Contacts of the helix formed by residues 1226 - 1245 (chain D) in PDB entry 6JBQ
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 VAL1226 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886D VAL* 4.3 26.2 - - + +
887D SER* 6.1 1.3 - - - -
1221D LEU* 4.2 9.4 - - + -
1225D GLY* 1.3 77.6 - - - -
1227D HIS* 1.3 79.8 + - + +
1228D ALA 3.4 0.7 - - - -
1229D VAL* 3.4 12.7 - - - +
1230D THR* 3.3 13.7 - - - +
1261D LEU* 4.6 18.7 - - + +
1304D ARG* 4.3 24.2 - - - +
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Residues in contact with HIS1227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818D GLU* 5.1 9.6 + - - +
819D GLY 3.7 21.7 + - - -
820D ILE* 3.4 29.2 - - + +
884D SER* 4.8 0.8 + - - -
886D VAL* 5.0 4.6 - - - +
887D SER* 3.7 29.9 - - - -
1225D GLY* 3.7 0.4 - - - -
1226D VAL* 1.3 88.1 - - + +
1228D ALA* 1.3 59.4 + - - +
1229D VAL 3.4 0.2 - - - -
1230D THR* 3.3 8.7 - - - +
1231D ARG* 2.9 31.6 + - - +
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Residues in contact with ALA1228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220D ILE* 4.4 3.8 - - + +
1224D ARG* 3.9 45.0 + - + +
1225D GLY 4.6 0.2 - - - -
1226D VAL 3.4 1.6 - - - +
1227D HIS* 1.3 79.7 - - - +
1229D VAL* 1.3 57.4 + - - +
1231D ARG* 3.4 18.4 + - - +
1232D TYR* 2.9 29.5 + - - +
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Residues in contact with VAL1229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217D PRO* 3.8 29.6 - - + +
1220D ILE* 3.8 18.3 - - + +
1221D LEU* 3.8 30.3 - - + +
1225D GLY 3.9 3.8 + - - +
1226D VAL 3.4 14.8 - - - +
1228D ALA* 1.3 78.3 - - - +
1230D THR* 1.3 62.2 + - - +
1232D TYR* 3.4 5.8 + - + +
1233D ILE* 2.9 33.5 + - + +
1261D LEU* 5.2 4.3 - - + -
1306D LEU* 3.8 27.6 - - + -
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Residues in contact with THR1230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820D ILE* 5.5 4.9 - - + -
886D VAL* 4.0 24.9 - - + +
1226D VAL 3.3 13.9 - - - +
1227D HIS* 3.3 20.6 - - - +
1229D VAL* 1.3 79.5 - - - +
1231D ARG* 1.3 59.8 + - - +
1233D ILE* 3.7 6.4 - - - +
1234D VAL* 2.9 37.2 + - - +
1254D GLU* 4.3 9.5 - - + +
1257D VAL* 3.2 33.0 - - - +
1261D LEU* 5.7 1.6 - - - -
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Residues in contact with ARG1231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820D ILE* 6.4 1.3 - - + -
821D MET 5.4 8.3 - - - -
823D THR* 5.1 17.1 - - - +
838D ARG* 6.1 3.1 - - - +
1227D HIS* 2.9 20.5 + - - +
1228D ALA* 3.6 17.8 + - - +
1229D VAL 3.3 0.2 - - - -
1230D THR* 1.3 77.9 - - - +
1232D TYR* 1.3 57.1 + - - +
1234D VAL* 3.4 8.7 - - + +
1235D ASN* 2.9 50.1 + - - +
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Residues in contact with TYR1232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140D ARG* 3.7 20.7 + - - -
1144D LEU* 5.1 3.7 - - + +
1214D PRO* 6.1 0.3 - - - +
1215D GLU* 4.2 39.5 + - + +
1216D ALA 5.8 0.2 - - - -
1217D PRO* 4.8 15.9 - - + -
1220D ILE* 5.5 9.9 - - + -
1228D ALA 2.9 17.7 + - - +
1229D VAL* 3.8 11.0 - - + +
1230D THR 3.4 0.2 - - - -
1231D ARG* 1.3 76.3 - - - +
1233D ILE* 1.3 75.0 + - + +
1235D ASN* 3.9 5.5 - - + +
1236D GLU* 2.9 48.8 + - + +
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Residues in contact with ILE1233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144D LEU* 3.8 43.7 - - + +
1145D PHE* 5.2 9.6 - - + -
1217D PRO* 4.9 9.6 - - + -
1229D VAL* 2.9 29.2 + - + +
1230D THR* 3.7 7.0 - - - +
1231D ARG 3.3 0.2 - - - -
1232D TYR* 1.3 88.5 - - + +
1234D VAL* 1.3 61.3 + - + +
1236D GLU* 3.4 3.4 + - - +
1237D VAL* 3.0 30.3 + - + +
1253D ILE* 4.5 15.5 - - + -
1257D VAL* 4.3 24.2 - - + -
1260D MET* 5.4 6.3 - - + -
1306D LEU* 5.7 0.9 - - + -
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Residues in contact with VAL1234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838D ARG* 5.3 11.4 - - - +
1230D THR* 2.9 33.0 + - - +
1231D ARG* 3.4 13.2 - - + +
1233D ILE* 1.3 78.5 - - + +
