Contacts of the helix formed by residues 250 - 257 (chain A) in PDB entry 4RG1
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 GLN 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A SER* 3.0 12.5 + - - +
249A SER* 1.3 101.7 + - - +
251A ASP* 1.3 58.1 + - - +
252A PRO* 3.5 1.8 - - - -
253A ARG* 2.9 42.3 + - - +
254A THR* 2.9 35.5 + - + +
403A 15P 3.0 57.2 + - - +
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Residues in contact with ASP 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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189A PHE* 4.3 8.1 - - + -
247A VAL* 3.5 27.0 - - + +
248A SER* 3.1 30.3 + - - +
250A GLN* 1.3 75.0 - - - +
252A PRO* 1.3 72.5 - - + +
254A THR* 3.7 7.4 + - - -
255A LYS* 2.8 66.8 + - + +
256A ALA 3.4 0.5 + - - -
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Residues in contact with PRO 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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189A PHE* 3.9 33.9 - - + -
228A THR* 4.0 6.7 - - + -
248A SER 3.8 5.2 - - - +
249A SER 3.6 13.0 - - - +
250A GLN 3.6 0.4 - - - -
251A ASP* 1.3 92.6 - - + +
253A ARG* 1.3 56.2 + - - +
256A ALA* 3.0 9.0 + - - +
257A GLY 3.0 10.7 + - - -
258A LEU* 2.9 24.7 + - + +
260A TRP* 3.7 51.6 - - + +
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Residues in contact with ARG 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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71A ARG* 2.9 68.3 + - + +
72A PRO 3.9 6.5 + - - -
73A TYR 3.3 23.6 + - - -
74A THR* 3.5 23.4 - - - +
110A ASP* 3.5 25.7 + - - -
249A SER 5.4 0.2 + - - -
250A GLN* 2.9 39.2 + - - +
251A ASP 3.2 0.4 - - - -
252A PRO* 1.3 79.8 - - - +
254A THR* 1.3 80.5 + - - +
257A GLY* 3.0 14.7 + - - -
258A LEU 3.2 16.7 + - - +
260A TRP* 5.0 5.7 - - + +
279A PHE* 6.0 0.6 - - - -
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Residues in contact with THR 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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70A GLY* 3.3 14.7 - - - -
71A ARG 3.7 10.4 - - - +
72A PRO* 5.0 6.0 - - + +
250A GLN* 2.9 30.5 + - + +
251A ASP* 3.7 10.7 + - - -
253A ARG* 1.3 106.4 - - - +
255A LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 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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69A ARG* 4.1 6.9 - - - +
70A GLY* 3.8 11.2 + - - -
189A PHE* 5.3 5.6 - - + -
251A ASP* 2.8 50.7 + - + +
254A THR* 1.3 89.7 - - - +
256A ALA* 1.3 59.2 + - + +
257A GLY 3.7 0.7 - - - -
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Residues in contact with ALA 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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69A ARG* 3.9 12.5 - - - +
188A GLU* 4.0 11.4 - - - +
189A PHE* 4.0 20.4 - - + -
251A ASP 3.4 0.2 + - - -
252A PRO 3.0 12.9 + - - +
255A LYS* 1.3 78.1 - - + +
257A GLY* 1.3 63.0 + - - +
258A LEU* 3.2 20.8 + - + +
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Residues in contact with GLY 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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69A ARG 3.3 19.0 + - - -
70A GLY* 4.1 1.3 - - - -
71A ARG* 3.5 24.2 + - - -
253A ARG 3.0 18.3 + - - -
255A LYS 3.7 0.4 - - - -
256A ALA* 1.3 76.8 - - - +
258A LEU* 1.3 62.3 + - - +
259A TYR 3.9 0.9 + - - -
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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