Contacts of the helix formed by residues 243 - 256 (chain A) in PDB entry 2Q5E
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 THR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PRO 5.6 0.2 - - - -
145A TYR* 4.1 20.6 - - + +
241A ALA 3.6 10.5 + - - +
242A ASP* 1.3 78.9 - - - +
244A GLU* 1.3 56.4 + - - +
245A LEU 3.3 2.9 - - - -
246A LEU* 3.2 20.9 - - + +
247A ASN* 2.7 53.1 + - - -
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Residues in contact with GLU 244 (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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143A ARG* 3.5 18.2 - - - +
232A PRO 5.3 0.5 - - - +
233A VAL* 4.1 13.8 - - + +
234A GLN* 3.6 31.9 + - + +
242A ASP* 3.3 19.5 + - - +
243A THR* 1.3 77.5 - - - +
245A LEU* 1.3 58.8 + - - +
247A ASN* 3.4 14.3 + - - +
248A LEU* 3.1 40.1 + - - +
119C PRO* 4.1 13.9 - - - +
120C ILE* 5.3 3.8 - - - +
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Residues in contact with LEU 245 (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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111A THR* 4.4 6.7 - - + +
112A LEU* 4.1 15.9 - - + -
143A ARG* 3.6 37.0 - - - +
144A PRO 4.0 12.0 + - - +
145A TYR* 4.4 1.8 - - + -
146A VAL* 3.8 31.9 - - + -
149A PHE* 3.6 34.9 - - + -
216A LEU* 5.0 3.6 - - + -
233A VAL* 4.6 5.2 - - + -
242A ASP* 4.4 0.8 + - - -
243A THR* 3.3 1.0 - - - +
244A GLU* 1.3 73.1 - - - +
246A LEU* 1.3 65.7 + - - +
248A LEU* 3.2 28.2 + - + +
249A ILE* 3.3 19.9 + - - +
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Residues in contact with LEU 246 (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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145A TYR* 3.6 54.7 - - + +
243A THR* 3.2 21.3 - - + +
245A LEU* 1.3 73.2 - - - +
247A ASN* 1.3 71.3 + - - +
248A LEU 3.1 0.5 + - - -
249A ILE* 3.4 23.2 + - + +
250A PRO* 3.5 8.7 - - - +
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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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243A THR* 2.7 44.2 + - - +
244A GLU* 3.4 17.7 + - - +
246A LEU* 1.3 75.8 - - - +
248A LEU* 1.3 56.9 + - - +
250A PRO* 3.2 23.0 - - - +
251A ILE* 3.9 10.9 - - + +
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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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149A PHE* 4.4 4.3 - - + -
216A LEU* 3.9 26.0 - - + -
231A VAL* 3.8 25.8 - - + -
232A PRO 4.8 4.5 - - - +
233A VAL* 4.0 17.7 - - + -
244A GLU* 3.1 26.9 + - - +
245A LEU* 3.2 16.1 + - + +
246A LEU 3.1 1.4 - - - -
247A ASN* 1.3 76.7 - - - +
249A ILE* 1.3 67.0 + - - +
250A PRO 3.4 0.4 - - - -
251A ILE* 3.2 26.4 + - + +
252A PHE* 3.0 39.4 + - + -
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Residues in contact with ILE 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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145A TYR* 5.6 2.0 - - + +
148A GLU* 4.4 11.2 - - + +
149A PHE* 3.8 36.3 - - + +
152A ARG* 4.3 17.0 - - + -
153A MET* 5.9 1.8 - - - -
156A LEU* 5.9 0.2 - - - +
245A LEU 3.3 16.6 + - - +
246A LEU* 3.9 17.0 - - + +
248A LEU* 1.3 78.9 - - - +
250A PRO* 1.3 66.0 - - + +
252A PHE* 3.2 4.4 + - - +
253A GLU* 2.8 51.4 + - - +
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Residues in contact with PRO 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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246A LEU 3.5 7.2 - - - +
247A ASN* 3.2 19.5 - - - +
249A ILE* 1.3 97.3 - - + +
251A ILE* 1.3 54.1 + - + +
253A GLU* 3.1 14.8 + - + +
254A GLU* 2.7 43.6 + - + +
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Residues in contact with ILE 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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231A VAL* 5.0 6.7 - - + -
247A ASN* 3.9 16.6 - - + +
248A LEU* 3.2 35.0 - - + +
250A PRO* 1.3 78.3 - - + +
252A PHE* 1.3 60.5 + - + +
254A GLU* 3.3 10.1 + - - +
255A LEU* 2.9 40.4 + - + +
265A LEU* 6.2 0.4 - - + -
268A LEU* 3.8 26.1 - - + +
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Residues in contact with PHE 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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104A VAL* 4.2 9.6 - - + -
149A PHE* 4.3 9.6 - + - -
153A MET* 3.4 38.4 - - + -
156A LEU* 4.9 0.9 - - + -
157A PHE* 3.4 29.3 - + + -
214A LEU* 3.7 24.9 - - + -
216A LEU* 4.2 23.1 - - + -
231A VAL* 4.0 20.6 - - + -
248A LEU* 3.0 55.8 + - + +
249A ILE 3.9 2.9 - - - +
251A ILE* 1.3 75.2 - - + +
253A GLU* 1.3 60.6 + - - +
255A LEU* 4.1 5.2 - - + +
256A SER* 2.9 27.4 + - - -
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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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152A ARG* 2.6 48.9 + - - +
156A LEU* 4.0 12.3 - - + +
249A ILE* 2.8 31.4 + - + +
250A PRO* 3.3 14.9 - - + +
252A PHE* 1.3 75.0 - - - +
254A GLU* 1.3 62.9 + - - +
256A SER* 2.9 20.5 + - - +
257A GLY 4.7 0.3 + - - -
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Residues in contact with GLU 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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250A PRO* 2.7 21.8 + - + +
251A ILE* 3.5 12.5 - - - +
253A GLU* 1.3 72.8 - - - +
255A LEU* 1.3 63.1 + - - +
256A SER 3.5 0.2 + - - -
257A GLY 4.4 2.6 + - - -
258A ALA* 5.1 1.4 + - - +
264A SER* 5.6 0.9 + - - -
268A LEU* 3.8 38.5 - - + +
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Residues in contact with LEU 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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102A ILE* 3.6 5.1 - - + +
157A PHE* 4.4 1.1 - - + -
214A LEU* 4.0 28.7 - - + -
231A VAL* 4.5 4.5 - - + -
251A ILE* 2.9 35.8 + - + +
252A PHE* 2.9 12.2 + - + +
254A GLU* 1.3 78.4 - - - +
256A SER* 1.3 59.4 + - - +
257A GLY 2.9 7.9 + - - -
258A ALA* 2.9 24.5 + - + +
261A VAL* 4.9 3.6 - - + +
264A SER* 3.7 30.3 - - - +
265A LEU* 3.7 38.1 - - + +
268A LEU* 4.5 10.5 - - + -
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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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101A ARG* 5.7 1.2 - - - -
102A ILE* 4.0 13.8 + - - +
156A LEU* 4.0 33.0 - - - +
157A PHE* 3.4 32.4 - - - -
252A PHE 2.9 8.4 + - - -
253A GLU* 2.9 15.4 + - - -
254A GLU 3.3 0.8 - - - -
255A LEU* 1.3 74.5 - - - +
257A GLY* 1.3 59.5 + - - +
258A ALA 3.5 0.4 - - - +
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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