Contacts of the helix formed by residues 149 - 158 (chain H) in PDB entry 5O9Z
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 CYS 149 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147H ASP 3.1 1.2 + - - +
148H LYS* 1.3 79.1 - - + +
150H LYS* 1.3 63.3 + - - +
152H ASN* 3.0 10.0 + - - +
153H GLU* 2.9 21.6 + - - +
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Residues in contact with LYS 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ASP* 3.4 19.0 + - + +
149H CYS* 1.3 78.8 - - - +
151H ASN* 1.3 56.8 - - - +
153H GLU* 3.0 10.0 + - - +
154H ASN* 2.9 30.0 + - - +
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Residues in contact with ASN 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H GLU 6.1 1.1 - - - -
142H LEU* 5.9 7.6 - - + -
145H SER 5.2 1.6 - - - +
146H LEU* 4.5 4.0 - - + -
147H ASP* 3.3 32.6 - - + +
148H LYS* 3.1 11.7 + - - +
150H LYS* 1.3 79.6 - - - +
152H ASN* 1.3 57.5 + - - +
154H ASN* 3.5 4.9 + - - +
155H LEU* 2.9 31.8 + - - +
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Residues in contact with ASN 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A ALA* 6.0 6.7 - - + -
148H LYS 2.8 12.5 + - - +
149H CYS* 3.0 10.3 + - - +
151H ASN* 1.3 77.5 - - - +
153H GLU* 1.3 57.7 + - - +
155H LEU* 4.4 5.2 - - - -
156H GLN* 2.9 31.8 + - - +
164H ILE* 5.2 7.1 - - + +
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Residues in contact with GLU 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H CYS 2.9 11.2 + - - +
150H LYS* 3.0 14.1 + - - +
152H ASN* 1.3 76.5 - - - +
154H ASN* 1.3 60.2 + - - +
156H GLN* 3.8 3.7 - - - +
157H GLN* 2.9 30.1 + - - +
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Residues in contact with ASN 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H GLU* 3.7 30.0 - - + +
150H LYS 2.9 14.5 + - - +
151H ASN* 4.0 4.9 - - - +
153H GLU* 1.3 74.7 - - - +
155H LEU* 1.3 60.2 + - - +
157H GLN* 3.2 6.5 + - - +
158H ILE* 2.9 30.8 + - - +
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H THR* 6.0 5.4 - - - +
141H GLU* 5.6 0.2 - - - +
151H ASN 2.9 19.9 + - - +
152H ASN* 4.3 2.5 - - - +
154H ASN* 1.3 77.3 - - - +
156H GLN* 1.3 58.0 + - - +
158H ILE* 4.4 2.7 - - - +
159H LEU* 2.7 40.3 + - + +
160H THR 4.3 0.7 - - - +
164H ILE* 4.1 22.7 - - + -
167H VAL* 6.1 3.1 - - + -
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Residues in contact with GLN 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ASN 2.9 23.0 + - - +
153H GLU* 4.0 4.0 - - - +
155H LEU* 1.3 77.6 - - - +
157H GLN* 1.3 59.2 + - - +
159H LEU 3.2 15.7 - - - +
160H THR 4.8 6.0 - - - -
161H ASN* 6.1 2.0 - - - -
164H ILE* 4.7 5.6 - - + +
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Residues in contact with GLN 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H GLU 2.9 19.9 + - - +
154H ASN* 3.7 7.2 - - - +
155H LEU 3.2 0.2 - - - -
156H GLN* 1.3 76.8 - - - +
158H ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H ASP* 5.5 9.9 - - + +
137H ARG* 5.0 9.6 - - + -
138H THR* 4.9 22.4 - - - +
154H ASN 2.9 17.7 + - - +
155H LEU* 4.0 2.5 - - - +
157H GLN* 1.3 78.7 - - - +
159H LEU* 1.3 66.9 + - + +
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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