Contacts of the helix formed by residues 246 - 253 (chain A) in PDB entry 3U4S
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLY* 3.0 29.1 + - - -
122A TRP* 3.5 28.9 - - - -
245A ILE* 1.3 77.3 - - - +
247A PRO* 1.3 76.0 - - - +
248A LEU* 3.6 8.6 + - - +
249A MET* 3.0 23.7 + - - +
250A LEU* 3.1 12.1 + - - +
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Residues in contact with PRO 247 (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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118A GLU* 3.6 10.3 - - - +
122A TRP* 3.2 22.0 - - + +
187A TRP* 6.3 0.4 - - + -
209A TYR* 3.3 31.9 - - + +
245A ILE 4.5 0.2 - - - +
246A SER* 1.3 91.1 - - - +
248A LEU* 1.3 67.8 + - + +
250A LEU* 3.1 9.6 + - + +
251A LYS* 2.9 28.2 + - + +
257A PHE* 3.7 30.1 - - + -
259A LYS* 4.4 7.4 - - - +
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Residues in contact with LEU 248 (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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246A SER* 3.2 8.6 - - - +
247A PRO* 1.3 84.8 - - + +
249A MET* 1.3 57.4 + - + +
251A LYS* 3.4 19.4 + - + +
252A LYS* 2.9 33.4 + - - +
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Residues in contact with MET 249 (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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79A SER* 3.5 27.4 - - - +
80A GLY* 3.6 9.6 - - - +
81A LEU* 4.4 10.5 - - + -
222A LEU* 4.8 1.5 - - - +
226A PHE* 3.6 20.0 - - + -
245A ILE* 3.8 13.2 - - + -
246A SER* 3.0 22.2 + - - +
248A LEU* 1.3 74.4 - - + +
250A LEU* 1.3 66.6 + - - +
252A LYS* 3.2 21.1 + - - -
253A TYR* 3.1 64.3 + - + +
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Residues in contact with LEU 250 (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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187A TRP* 3.7 28.3 - - + -
211A VAL* 4.3 6.7 - - + -
219A LEU* 4.0 22.7 - - + -
222A LEU* 4.7 4.0 - - + -
245A ILE* 3.8 22.7 - - + -
246A SER 3.1 12.5 + - - +
247A PRO* 3.1 9.7 + - + +
249A MET* 1.3 74.5 - - - +
251A LYS* 1.3 65.6 + - - +
253A TYR 3.1 2.8 + - - -
254A GLY 2.9 18.4 + - - -
255A ILE* 3.0 29.5 + - + +
257A PHE* 3.7 40.4 - - + -
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Residues in contact with LYS 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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247A PRO 2.9 10.5 + - - +
248A LEU* 3.5 24.0 - - + +
250A LEU* 1.3 76.8 - - - +
252A LYS* 1.3 59.9 + - - +
254A GLY* 2.9 21.1 + - - +
255A ILE 5.0 1.3 - - - -
257A PHE* 3.6 27.3 - - + -
16B THR* 3.9 10.4 - - - -
18B TYR* 3.4 57.8 + - + +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LEU* 2.9 19.4 + - - +
249A MET* 3.2 25.1 + - - +
251A LYS* 1.3 76.4 - - - +
253A TYR* 1.3 73.7 + - + +
15B MET* 3.0 40.4 - - + +
16B THR 2.7 40.5 + - - +
17B PHE* 4.4 9.2 - - + -
18B TYR* 6.0 0.2 - - - -
33B TYR* 5.2 2.4 + - - -
37B GLN* 3.0 23.8 + - - +
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Residues in contact with TYR 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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218A ARG* 5.1 3.3 + - - -
222A LEU* 3.7 38.6 - - + -
226A PHE* 3.8 16.5 - + - -
249A MET* 3.1 46.0 + - + +
250A LEU 4.1 0.9 - - - +
251A LYS 3.1 0.4 - - - -
252A LYS* 1.3 90.8 - - + +
254A GLY* 1.3 64.3 + - - +
255A ILE* 3.3 8.1 + - - +
9B ASN* 3.0 38.9 + - - +
10B PRO* 5.4 0.5 - - - +
11B SER* 4.8 1.2 + - - -
13B ARG* 3.7 25.5 + - + -
14B ILE 4.1 15.0 - - - +
15B MET* 3.9 16.7 - - + +
16B THR* 5.0 1.3 - - - -
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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