Contacts of the helix formed by residues 239 - 253 (chain A) in PDB entry 4OE4
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 ALA 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLN* 3.8 3.8 - - - +
151A GLN* 3.7 24.0 - - - +
210A PRO 4.5 1.8 - - - +
211A PHE* 3.8 19.7 - - - +
213A PHE 6.2 0.2 - - - +
236A SER* 3.2 12.0 + - - +
238A THR* 1.3 78.4 - - - +
240A ALA* 1.3 65.3 + - - +
241A LEU 3.3 2.9 + - - -
242A SER* 3.4 2.2 + - - -
243A ASN* 2.9 42.1 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.8 4.7 - - + -
81A GLN* 3.6 4.4 + - - +
94A VAL* 3.5 39.5 - - + -
235A PRO* 5.1 4.0 - - + -
236A SER 3.4 7.6 + - - +
237A GLN* 3.5 17.8 + - - +
239A ALA* 1.3 78.0 - - - +
241A LEU* 1.3 59.5 + - - +
243A ASN* 3.9 4.0 - - - +
244A TYR* 2.7 33.7 + - - +
262A PHE* 4.1 6.4 - - + -
264A PRO* 5.5 0.7 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.9 29.8 - - + -
59A LEU* 3.7 35.4 - - + -
61A VAL* 4.6 4.7 - - + +
81A GLN* 2.9 23.3 + - - +
91A LEU* 4.4 25.1 - - + +
92A ALA* 4.6 8.5 - - + -
145A ALA 5.3 0.2 - - - +
146A ALA* 3.6 34.8 - - + +
149A LEU* 5.3 0.9 - - + -
150A GLY 5.2 0.4 - - - +
239A ALA 3.3 0.6 - - - -
240A ALA* 1.3 76.0 - - - +
242A SER* 1.3 61.7 + - - +
244A TYR* 3.4 4.7 + - + +
245A LEU* 3.2 22.9 + - + +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLN* 5.4 0.4 - - - +
143A MET* 3.7 10.2 - - - +
146A ALA* 3.9 15.8 + - - +
147A THR* 3.4 20.0 - - - -
151A GLN* 2.9 27.5 + - - -
214A THR* 3.0 11.6 + - - +
239A ALA 3.4 2.4 + - - -
241A LEU* 1.3 80.5 - - - +
243A ASN* 1.3 74.3 + - - +
245A LEU* 3.4 4.1 + - - +
246A LEU* 3.0 27.2 + - - +
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Residues in contact with ASN 243 (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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209A SER* 3.6 4.2 + - - -
210A PRO 4.9 2.7 + - - +
213A PHE 5.4 0.4 + - - -
214A THR* 4.4 10.3 - - - +
217A ALA* 3.3 27.3 - - - +
233A TRP* 3.4 29.2 - - + -
235A PRO* 3.4 21.7 - - + +
236A SER 4.6 0.5 + - - -
239A ALA* 2.9 30.1 + - - +
240A ALA 3.9 2.0 - - - +
242A SER* 1.3 93.9 + - - +
244A TYR* 1.3 64.7 + - - +
246A LEU* 3.2 8.1 + - - +
247A MET* 3.0 18.5 + - - +
262A PHE* 3.9 4.0 - - + -
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Residues in contact with TYR 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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59A LEU* 4.2 19.3 - - + -
60A GLU 4.9 1.3 - - - -
61A VAL* 3.8 22.0 - - + -
62A PRO* 3.4 37.4 - - + +
64A VAL* 3.8 15.9 - - + -
69A ARG* 3.6 23.8 + - + +
71A TYR* 4.5 1.6 + - - -
240A ALA 2.7 24.0 + - - +
241A LEU 3.7 3.6 - - - +
243A ASN* 1.3 70.3 - - - +
245A LEU* 1.3 63.4 + - + +
247A MET* 3.0 6.2 + - + +
248A THR* 2.8 51.3 + - + +
262A PHE* 3.6 29.1 - + + -
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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
----------------------------------------------------------
54A PHE* 3.8 30.5 - - + -
59A LEU* 6.2 1.6 - - + -
139A TYR* 4.5 8.5 - - + -
142A ASP* 4.2 15.9 - - + +
143A MET* 3.8 41.5 - - + +
146A ALA* 4.3 7.9 - - + -
241A LEU* 3.2 10.2 + - + +
242A SER* 3.4 10.3 - - - +
244A TYR* 1.3 80.9 - - + +
246A LEU* 1.3 63.9 + - - +
248A THR* 2.8 24.9 + - - +
249A VAL* 2.9 25.0 + - + +
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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
----------------------------------------------------------
131A ALA* 5.5 0.4 - - + -
135A ILE* 3.9 20.9 - - + -
143A MET* 3.8 12.4 - - + +
166A LEU* 4.4 9.2 - - + -
