Contacts of the helix formed by residues 1223 - 1244 (chain A) in PDB entry 2N1G
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 SER1223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180A SER 5.4 4.7 - - - -
1220A SER* 5.0 7.9 - - - -
1221A VAL 5.4 0.5 + - - -
1222A GLU* 1.3 82.9 + - - +
1224A VAL* 1.4 63.0 + - - +
1225A TRP* 3.0 31.6 + - - -
1226A ASN* 3.2 21.8 + - - +
1227A MET* 4.3 4.6 + - - +
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Residues in contact with VAL1224 (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 SER 4.5 8.5 + - - +
1181A ASP* 4.2 18.6 - - - +
1182A PRO* 3.7 34.5 - - + +
1187A ILE* 5.5 4.0 - - + -
1223A SER* 1.4 72.7 - - - +
1225A TRP* 1.3 56.5 + - + +
1227A MET* 3.0 35.5 + - + +
1228A ALA* 2.9 28.6 + - + +
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Residues in contact with TRP1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A TRP* 3.0 70.2 - + - -
1176A ILE* 3.0 30.5 + - + -
1177A THR 5.4 0.4 + - - -
1179A ILE* 3.0 29.3 + - + -
1180A SER* 4.7 2.0 + - - +
1182A PRO* 3.4 37.5 - - + +
1217A MET* 3.2 36.0 - - + +
1220A SER* 3.6 19.7 - - - +
1223A SER* 3.0 22.1 - - - -
1224A VAL* 1.3 77.4 - - - +
1226A ASN* 1.3 58.7 + - - +
1228A ALA* 3.8 3.8 - - + -
1229A PHE 2.9 22.0 + - - -
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Residues in contact with ASN1226 (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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1217A MET 3.1 9.6 + - - -
1218A GLN 5.0 1.8 - - - +
1220A SER* 2.8 41.1 + - - +
1221A VAL 3.1 20.3 + - - +
1222A GLU* 4.6 1.0 - - - -
1223A SER 3.2 17.2 + - - +
1224A VAL 3.2 0.8 - - - -
1225A TRP* 1.3 75.1 - - - +
1227A MET* 1.3 63.4 + - + +
1229A PHE* 3.3 20.8 - - + +
1230A ASP* 3.3 10.6 + - - +
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Residues in contact with MET1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223A SER 4.8 3.4 - - - +
1224A VAL* 3.0 41.1 + - + +
1226A ASN* 1.3 76.6 - - + +
1228A ALA* 1.3 61.1 + - - +
1230A ASP* 3.4 6.8 + - - +
1231A PHE* 2.9 29.9 + - - +
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Residues in contact with ALA1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A TRP* 5.7 0.2 - - + -
1182A PRO* 5.4 0.4 - - + -
1187A ILE* 5.2 14.8 - - + -
1217A MET* 3.8 21.3 - - + -
1224A VAL* 2.9 20.9 + - + +
1225A TRP* 3.7 14.1 - - + +
1227A MET* 1.3 74.7 - - - +
1229A PHE* 1.3 63.9 + - - +
1231A PHE* 4.3 6.5 - - - -
1232A ILE* 3.0 37.6 + - + +
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Residues in contact with PHE1229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214A LYS* 3.6 53.8 - - + -
1217A MET* 3.3 21.9 - - + +
1218A GLN* 3.5 29.8 - - - -
1225A TRP 2.9 16.0 + - - +
1226A ASN* 3.3 18.2 - - + +
1228A ALA* 1.3 73.6 - - - +
1230A ASP* 1.3 74.2 + - + +
1232A ILE* 4.5 1.1 - - - +
1233A LEU* 3.1 52.6 + - + +
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Residues in contact with ASP1230 (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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1226A ASN 3.3 10.5 + - - +
1227A MET* 3.8 9.8 - - - +
1228A ALA 3.3 0.4 - - - -
1229A PHE* 1.3 89.1 - - + +
1231A PHE* 1.3 57.5 + - - +
1233A LEU* 4.1 2.9 - - - +
1234A ASP* 3.1 31.9 + - - +
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Residues in contact with PHE1231 (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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1187A ILE* 4.1 23.8 - - + -
1188A LEU* 6.3 0.4 - - - -
1191A VAL* 3.9 24.0 - - + -
1227A MET 2.9 17.6 + - - +
1228A ALA* 3.8 6.5 - - - +
1229A PHE 3.3 0.2 - - - -
1230A ASP* 1.3 76.5 - - - +
1232A ILE* 1.3 67.3 + - + +
1234A ASP* 3.2 5.6 + - - +
1235A ASN* 2.9 52.6 + - - -
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Residues in contact with ILE1232 (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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1175A TRP* 4.5 4.3 - - + -
1187A ILE* 4.6 5.8 - - + -
1190A VAL* 3.7 17.3 - - + -
1191A VAL* 3.7 29.4 - - + +
1194A CYS* 3.9 22.3 - - - +
1210A ILE* 4.3 3.8 - - + -
1213A MET* 3.4 37.9 - - + -
1217A MET* 3.8 16.6 - - + -
1228A ALA* 3.0 22.9 + - + +
1229A PHE* 4.5 1.3 - - - +
1231A PHE* 1.3 80.6 - - + +
1233A LEU* 1.3 57.2 + - - +
1235A ASN* 3.5 2.4 + - - +
1236A VAL* 3.1 29.8 + - - +
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Residues in contact with LEU1233 (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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1210A ILE* 3.8 29.8 - - + -
1214A LYS* 5.2 7.6 - - + +
1229A PHE* 3.1 49.0 + - + +
1230A ASP* 4.4 3.1 - - - +
1232A ILE* 1.3 75.3 - - - +
1234A ASP* 1.3 66.4 + - - +
1236A VAL* 3.2 9.5 - - + +
1237A GLN* 3.2 59.7 - - + +
1248A LEU* 5.1 1.3 - - + +
