Contacts of the helix formed by residues 255 - 265 (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 VAL 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LEU 4.2 1.8 - - - +
225A MET* 4.4 13.7 - - + +
250A PHE* 3.3 22.9 + - + -
251A ARG* 3.3 61.2 - - - +
254A ILE* 1.3 73.0 - - - +
256A LYS* 1.3 66.6 + - - +
258A ASN* 3.4 16.8 + - + +
259A ALA* 3.5 10.7 + - - +
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Residues in contact with LYS 256 (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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160A GLN* 4.3 15.5 + - - +
251A ARG 3.7 4.6 + - - +
252A ARG* 3.4 25.8 + - - +
253A ILE* 3.5 4.9 + - - +
254A ILE 3.2 0.4 - - - -
255A VAL* 1.3 79.7 - - - +
257A ASN* 1.3 68.5 - - - +
259A ALA* 3.4 19.6 + - - +
260A LYS* 3.7 19.2 + - - +
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Residues in contact with ASN 257 (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 LEU 4.6 7.4 - - - +
155A ASN* 2.6 44.9 + - - +
156A LEU* 3.7 19.0 - - + +
160A GLN* 4.7 5.6 - - - +
253A ILE 2.9 19.1 + - - +
254A ILE* 3.1 5.7 + - - +
256A LYS* 1.3 81.6 - - - +
258A ASN* 1.3 70.8 + - - +
260A LYS* 3.2 26.2 + - - +
261A LYS* 3.1 19.8 + - - +
264A MET* 6.1 0.2 - - - +
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Residues in contact with ASN 258 (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 LEU* 4.5 1.8 - - - +
225A MET* 3.6 25.5 - - - +
254A ILE* 2.8 29.6 + - - +
255A VAL* 3.7 10.5 - - + +
256A LYS 3.3 0.4 - - - -
257A ASN* 1.3 78.9 - - - +
259A ALA* 1.3 56.5 + - - +
261A LYS* 3.1 29.8 + - - +
262A ARG* 2.7 36.4 + - - +
287A VAL* 5.2 0.9 - - - +
288A ASP* 3.4 37.3 + - - +
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Residues in contact with ALA 259 (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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255A VAL 3.5 7.6 + - - +
256A LYS* 3.4 13.8 + - - +
257A ASN 3.2 0.4 - - - -
258A ASN* 1.3 78.6 - - - +
260A LYS* 1.3 61.5 + - - +
262A ARG* 3.3 10.3 + - - +
263A LYS* 3.2 32.0 + - - +
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Residues in contact with LYS 260 (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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155A ASN* 5.3 2.3 + - + +
157A ASP* 5.5 1.2 + - - -
160A GLN* 4.6 13.5 - - - +
256A LYS* 3.7 19.2 + - + +
257A ASN* 3.2 28.8 + - - +
258A ASN 3.2 0.2 - - - -
259A ALA* 1.3 80.8 - - - +
261A LYS* 1.3 61.4 + - - +
263A LYS* 3.2 18.7 + - - +
264A MET* 3.3 32.6 + - + +
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Residues in contact with LYS 261 (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 LEU 5.2 0.6 + - - -
152A LEU* 4.2 12.1 + - - +
155A ASN* 3.6 42.5 + - + +
257A ASN* 3.1 11.0 + - - +
258A ASN* 3.2 32.1 + - - +
260A LYS* 1.3 79.2 - - - +
262A ARG* 1.3 63.7 + - - +
264A MET* 3.1 10.5 + - + -
265A TYR* 3.0 43.3 + - + +
287A VAL* 3.2 25.2 - - + +
288A ASP 3.3 12.7 + - - -
290A ILE* 2.8 26.0 + - + +
292A THR* 5.7 0.2 - - - +
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Residues in contact with ARG 262 (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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258A ASN 2.7 16.2 + - - +
259A ALA* 3.5 10.9 - - - +
260A LYS 3.2 0.2 - - - -
261A LYS* 1.3 77.8 - - - +
263A LYS* 1.3 58.7 + - + +
266A GLU* 2.9 70.1 + - + +
284A LEU* 2.8 46.9 + - - +
287A VAL* 3.7 24.5 - - + +
288A ASP* 2.7 35.5 + - - -
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Residues in contact with LYS 263 (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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259A ALA* 3.2 18.4 + - - +
260A LYS* 3.6 11.0 - - - +
261A LYS 3.2 0.4 - - - -
262A ARG* 1.3 78.1 - - + +
264A MET* 1.3 62.0 + - + +
266A GLU 5.0 0.7 + - - -
267A SER* 5.7 2.6 + - - -
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Residues in contact with MET 264 (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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155A ASN* 4.0 22.4 - - + +
260A LYS* 3.3 27.1 + - + +
261A LYS* 3.1 26.1 + - - +
263A LYS* 1.3 81.3 - - + +
265A TYR* 1.3 87.8 + - + +
267A SER* 5.4 2.2 + - - -
268A PHE* 5.0 3.8 + - - +
370A LYS* 6.1 0.7 - - - -
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Residues in contact with TYR 265 (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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155A ASN* 4.5 1.2 + - - -
261A LYS* 3.0 35.2 + - + +
264A MET* 1.3 113.0 - - + +
266A GLU* 1.3 66.4 + - - +
267A SER 3.2 2.9 - - - -
268A PHE* 3.0 12.5 + + + +
269A ILE* 2.9 40.1 + - + +
287A VAL* 4.7 2.0 - - + -
290A ILE* 4.5 6.5 - - + -
292A THR* 3.0 30.1 + - - +
315A GLU* 3.9 25.1 - - + -
370A LYS* 3.6 20.2 + - - -
372A LEU* 3.9 28.5 - - + -
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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