Contacts of the helix formed by residues 246 - 259 (chain A) in PDB entry 4RA2
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 GLY 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ARG* 5.1 3.6 - - - -
242A TRP* 4.4 2.5 - - - -
245A MET* 1.3 75.1 - - - +
247A ASN* 1.3 67.4 + - - -
248A GLU 3.4 2.5 - - - -
249A GLU* 3.0 19.9 + - - -
250A LEU* 3.0 22.0 + - - +
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Residues in contact with ASN 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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148A ARG* 3.0 36.6 + - - +
150A LEU* 3.7 21.0 - - + +
157A VAL* 4.1 11.9 - - + -
160A PHE* 3.4 45.4 - - + -
242A TRP* 3.5 8.6 - - - -
246A GLY* 1.3 70.7 - - - +
248A GLU* 1.3 59.7 + - - +
250A LEU* 4.0 0.5 - - - +
251A CYS* 3.0 30.3 + - - +
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Residues in contact with GLU 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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155A ARG 4.5 7.8 - - - +
156A LYS* 4.9 2.6 - - - +
157A VAL* 3.4 27.8 + - + +
246A GLY 3.4 0.2 - - - -
247A ASN* 1.3 77.4 - - - +
249A GLU* 1.3 60.8 + - + +
251A CYS* 4.0 9.7 - - - +
252A ASP* 2.8 66.4 + - - +
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Residues in contact with GLU 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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244A VAL 4.3 4.2 - - - +
245A MET* 3.6 14.6 - - + +
246A GLY* 3.0 29.0 + - - +
247A ASN 3.4 0.2 - - - -
248A GLU* 1.3 78.2 - - + +
250A LEU* 1.3 57.3 + - - +
252A ASP* 3.7 4.9 - - - +
253A PHE* 2.8 30.0 + - - +
278A LYS* 5.0 3.9 + - - -
348A GLY* 3.7 31.6 - - - +
350A GLU* 5.9 1.0 - - - +
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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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235A ILE* 3.9 23.3 - - + -
241A ILE* 3.7 21.8 - - + -
242A TRP* 3.6 31.9 - - + -
245A MET* 3.8 28.0 - - + -
246A GLY 3.0 17.4 + - - +
247A ASN 4.1 2.9 - - - +
249A GLU* 1.3 74.6 - - - +
251A CYS* 1.3 61.0 + - - +
253A PHE* 3.5 3.5 - - + +
254A VAL* 2.8 37.7 + - + +
271A VAL* 3.8 35.4 - - + -
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Residues in contact with CYS 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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150A LEU* 4.7 6.5 - - + -
152A CYS* 3.4 42.6 - - - -
155A ARG 4.9 0.2 - - - -
156A LYS 4.5 3.4 - - - -
157A VAL* 3.9 22.0 - - + -
233A PHE* 3.8 9.8 - - - -
235A ILE* 4.5 6.2 - - - +
247A ASN 3.0 19.5 + - - +
248A GLU* 3.7 9.4 - - - +
250A LEU* 1.3 77.7 - - - +
252A ASP* 1.3 62.4 + - - +
255A ARG* 3.0 29.2 + - - +
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Residues in contact with ASP 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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155A ARG 4.8 0.2 - - - +
248A GLU* 2.8 49.9 + - - +
249A GLU* 3.7 6.2 - - - +
251A CYS* 1.3 73.1 - - - +
253A PHE* 1.3 57.3 + - - +
255A ARG* 2.9 30.4 + - - +
256A SER* 3.0 28.2 + - - -
347A PRO* 3.7 26.6 - - + +
348A GLY 5.1 0.2 - - - +
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Residues in contact with PHE 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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245A MET* 3.9 17.5 - - + -
249A GLU 2.8 22.1 + - - +
250A LEU* 3.5 6.1 - - + +
251A CYS 3.3 0.2 - - - -
