Contacts of the helix formed by residues 239 - 255 (chain A) in PDB entry 3Q72
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 ASN 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ILE* 3.8 20.3 - - + +
231A GLU 3.0 27.3 + - - +
232A THR* 3.7 4.9 - - + +
237A HIS 3.8 1.6 + - - -
238A HIS* 1.3 102.0 + - - +
240A VAL* 1.3 59.3 + - - +
241A GLN 3.4 1.8 - - - +
242A ALA* 3.7 15.5 - - - +
243A LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.6 39.9 - - + +
110A ILE* 3.9 36.6 - - + -
111A PHE* 4.3 6.1 - - + +
232A THR* 4.6 2.0 - - - -
233A SER 4.4 4.0 - - - +
237A HIS* 4.2 18.9 + - + +
238A HIS 3.0 11.1 - - - +
239A ASN* 1.3 78.0 - - - +
241A GLN* 1.3 64.4 + - - +
243A LEU* 3.3 9.9 + - - +
244A PHE* 3.3 29.9 - - + -
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 4.4 10.5 - - - -
129A ARG* 3.4 40.2 + - - +
131A ILE* 3.5 24.2 - - - +
237A HIS 5.4 0.8 + - - -
239A ASN* 3.4 0.4 - - - +
240A VAL* 1.3 81.9 - - - +
242A ALA* 1.3 61.0 + - - +
244A PHE* 3.2 3.1 + - - -
245A GLU* 3.0 48.2 + - - +
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Residues in contact with ALA 242 (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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230A ILE* 3.9 17.1 - - + +
239A ASN* 3.5 24.5 + - - +
240A VAL 3.3 0.2 - - - -
241A GLN* 1.3 78.4 - - - +
243A LEU* 1.3 64.6 + - - +
245A GLU* 3.4 9.6 + - - +
246A GLY* 2.9 20.6 + - - -
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Residues in contact with LEU 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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96A LEU* 6.1 0.2 - - + -
107A LEU* 4.7 16.2 - - + -
166A VAL* 4.5 10.1 - - + -
199A ILE* 3.5 19.8 - - + +
201A VAL* 3.3 34.1 - - + -
230A ILE* 3.8 15.6 - - + +
232A THR* 4.3 9.6 - - + -
239A ASN 2.9 18.1 + - - +
240A VAL* 3.4 4.5 - - - +
241A GLN 3.2 0.2 - - - -
242A ALA* 1.3 76.5 - - - +
244A PHE* 1.3 88.3 + - + +
246A GLY* 3.1 4.4 + - - -
247A VAL* 3.0 31.2 + - + +
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Residues in contact with PHE 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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94A VAL* 4.6 10.3 - - + -
96A LEU* 4.5 9.6 - - + -
107A LEU* 4.1 14.4 - - + -
108A ALA* 4.9 2.7 - - - -
111A PHE* 3.4 48.0 - + + -
131A ILE* 3.6 4.8 - - + +
140A LEU* 3.6 21.2 - - + +
142A VAL* 3.4 37.9 - - + -
166A VAL* 5.2 2.2 - - + -
240A VAL* 3.3 24.8 + - + +
241A GLN* 3.2 5.3 + - - +
243A LEU* 1.3 97.8 - - + +
245A GLU* 1.3 63.8 + - - +
247A VAL* 3.7 11.8 + - + +
248A VAL* 3.3 25.5 + - - +
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Residues in contact with GLU 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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131A ILE* 4.0 9.1 - - + +
132A VAL 4.5 8.5 - - - +
133A VAL* 3.7 32.0 - - + +
241A GLN* 3.0 42.1 + - - +
242A ALA* 3.8 8.5 - - - +
244A PHE* 1.3 76.9 - - - +
246A GLY* 1.3 58.6 + - - +
248A VAL* 3.3 4.2 + - - +
249A ARG* 3.0 44.8 + - - +
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Residues in contact with GLY 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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199A ILE* 5.1 3.4 - - - -
228A LYS* 5.5 14.4 - - - -
242A ALA 2.9 15.6 + - - -
243A LEU* 3.1 4.9 + - - -
245A GLU* 1.3 74.1 - - - +
247A VAL* 1.3 55.3 + - - +
249A ARG* 2.9 10.8 + - - +
250A GLN* 2.6 40.0 + - - +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 3.8 22.2 - - + -
140A LEU* 4.8 4.3 - - + -
164A ALA* 3.9 9.8 - - + +
166A VAL* 3.7 21.1 - - + -
199A ILE* 3.5 30.0 - - + +
243A LEU* 3.0 22.0 + - + +
244A PHE* 3.7 17.7 - - + +
245A GLU 3.4 0.2 - - - -
246A GLY* 1.3 73.9 - - - +
248A VAL* 1.3 57.8 + - - +