170A PHE* 4.5 9.0 - - + -
214A THR* 4.5 6.7 - - + +
217A ALA* 4.3 4.9 - - + -
218A ALA* 3.7 38.4 - - + +
221A ILE* 4.1 4.0 - - + -
233A TRP* 4.0 18.8 - - + -
242A SER 3.0 14.4 + - - +
243A ASN* 3.3 8.7 - - - +
245A LEU* 1.3 75.0 - - - +
247A MET* 1.3 61.6 - - - +
249A VAL* 3.2 5.0 + - - +
250A LEU* 3.0 39.8 + - + +
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Residues in contact with MET 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.1 33.9 - - + -
67A GLY 6.2 0.2 - - - +
233A TRP* 4.0 15.2 - - + -
243A ASN 3.0 12.9 + - - +
244A TYR* 3.0 11.6 + - + +
246A LEU* 1.3 76.9 - - - +
248A THR* 1.3 63.6 + - - +
250A LEU* 3.2 13.3 + - - +
251A GLU* 3.1 29.2 + - + +
255A LEU* 4.3 14.6 - - + -
260A ILE* 3.1 48.0 - - + +
262A PHE* 3.9 24.2 - - + +
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 5.8 1.6 - - - +
244A TYR* 2.8 60.0 + - + +
245A LEU* 2.8 24.6 + - - +
247A MET* 1.3 71.7 - - + +
249A VAL* 1.3 60.1 + - - +
251A GLU* 3.4 17.3 + - - +
252A GLU* 3.0 28.1 + - - +
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Residues in contact with VAL 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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131A ALA* 3.7 34.5 - - + +
134A LEU* 3.9 14.7 - - + +
135A ILE* 3.9 20.0 - - + -
139A TYR* 3.5 30.5 - - + -
245A LEU* 2.9 27.6 + - + +
246A LEU 3.6 4.7 - - - +
248A THR* 1.3 78.5 + - - +
250A LEU* 1.3 60.2 + - - +
252A GLU* 3.2 7.9 + - - +
253A ALA* 2.8 27.9 + - - +
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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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127A ILE* 4.2 10.1 - - + +
128A PHE* 3.8 28.5 - - + -
131A ALA* 3.7 21.3 - - + -
170A PHE* 4.4 4.7 - - + -
221A ILE* 3.7 30.3 - - + -
246A LEU* 3.0 28.8 + - + +
247A MET* 3.4 16.8 - - - +
249A VAL* 1.3 76.3 - - - +
251A GLU* 1.3 59.4 + - - +
253A ALA* 3.3 6.9 + - - +
254A GLY 3.3 5.2 + - - -
255A LEU* 3.0 36.5 + - + +
260A ILE* 4.1 15.3 - - + -
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Residues in contact with GLU 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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64A VAL* 3.3 32.9 - - - +
67A GLY* 3.5 21.8 - - - +
69A ARG* 5.3 7.9 - - - +
247A MET* 3.1 23.1 + - + +
248A THR* 3.6 25.0 + - - +
249A VAL 3.2 0.2 - - - -
250A LEU* 1.3 74.2 - - + +
252A GLU* 1.3 62.0 + - - +
254A GLY* 2.8 21.1 + - - -
255A LEU* 3.8 16.0 + - + +
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Residues in contact with GLU 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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130A LYS* 5.3 3.7 - - - -
134A LEU* 3.9 16.0 - - + +
138A LYS* 3.0 27.7 + - - -
139A TYR* 2.3 36.7 + - - -
248A THR 3.0 16.8 + - - +
249A VAL* 3.6 6.9 - - - +
251A GLU* 1.3 76.1 - - - +
253A ALA* 1.3 58.0 + - - +
254A GLY* 3.1 5.0 + - - -
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Residues in contact with ALA 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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126A ALA 5.3 0.2 - - - -
127A ILE* 3.4 39.6 - - - +
130A LYS* 3.8 25.2 - - + +
131A ALA* 3.7 17.7 - - + +
134A LEU* 4.1 3.1 - - + +
249A VAL 2.8 16.8 + - - +
250A LEU 3.6 7.2 - - - +
251A GLU 3.2 0.6 - - - -
252A GLU* 1.3 74.5 - - - +
254A GLY* 1.3 58.0 + - - +
255A LEU 3.7 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
------------------------------------------------------------
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