Contacts of the helix formed by residues 150 - 155 (chain A) in PDB entry 5H8N
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLN 4.2 2.4 - - - +
145A VAL* 3.4 15.4 - - + -
146A THR* 2.9 43.8 + - - +
147A GLY 2.8 18.3 + - - +
148A LEU 3.2 0.6 - - - -
149A SER* 1.3 75.4 - - - +
151A LYS* 1.4 60.8 + - - +
152A LYS* 3.0 42.1 + - - +
153A PHE* 3.0 16.7 + - + +
154A GLN* 2.9 24.8 + - - +
159A TYR* 4.9 1.0 + - - -
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Residues in contact with LYS 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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149A SER 3.5 3.2 + - - -
150A ASP* 1.4 72.0 + - - +
152A LYS* 1.4 59.8 + - - +
154A GLN* 4.1 9.9 - - - -
155A ARG* 2.8 43.7 + - + +
158A ASP* 5.7 1.6 - - - +
159A TYR* 3.5 24.9 - - + +
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Residues in contact with LYS 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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144A GLN* 2.9 29.7 + - - +
145A VAL* 4.0 10.1 - - + -
150A ASP* 3.0 20.3 + - - +
151A LYS* 1.4 74.8 - - - +
153A PHE* 1.3 57.9 + - - +
156A PRO* 3.4 24.4 - - - +
159A TYR* 3.6 43.7 - - + -
163A PHE* 4.0 44.2 - - + +
165A PHE* 3.6 7.7 - - - -
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Residues in contact with PHE 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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137A VAL* 3.7 35.2 - - + -
145A VAL* 4.3 14.4 - - + -
147A GLY 3.3 31.2 - - - -
148A LEU* 3.5 19.1 - - + +
150A ASP* 3.0 9.6 + - + +
152A LYS* 1.3 78.6 - - + +
154A GLN* 1.3 63.5 + - - +
156A PRO* 3.2 11.4 - - - +
163A PHE* 3.6 21.1 - + - -
165A PHE* 3.6 46.0 - + + -
184A MET* 3.2 32.1 - - + +
210A ALA* 3.9 6.1 - - + -
212A ILE* 4.0 7.0 - - + -
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Residues in contact with GLN 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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148A LEU 3.0 20.1 + - - -
149A SER* 3.3 23.6 - - - +
150A ASP 2.9 17.9 + - - +
151A LYS* 4.1 6.5 - - - -
153A PHE* 1.3 75.7 - - - +
155A ARG* 1.4 65.9 + - + +
156A PRO* 3.4 6.5 - - - +
181A TYR* 3.2 40.4 - - - +
183A TYR* 3.6 14.9 - - - +
184A MET* 3.2 21.0 + - - +
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Residues in contact with ARG 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 LYS* 2.8 26.1 + - + +
154A GLN* 1.4 78.9 - - + +
156A PRO* 1.4 66.2 - - - +
157A HIS 3.2 4.2 + - - -
158A ASP* 2.7 57.4 + - - +
159A TYR* 4.0 2.1 - - - -
183A TYR* 4.3 8.3 - - + -
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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