252A ASP* 1.3 70.6 - - - +
254A VAL* 1.3 67.2 + - - +
256A SER* 2.6 27.3 + - - -
257A ARG* 3.0 36.3 + - + +
270A GLU* 4.2 5.2 - - + -
271A VAL* 4.2 32.8 - - + -
274A THR* 3.7 14.6 - - - -
346A PRO* 3.7 13.9 - - + -
347A PRO 3.3 19.7 + - - +
349A GLY* 3.5 8.5 - - - -
353A SER* 3.5 33.4 - - - -
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Residues in contact with VAL 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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233A PHE* 3.8 23.6 - - + -
235A ILE* 3.8 17.0 - - + -
250A LEU* 2.8 27.1 + - + +
251A CYS 3.9 2.9 - - - +
253A PHE* 1.3 71.3 - - - +
255A ARG* 1.3 64.0 + - - +
257A ARG* 3.0 8.5 + - - +
258A LEU* 2.9 34.8 + - + +
267A VAL* 4.3 4.7 - - + -
271A VAL* 4.0 26.5 - - + -
288A LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 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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152A CYS* 4.1 11.7 - - - -
155A ARG* 3.6 65.0 + - - +
232A GLN* 4.9 2.0 + - - +
233A PHE* 4.3 4.6 - - + -
251A CYS* 3.0 19.2 + - - +
252A ASP* 2.9 34.0 + - - +
254A VAL* 1.3 76.2 - - - +
256A SER* 1.3 65.2 + - - +
258A LEU* 3.2 1.7 + - - +
259A GLU* 3.1 42.2 + - - +
295A PRO* 4.1 26.5 - - + -
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Residues in contact with SER 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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252A ASP 3.0 14.2 + - - -
253A PHE* 2.6 25.4 + - - -
255A ARG* 1.3 79.4 - - - +
257A ARG* 1.3 87.4 + - - +
259A GLU* 3.6 18.7 + - - +
260A VAL* 3.8 8.8 - - - +
301A ALA* 5.6 0.2 - - - +
347A PRO* 3.7 24.1 - - - +
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Residues in contact with ARG 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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253A PHE* 3.0 44.2 + - + +
254A VAL* 3.0 6.2 + - - +
256A SER* 1.3 110.9 + - - +
258A LEU* 1.3 60.8 + - - +
259A GLU 3.2 0.4 - - - -
260A VAL* 3.0 26.2 + - - +
261A THR* 3.0 19.1 + - - +
267A VAL* 3.9 17.9 - - + -
270A GLU* 3.5 35.1 + - + +
305A GLU* 2.7 42.1 + - - -
346A PRO* 3.5 26.0 - - - +
353A SER 5.5 2.8 + - - -
354A LYS* 4.6 3.6 - - - +
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Residues in contact with LEU 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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233A PHE* 3.8 22.0 - - + -
254A VAL* 2.9 28.2 + - + +
255A ARG 3.8 3.8 - - - +
257A ARG* 1.3 71.7 - - - +
259A GLU* 1.3 61.4 + - - +
260A VAL 3.0 5.2 - - - -
261A THR 3.1 18.0 - - - +
262A ASP* 5.2 1.5 - - - -
264A LEU* 3.7 30.5 - - + -
267A VAL* 4.0 14.4 - - + -
288A LEU* 4.2 4.3 - - + -
290A CYS* 4.0 15.5 - - - -
294A ALA* 4.8 1.3 - - + -
295A PRO* 3.8 37.2 - - + +
296A LYS 3.8 2.3 - - - -
297A VAL* 3.7 16.3 + - - +
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Residues in contact with GLU 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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155A ARG* 4.5 11.4 + - - -
255A ARG* 3.1 35.4 + - - +
256A SER* 3.8 11.6 - - - +
257A ARG 3.2 0.4 - - - -
258A LEU* 1.3 77.3 - - - +
260A VAL* 1.3 58.6 + - - +
295A PRO* 4.2 11.3 - - + +
296A LYS 3.6 16.4 - - - +
297A VAL* 3.4 2.0 - - - +
298A SER* 2.8 31.8 + - - +
301A ALA* 3.5 25.1 - - + +
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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