250A GLN* 3.7 1.3 - - - +
251A ILE* 2.9 53.3 + - + +
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Residues in contact with VAL 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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92A TYR* 4.6 6.5 - - + -
131A ILE* 4.0 14.1 - - + -
133A VAL* 4.0 9.9 - - + -
138A ALA* 3.8 17.9 - - + -
140A LEU* 3.8 27.1 - - + -
244A PHE 3.3 15.0 + - - +
245A GLU 3.3 8.2 + - - +
246A GLY 3.1 0.6 - - - -
247A VAL* 1.3 73.2 - - - +
249A ARG* 1.3 66.6 + - - +
251A ILE* 3.4 8.7 + - - +
252A ARG* 3.0 61.1 + - + +
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 2.9 29.2 - - - +
134A ASP* 3.0 34.1 + - - +
245A GLU* 3.0 30.4 + - - +
246A GLY* 2.9 12.7 + - - +
248A VAL* 1.3 76.6 - - - +
250A GLN* 1.3 62.4 + - - +
252A ARG* 2.9 16.5 + - + +
253A LEU* 2.9 28.3 + - + +
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Residues in contact with GLN 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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197A PRO* 3.6 28.2 - - + +
198A ILE 5.2 2.0 - - - +
199A ILE* 4.5 9.2 - - + -
228A LYS* 4.1 28.1 - - + +
246A GLY* 2.6 21.2 + - - +
247A VAL* 3.7 6.7 - - - +
249A ARG* 1.3 72.4 - - - +
251A ILE* 1.3 68.1 + - - +
252A ARG 2.9 1.6 - - - -
253A LEU* 2.8 37.2 + - - +
254A ARG* 3.2 17.8 + - - +
182B GLU* 3.7 18.9 - - - +
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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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92A TYR* 3.7 50.0 - - + +
94A VAL* 4.8 3.4 - - + -
140A LEU* 5.3 1.1 - - + -
163A ASP* 3.5 26.9 - - + +
164A ALA* 3.9 11.7 - - + -
197A PRO* 3.5 9.6 - - + +
247A VAL* 2.9 46.6 + - + +
248A VAL* 3.7 8.3 - - - +
250A GLN* 1.3 71.4 - - - +
252A ARG* 1.3 58.9 + - - +
255A ARG* 2.6 56.4 + - + +
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Residues in contact with ARG 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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1A CA 2.6 28.1 - - - -
92A TYR* 4.3 19.8 + - + +
133A VAL* 2.6 31.5 + - - +
134A ASP* 3.6 7.3 + - - +
136A GLU* 3.2 50.2 + - - +
137A GLU 3.6 10.1 + - - -
138A ALA* 3.7 9.3 - - - +
248A VAL* 3.0 37.1 + - - +
249A ARG* 2.9 15.4 + - + +
250A GLN 2.9 0.8 - - - -
251A ILE* 1.3 77.6 - - + +
253A LEU* 1.3 60.6 + - - +
255A ARG* 3.8 5.9 + - - +
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Residues in contact with LEU 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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249A ARG* 2.9 12.2 + - + +
250A GLN* 2.8 40.9 + - - +
252A ARG* 1.3 74.0 - - - +
254A ARG* 1.3 65.9 + - + +
255A ARG 4.6 1.7 - - - -
178B GLU* 5.8 4.0 - - - +
182B GLU* 4.6 22.0 - - + +
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Residues in contact with ARG 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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184A ARG* 5.2 3.0 - - - +
195A ASP* 3.3 29.2 + - - +
196A VAL 3.8 16.6 + - - -
197A PRO* 3.7 26.9 - - + +
198A ILE* 4.9 2.2 - - - +
226A ASP* 3.5 25.7 + - - -
250A GLN* 3.2 14.2 + - - +
253A LEU* 1.3 79.2 - - + +
255A ARG* 1.3 85.8 + - - +
179B LYS* 3.3 14.6 - - - +
182B GLU* 3.3 35.2 + - - -
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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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1A CA 3.3 24.4 - - - -
92A TYR* 5.9 2.5 - - + +
163A ASP* 3.2 38.6 + - - +
195A ASP 4.5 2.6 + - - -
196A VAL* 4.2 10.3 - - - +
197A PRO* 3.3 9.5 - - - +
251A ILE* 2.6 61.4 + - + +
252A ARG* 3.8 3.6 + - - +
253A LEU 3.5 2.1 - - - -
254A ARG* 1.3 107.6 - - - +
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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