Contacts of the helix formed by residues 151 - 154 (chain A) in PDB entry 1CX4
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP 3.3 9.8 + - - +
150A ILE* 1.3 71.9 - - - +
152A LEU* 1.3 58.3 + - - +
153A PHE 3.0 5.1 + - - -
154A LYS* 3.1 34.8 + - + +
155A ASN* 4.6 1.2 + - - +
261A LYS* 5.2 0.9 + - - -
289A VAL 4.2 9.0 - - - +
290A ILE 4.3 1.8 - - - +
291A GLY* 3.6 24.8 - - - +
293A LYS* 4.4 12.3 - - + -
310A SER* 4.5 7.9 - - - +
373A ALA* 3.5 30.3 - - + +
374A MET* 3.5 11.2 - - - +
375A ASP* 3.5 38.4 - - + +
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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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150A ILE* 3.2 11.3 + - + +
151A LEU* 1.3 76.5 - - + +
153A PHE* 1.3 68.3 + - + +
154A LYS 3.5 0.2 - - - -
155A ASN 4.9 1.2 + - - -
156A LEU* 4.6 0.7 - - - +
189A PHE* 4.0 17.7 - - + -
218A SER* 5.4 2.0 - - - +
221A GLU* 3.8 35.9 - - + +
225A MET* 5.1 2.7 - - - -
250A PHE* 4.6 10.5 - - + -
254A ILE* 4.0 21.3 - - + +
257A ASN* 4.6 10.4 - - - +
258A ASN* 4.5 8.6 - - - +
261A LYS* 4.2 11.5 + - - +
288A ASP 3.2 27.4 - - - +
289A VAL* 4.1 16.2 - - + +
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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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147A CYS* 3.8 39.0 - - + +
150A ILE* 2.9 29.3 + - + +
152A LEU* 1.3 85.9 - - + +
154A LYS* 1.3 65.6 + - - +
155A ASN 3.4 3.0 + - - -
156A LEU* 3.5 20.5 + - + +
161A MET* 3.2 38.0 - - + +
164A VAL* 4.0 22.4 - - + -
168A MET* 4.3 5.2 - - + -
189A PHE* 3.8 30.7 - + - -
191A VAL* 4.2 7.4 - - + -
245A LEU* 4.9 1.6 - - + -
254A ILE* 3.7 24.5 - - + -
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Residues in contact with LYS 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 LYS 2.8 28.0 + - - -
149A ASP* 3.9 18.0 + - - +
150A ILE 4.2 3.4 + - - -
151A LEU* 3.1 32.4 + - + +
153A PHE* 1.3 79.5 - - - +
155A ASN* 1.3 65.4 + - - +
156A LEU 3.2 8.4 + - - +
292A THR* 3.6 27.3 - - - +
293A LYS* 4.1 26.0 - - + +
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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