Contacts of the helix formed by residues 1233 - 1248 (chain A) in PDB entry 5W0N
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 SER1233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998A LEU* 5.1 4.2 + - - +
1002A ASP* 2.9 31.3 + - - -
1143A ARG* 4.7 1.8 - - - +
1231A THR 3.6 2.6 + - - -
1232A GLU* 1.3 77.7 - - - +
1234A VAL* 1.3 65.1 + - - +
1236A GLN* 3.4 22.4 + - - +
1237A LEU* 3.1 22.3 + - - +
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Residues in contact with VAL1234 (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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1002A ASP* 3.6 7.3 + - + +
1005A CYS* 3.4 28.7 - - + -
1006A ILE* 4.6 10.8 - - + -
1143A ARG* 4.0 16.8 - - + +
1146A TYR* 3.5 42.6 - - + -
1147A LEU* 3.9 14.7 - - + +
1233A SER* 1.3 73.8 - - - +
1235A GLY* 1.3 58.4 + - - +
1237A LEU* 3.1 9.5 + - - +
1238A TRP* 2.8 27.0 + - - +
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Residues in contact with GLY1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A LEU* 5.8 0.2 - - - -
1001A LEU* 3.8 35.7 - - - +
1002A ASP* 2.7 24.2 + - - +
1005A CYS* 4.2 6.3 - - - -
1234A VAL* 1.3 74.1 - - - +
1236A GLN* 1.3 61.3 + - - +
1238A TRP* 3.8 2.0 - - - +
1239A LEU* 3.0 25.5 + - - +
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Residues in contact with GLN1236 (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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998A LEU* 5.4 17.6 + - + +
1001A LEU* 6.0 0.2 - - - -
1002A ASP* 3.9 0.2 + - - -
1184A ARG* 4.3 4.1 + - - +
1232A GLU* 3.5 33.4 + - - +
1233A SER* 3.4 33.8 + - - +
1234A VAL 3.3 0.2 - - - -
1235A GLY* 1.3 76.3 - - - +
1237A LEU* 1.3 56.1 + - - +
1239A LEU* 3.7 4.8 + - - +
1240A GLY* 3.0 23.6 + - - -
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Residues in contact with LEU1237 (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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1143A ARG* 3.8 37.0 - - + +
1147A LEU* 3.8 26.0 - - + +
1180A PHE* 3.4 20.5 - - + -
1181A LEU* 4.4 0.9 - - + -
1184A ARG* 3.9 10.8 - - + +
1188A VAL* 4.1 22.2 - - + -
1232A GLU* 3.6 33.9 - - + +
1233A SER 3.1 19.7 + - - +
1234A VAL* 3.1 6.9 + - - +
1236A GLN* 1.3 74.8 - - - +
1238A TRP* 1.3 61.7 + - - +
1240A GLY* 3.2 0.8 + - - +
1241A LEU* 2.8 24.8 + - - +
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Residues in contact with TRP1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A LEU* 5.6 3.1 - - + -
1005A CYS* 3.6 24.2 - - - -
1147A LEU* 3.5 21.7 - - + +
1150A THR* 3.5 18.3 - - + +
1151A MET* 3.9 32.5 - - + -
1154A PHE* 3.9 37.0 - + + -
1234A VAL 2.8 20.4 + - - +
1235A GLY* 3.3 4.2 + - - +
1237A LEU* 1.3 69.7 - - - +
1239A LEU* 1.3 67.3 + - + +
1241A LEU* 3.2 24.7 + - + +
1242A LEU* 3.1 46.1 + - + +
1311A PHE* 3.4 45.5 - + + -
1330A PHE* 5.0 0.2 - + - -
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Residues in contact with LEU1239 (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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990A LEU* 4.5 9.2 - - + -
993A LEU* 4.0 27.8 - - + -
998A LEU* 6.0 0.4 - - + -
1001A LEU* 4.6 8.1 - - + -
1235A GLY 3.0 15.8 + - - +
1236A GLN* 4.1 4.5 - - - +
1238A TRP* 1.3 78.3 - - - +
1240A GLY* 1.3 61.6 + - - +
1242A LEU* 3.3 12.0 + - + +
1243A ARG* 3.0 49.1 + - + +
1308A ARG* 4.2 7.6 - - - +
1311A PHE* 4.1 11.9 - - + +
1312A GLY* 3.7 33.9 - - - +
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Residues in contact with GLY1240 (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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1180A PHE* 3.7 7.8 - - - -
1184A ARG* 4.0 20.8 + - - -
1236A GLN 3.0 17.0 + - - -
1237A LEU 3.6 3.6 - - - -
1238A TRP 3.2 0.4 - - - -
1239A LEU* 1.3 77.2 - - - +
1241A LEU* 1.3 50.2 + - - +
1243A ARG* 3.4 8.1 + - - +
