Contacts of the helix formed by residues 250 - 258 (chain A) in PDB entry 3C9S
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 ASN 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A CYS* 3.9 2.2 - - - -
249A LYS* 1.3 75.7 - - - +
251A PRO* 1.3 73.6 - - - +
252A ILE* 3.7 19.3 + - - +
253A GLU* 3.2 40.8 + - + +
254A TYR* 3.3 14.4 - - - -
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Residues in contact with PRO 251 (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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236A LEU* 3.6 29.4 - - + -
240A LEU* 4.1 10.6 - - + +
241A LYS* 4.5 15.5 - - + -
244A CYS* 3.5 26.6 - - + -
249A LYS 3.6 7.4 - - - +
250A ASN* 1.3 91.8 - - - +
252A ILE* 1.3 63.6 + - + +
254A TYR* 3.0 7.0 + - + +
255A ALA* 3.0 20.6 + - - +
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Residues in contact with ILE 252 (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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231A SER* 3.7 43.5 - - - +
232A GLU* 4.9 3.1 - - - +
234A LEU* 4.1 7.2 - - + +
236A LEU* 4.1 21.1 - - + -
250A ASN* 3.3 19.4 + - - +
251A PRO* 1.3 77.0 - - + +
253A GLU* 1.3 56.6 + - - +
255A ALA* 3.1 4.9 + - - +
256A LEU* 2.9 49.6 + - + +
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Residues in contact with GLU 253 (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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250A ASN* 3.2 28.5 + - + +
252A ILE* 1.3 79.0 - - - +
254A TYR* 1.3 69.6 + - + +
256A LEU* 4.7 2.9 - - - -
257A PHE* 2.9 51.2 + - + +
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Residues in contact with TYR 254 (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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158A GLY* 3.3 32.8 + - - -
161A ARG* 3.9 14.6 - - + -
162A ALA* 4.1 4.0 - - - -
165A GLU* 2.6 41.6 + - - -
240A LEU* 4.0 17.3 - - + -
243A TYR* 3.7 14.9 - + - -
244A CYS* 4.1 4.3 - - - -
249A LYS* 3.1 45.1 - - + +
250A ASN 3.3 14.6 - - - -
251A PRO 3.0 8.8 + - - +
253A GLU* 1.3 89.5 - - + +
255A ALA* 1.3 59.1 + - - +
258A GLY* 2.7 32.7 + - - +
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Residues in contact with ALA 255 (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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157A LEU* 3.6 42.5 + - + +
158A GLY* 4.1 0.2 - - - -
212A LEU* 3.7 8.0 + - - +
234A LEU* 3.8 20.0 - - + -
236A LEU* 3.8 21.8 - - + -
251A PRO 3.0 11.1 + - - +
252A ILE 3.1 9.2 + - - +
254A TYR* 1.3 79.4 - - - +
256A LEU* 1.3 60.7 + - - +
258A GLY 4.7 2.6 + - - +
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Residues in contact with LEU 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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211A GLY 4.1 0.5 - - - -
212A LEU* 3.4 22.0 + - + -
213A VAL* 3.1 43.6 + - + +
214A ALA 4.9 0.3 + - - -
229A ILE* 4.8 2.5 - - + -
234A LEU* 3.4 25.4 - - + -
252A ILE* 2.9 34.4 + - + +
253A GLU* 5.0 1.1 - - - -
255A ALA* 1.3 78.8 - - - +
257A PHE* 1.3 80.3 + - + +
293A VAL* 4.4 31.0 - - + -
298A VAL* 6.3 1.3 - - + -
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Residues in contact with PHE 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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210A ASP 3.8 9.7 - - - +
211A GLY* 4.4 3.4 - - - -
213A VAL* 4.1 23.3 - - + -
214A ALA* 5.8 1.6 - - + -
253A GLU* 2.9 34.8 + - + +
256A LEU* 1.3 96.8 - - + +
258A GLY* 1.3 66.8 + - - +
259A GLY 3.4 2.3 + - - -
298A VAL* 3.9 25.4 - - + -
299A GLU 4.8 3.6 - - - -
300A PRO* 5.6 2.7 - - + -
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Residues in contact with GLY 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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158A GLY* 4.8 1.8 - - - -
161A ARG* 3.7 25.6 - - - -
208A ILE* 5.1 2.3 - - - +
211A GLY* 3.3 15.1 - - - -
212A LEU 4.5 1.4 + - - -
253A GLU 4.0 0.4 + - - -
254A TYR* 2.7 29.3 + - - +
255A ALA 5.0 2.3 - - - +
256A LEU 3.8 0.2 - - - -
257A PHE* 1.3 70.5 - - - +
259A GLY* 1.3 61.6 + - - -
261A ASP* 3.7 13.2 + - - +
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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