helix formed by residues 144 - 153 (chain A) in PDB entry 2OO3
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 ASP 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.4 29.4 - - + +
143A THR* 1.3 74.1 + - - +
145A GLY* 1.3 62.9 + - - +
146A VAL* 3.1 22.3 + - - +
147A SER* 2.7 44.3 + - - +
148A LYS* 3.2 8.0 + - - +
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Residues in contact with GLY 145 (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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39A LEU* 5.7 0.9 - - - +
41A THR* 3.3 38.3 + - - +
118A CYS* 3.5 22.3 - - - -
120A LEU* 5.7 0.2 - - - +
143A THR 3.0 7.9 + - - -
144A ASP* 1.3 71.8 + - - +
146A VAL* 1.3 61.8 + - - +
148A LYS* 3.0 16.8 + - - +
149A LEU* 3.4 5.7 + - - +
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Residues in contact with VAL 146 (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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41A THR* 4.4 9.0 - - + -
42A HIS* 3.4 35.2 - - + +
144A ASP* 3.1 10.9 + - - +
145A GLY* 1.3 74.8 - - - +
147A SER* 1.3 62.1 + - - +
148A LYS 3.4 0.3 + - - -
149A LEU* 3.4 22.5 + - + +
150A ASN* 4.6 0.7 + - - +
164A ILE* 5.4 0.2 - - + -
176A GLU* 4.7 9.2 - - + +
177A ILE* 3.5 22.9 - - + -
180A ALA* 3.5 28.8 - - + +
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Residues in contact with SER 147 (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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143A THR* 4.7 4.2 + - - -
144A ASP* 2.7 37.6 + - - +
146A VAL* 1.3 78.6 - - - +
148A LYS* 1.3 61.4 + - - +
149A LEU 3.4 0.7 + - - -
150A ASN* 3.6 17.7 + - - +
151A ALA* 4.3 2.8 + - - +
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Residues in contact with LYS 148 (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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39A LEU* 5.3 1.8 - - + -
116A TYR* 3.7 18.5 + - - +
118A CYS* 4.2 8.3 - - - -
141A ASN* 5.8 0.2 - - - -
143A THR* 3.7 38.6 - - + +
144A ASP 3.2 4.4 + - - +
145A GLY* 3.0 13.9 + - - +
147A SER* 1.3 78.3 + - - +
149A LEU* 1.3 64.5 + - - +
150A ASN 3.1 2.7 - - - -
151A ALA* 3.0 21.5 + - + +
152A LEU* 3.1 35.0 + - + +
301A SO4 2.6 39.0 + - - -
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Residues in contact with LEU 149 (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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39A LEU* 3.6 19.0 - - + +
41A THR* 3.9 20.0 - - + -
145A GLY 3.4 1.2 + - - -
146A VAL* 3.5 19.3 - - + +
147A SER 3.3 0.6 - - - -
148A LYS* 1.3 78.7 - - - +
150A ASN* 1.3 62.3 + - - +
152A LEU 3.5 0.2 + - - -
153A LEU* 3.5 36.3 + - + +
162A ILE* 3.5 31.2 - - + -
164A ILE* 4.4 13.2 - - + -
177A ILE* 6.5 0.2 - - + -
180A ALA* 3.9 31.9 - - + +
181A ILE* 4.4 3.6 - - + +
183A ASN* 5.9 0.2 - - - +
184A ALA* 4.2 17.4 - - + +
187A LYS* 5.5 0.2 - - - +
193A TYR* 6.0 0.2 - - + -
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Residues in contact with ASN 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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146A VAL 4.6 0.4 + - - -
147A SER 3.6 12.0 + - - +
148A LYS 3.1 1.0 - - - -
149A LEU* 1.3 80.0 - - - +
151A ALA* 1.3 60.8 + - - +
152A LEU 3.7 0.2 + - - -
153A LEU 3.8 3.3 - - - +
183A ASN* 3.0 31.3 + - - +
184A ALA* 5.8 0.7 - - - +
187A LYS* 2.7 56.6 + - - +
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Residues in contact with ALA 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 SER 4.3 1.8 + - - +
148A LYS* 3.0 25.7 + - + +
150A ASN* 1.3 80.1 - - - +
152A LEU* 1.3 62.6 + - + +
153A LEU 3.6 2.3 + - - +
301A SO4 3.8 23.7 + - - +
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Residues in contact with LEU 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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37A PHE* 4.0 16.6 - - + -
39A LEU* 3.9 19.3 - - + -
114A ARG* 5.5 4.5 + - - +
116A TYR* 3.5 55.0 - - + +
148A LYS* 3.1 29.1 + - + +
149A LEU 4.6 1.1 - - - +
151A ALA* 1.3 82.5 - - - +
153A LEU* 1.3 66.4 + - - +
154A PRO 3.8 1.5 - - - +
155A PRO* 3.7 18.2 - - - +
156A PRO* 5.3 0.9 - - - +
301A SO4 4.1 19.7 - - - +
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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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37A PHE* 4.0 20.4 - - + -
39A LEU* 4.6 3.8 - - + -
149A LEU* 3.5 24.2 + - + +
150A ASN 3.8 1.9 - - - +
151A ALA 3.6 1.6 - - - +
152A LEU* 1.3 85.0 - - - +
154A PRO* 1.4 65.6 - - + +
155A PRO* 3.9 16.8 - - + -
162A ILE* 4.0 24.2 - - + -
184A ALA* 3.9 22.9 - - + +
187A LYS* 3.7 26.6 + - + +
188A PHE* 4.0 15.5 - - + -
193A TYR* 3.7 21.1 - - + +
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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