1244A PHE* 2.7 36.2 + - - +
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Residues in contact with LEU1241 (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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1147A LEU* 5.4 3.6 - - + -
1151A MET* 3.7 23.1 - - + -
1177A VAL* 4.0 36.8 - - + -
1180A PHE* 3.5 32.0 - - + -
1237A LEU 2.8 13.5 + - - +
1238A TRP* 3.2 30.0 + - + +
1240A GLY* 1.3 74.3 - - - +
1242A LEU* 1.3 76.4 + - + +
1244A PHE* 3.1 1.9 + - - +
1245A TYR* 3.1 40.1 + - + +
1304A PHE* 4.4 3.6 - - + -
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Residues in contact with LEU1242 (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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1154A PHE* 4.5 9.2 - - + -
1238A TRP* 3.1 55.2 + - + +
1239A LEU* 3.7 9.0 - - + +
1241A LEU* 1.3 79.6 - - + +
1243A ARG* 1.3 61.1 + - - +
1245A TYR* 3.7 0.9 + - - +
1246A THR* 2.7 33.2 + - - +
1304A PHE* 3.9 34.5 - - + +
1307A GLY* 3.7 23.1 - - - +
1308A ARG* 4.2 15.9 - - + +
1311A PHE* 3.8 14.8 - - + -
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Residues in contact with ARG1243 (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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990A LEU* 3.5 31.3 - - + +
1239A LEU* 3.0 35.2 + - + +
1240A GLY* 3.8 7.4 - - - +
1242A LEU* 1.3 73.5 - - - +
1244A PHE* 1.3 59.2 + - - +
1246A THR* 3.4 6.3 - - - -
1247A GLU* 2.7 75.4 + - - +
1248A GLU* 5.2 0.4 - - - -
1308A ARG* 4.4 5.3 - - + +
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Residues in contact with PHE1244 (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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1179A TYR* 4.3 11.2 - + - -
1180A PHE* 3.7 35.0 - + + -
1183A GLN* 4.7 15.9 - - + -
1184A ARG* 5.4 1.1 - - - +
1240A GLY 2.7 21.3 + - - +
1241A LEU 3.1 4.0 + - - +
1243A ARG* 1.3 73.3 - - - +
1245A TYR* 1.3 94.0 + + - +
1248A GLU* 3.0 50.3 + - + +
1249A PHE* 2.7 57.1 + + + +
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Residues in contact with TYR1245 (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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1151A MET* 5.0 0.2 - - + -
1176A MET* 2.6 67.0 + - + +
1179A TYR* 3.7 15.3 - + - -
1180A PHE* 3.9 1.9 + - + -
1241A LEU* 3.1 43.9 + - + +
1242A LEU 4.6 1.3 - - - +
1244A PHE* 1.3 104.5 - + - +
1246A THR* 1.3 60.1 + - - +
1249A PHE* 4.0 13.0 - + + +
1251A PHE* 3.2 43.1 - + + -
1256A ILE* 3.8 15.3 - - + +
1301A MET* 3.6 9.4 - - - +
1304A PHE* 4.8 15.0 - + + +
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Residues in contact with THR1246 (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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987A LEU* 3.8 20.6 - - - +
1242A LEU 2.7 23.6 + - - +
1243A ARG* 3.2 4.0 + - - -
1245A TYR* 1.3 82.1 - - + +
1247A GLU* 1.3 62.5 + - - +
1249A PHE 5.6 1.3 - - - -
1301A MET* 4.9 7.1 - - + +
1304A PHE* 3.9 38.4 - - + +
1305A ILE* 4.0 14.6 - - + +
1308A ARG* 3.4 18.7 - - - -
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Residues in contact with GLU1247 (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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987A LEU* 3.8 14.4 - - + -
1243A ARG* 2.7 62.8 + - - +
1246A THR* 1.3 81.4 - - - +
1248A GLU* 1.3 61.0 + - + +
1249A PHE 5.1 1.7 - - - +
1308A ARG* 2.7 31.6 + - - -
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Residues in contact with GLU1248 (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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1184A ARG* 5.1 6.9 + - - -
1243A ARG 4.5 0.4 - - - +
1244A PHE* 3.0 42.2 + - + +
1247A GLU* 1.3 81.6 - - + +
1249A PHE* 1.3 68.0 + - - +
1250A ASP* 3.4 4.7 + - - +
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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