1250A VAL* 4.9 8.5 - - + -
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Residues in contact with ASP1234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A ASP* 3.1 25.0 + - - +
1231A PHE* 3.2 7.1 + - - +
1233A LEU* 1.3 79.1 - - - +
1235A ASN* 1.3 69.7 + - - +
1237A GLN* 3.2 4.6 + - - +
1238A VAL* 3.0 45.5 + - - +
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Residues in contact with ASN1235 (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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1191A VAL* 4.0 24.4 - - + +
1195A THR* 4.5 3.6 - - + -
1231A PHE* 2.9 59.8 + - - +
1232A ILE 4.1 1.6 - - - +
1234A ASP* 1.3 90.9 + - - +
1236A VAL* 1.4 61.6 + - - +
1238A VAL* 3.6 5.5 + - - +
1239A VAL* 3.2 32.0 + - + +
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Residues in contact with VAL1236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A VAL* 5.6 0.4 - - - +
1194A CYS* 3.8 16.8 - - + -
1195A THR* 4.5 6.2 - - - +
1198A ILE* 3.1 27.2 - - + +
1206A LEU* 3.6 36.6 - - + -
1210A ILE* 4.0 14.4 - - + -
1232A ILE 3.1 15.7 + - - +
1233A LEU* 3.2 25.1 - - + +
1235A ASN* 1.4 76.8 - - - +
1237A GLN* 1.3 66.0 + - + +
1238A VAL 3.4 0.2 + - - -
1239A VAL 3.4 1.0 + - - -
1240A LEU* 3.0 25.9 + - + +
1248A LEU* 6.2 3.1 - - + -
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Residues in contact with GLN1237 (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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1233A LEU* 3.2 47.0 - - + +
1234A ASP* 3.2 4.6 + - - +
1236A VAL* 1.3 79.6 - - + +
1238A VAL* 1.3 57.7 + - + +
1240A LEU* 3.6 8.9 - - + +
1241A GLN* 2.9 24.8 + - - +
1247A THR* 3.3 35.9 - - + +
1248A LEU* 2.8 34.7 + - + +
1249A LYS* 4.0 18.2 - - - +
1250A VAL 5.2 0.6 - - - +
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Residues in contact with VAL1238 (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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1234A ASP* 3.0 40.4 + - - +
1235A ASN* 3.8 7.4 - - - +
1237A GLN* 1.3 73.9 - - + +
1239A VAL* 1.3 66.2 + - + +
1241A GLN* 3.1 32.6 - - + +
1242A GLN* 3.2 34.7 + - + +
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Residues in contact with VAL1239 (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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1195A THR* 3.6 29.4 - - + +
1198A ILE* 3.8 25.4 - - + -
1199A GLU* 5.8 2.7 - - + +
1235A ASN* 3.2 16.4 + - + +
1238A VAL* 1.3 77.2 - - + +
1240A LEU* 1.3 51.7 + - - +
1242A GLN* 3.2 17.0 + - - +
1243A THR* 2.8 50.6 + - - +
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Residues in contact with LEU1240 (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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1198A ILE* 3.7 24.9 - - + +
1203A LEU* 4.6 9.9 - - + -
1206A LEU* 4.6 8.1 - - + -
1236A VAL* 3.0 18.7 + - + +
1237A GLN* 3.6 8.7 - - + +
1238A VAL 3.3 0.2 - - - -
1239A VAL* 1.3 78.0 - - - +
1241A GLN* 1.4 55.5 + - - +
1243A THR 4.5 0.2 - - - +
1244A TYR* 2.8 59.6 + - + +
1245A GLY 3.0 4.5 + - - -
1246A SER* 3.2 22.8 - - - +
1247A THR* 4.1 1.1 - - - -
1248A LEU* 3.5 45.5 - - + +
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Residues in contact with GLN1241 (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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1237A GLN 2.9 17.8 + - - +
1238A VAL* 3.1 34.6 - - - +
1240A LEU* 1.4 74.9 - - - +
1242A GLN* 1.3 65.1 + - + +
1245A GLY* 3.1 20.0 - - - -
1246A SER* 3.3 14.5 + - - +
1247A THR* 3.6 21.7 - - + +
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Residues in contact with GLN1242 (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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1238A VAL* 3.2 35.0 + - - +
1239A VAL* 3.5 19.8 - - + +
1241A GLN* 1.3 84.1 - - + +
1243A THR* 1.3 61.5 + - - +
1245A GLY 4.6 0.4 - - - -
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Residues in contact with THR1243 (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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1198A ILE* 3.9 15.8 - - + +
1199A GLU* 5.2 6.4 - - + +
1201A LYS* 6.3 0.4 - - - +
1239A VAL* 2.8 35.5 + - - +
1240A LEU 4.3 0.2 - - - -
1242A GLN* 1.3 80.6 - - - +
1244A TYR* 1.3 82.0 + - + +
1245A GLY 3.5 0.2 - - - -
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Residues in contact with TYR1244 (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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1198A ILE* 3.2 35.8 + - + -
1201A LYS* 3.6 28.8 + - - +
1203A LEU* 3.6 27.7 - - + +
1240A LEU* 2.8 36.1 + - + +
1243A THR* 1.3 89.9 - - + +
1245A GLY* 1.3 60.3 + - - +
1246A SER* 3.4 8.8 + - - +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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