1235D ASN* 1.3 63.1 + - - +
1237D VAL* 3.6 7.8 - - + +
1238D GLN* 2.9 33.1 + - - +
1250D ASP* 4.7 17.2 - - + +
1253D ILE* 3.8 29.2 - - + -
1254D GLU* 4.5 21.1 - - + +
1257D VAL* 5.3 0.2 - - + -
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Residues in contact with ASN1235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825D VAL* 4.7 23.0 - - - +
838D ARG* 4.8 13.8 + - - +
1231D ARG* 2.9 44.5 + - - +
1232D TYR* 3.9 6.7 - - + +
1234D VAL* 1.3 82.6 - - - +
1236D GLU* 1.3 57.3 + - - +
1238D GLN* 3.8 4.5 - - - +
1239D ASP* 2.9 38.6 + - - +
1242D ARG* 5.7 1.4 - - - +
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Residues in contact with GLU1236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140D ARG* 3.8 30.4 + - - +
1144D LEU* 3.8 24.9 - - + -
1232D TYR* 2.9 38.4 + - + +
1233D ILE 3.8 2.7 - - - +
1235D ASN* 1.3 76.6 - - - +
1237D VAL* 1.3 58.1 + - - +
1239D ASP* 3.3 8.2 + - - +
1240D VAL* 3.0 40.6 + - + +
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Residues in contact with VAL1237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141D VAL* 4.6 14.6 - - + -
1144D LEU* 4.1 17.3 - - + -
1145D PHE* 4.8 11.9 - - + -
1233D ILE* 3.0 22.3 + - + +
1234D VAL* 3.6 6.7 - - - +
1236D GLU* 1.3 77.4 - - - +
1238D GLN* 1.3 59.7 + - - +
1240D VAL* 3.4 4.6 + - + +
1241D TYR* 2.9 56.9 + - + +
1253D ILE* 3.7 37.2 - - + -
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Residues in contact with GLN1238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833D GLU* 4.3 7.9 + - - +
838D ARG* 5.3 4.0 - - - +
1234D VAL 2.9 20.3 + - - +
1235D ASN* 3.9 6.3 - - - +
1237D VAL* 1.3 76.3 - - - +
1239D ASP* 1.3 59.1 + - - +
1241D TYR* 3.7 8.6 - - - +
1242D ARG* 2.9 58.7 + - - +
1246D VAL 5.0 2.0 + - - -
1247D LYS* 4.1 13.3 - - - +
1248D ILE* 2.8 37.9 + - - +
1250D ASP* 3.0 23.7 - - - +
1253D ILE* 3.7 17.0 - - - +
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Residues in contact with ASP1239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825D VAL* 4.7 6.4 - - - +
832D LYS* 3.4 22.5 + - - +
1235D ASN* 2.9 24.0 + - - +
1236D GLU* 3.3 9.4 + - - +
1238D GLN* 1.3 76.8 - - - +
1240D VAL* 1.3 57.1 + - + +
1242D ARG* 2.5 32.6 + - - +
1243D LEU* 2.9 30.1 + - - +
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Residues in contact with VAL1240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930D LEU* 4.6 6.4 - - + +
1136D GLY* 5.7 2.7 - - - -
1137D GLY* 4.2 17.5 - - - +
1140D ARG* 4.1 23.3 - - + -
1141D VAL* 3.8 28.5 - - + -
1144D LEU* 5.2 1.6 - - + -
1236D GLU* 3.0 30.3 + - + +
1237D VAL* 3.7 7.4 - - - +
1239D ASP* 1.3 77.3 - - + +
1241D TYR* 1.3 68.2 + - + +
1242D ARG 3.4 0.5 + - - -
1243D LEU* 3.4 18.1 + - - +
1244D GLN* 3.8 7.3 + - - +
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Residues in contact with TYR1241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D LEU* 5.5 1.0 - - - +
923D ILE* 3.3 35.2 + - + +
926D PRO* 5.3 7.9 - - + -
927D GLY* 5.9 0.6 + - - -
930D LEU* 3.6 36.5 - - + +
1138D LEU* 5.9 0.5 - - - +
1141D VAL* 3.4 22.9 - - + +
1237D VAL* 2.9 40.0 + - + +
1238D GLN* 4.1 10.3 - - - +
1240D VAL* 1.3 78.5 - - + +
1242D ARG* 1.3 57.5 + - - +
1244D GLN* 3.8 3.1 + - - +
1245D GLY 3.4 4.7 + - - -
1246D VAL* 2.9 43.4 + - + +
1248D ILE* 3.7 39.0 - - + -
1253D ILE* 5.1 5.4 - - + -
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Residues in contact with ARG1242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825D VAL* 3.7 13.5 - - - +
832D LYS* 3.4 43.5 + - - +
833D GLU* 3.0 38.7 + - - +
838D ARG* 5.3 0.6 - - - +
1235D ASN* 5.7 1.4 - - - +
1238D GLN* 2.9 47.1 + - + +
1239D ASP* 2.5 33.7 + - - +
1240D VAL 3.3 0.2 - - - -
1241D TYR* 1.3 73.8 - - - +
1243D LEU* 1.3 63.5 + - - +
1244D GLN 3.2 2.8 + - - -
1245D GLY* 3.6 11.6 + - - +
1246D VAL 4.5 4.0 - - - +
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Residues in contact with LEU1243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832D LYS* 6.3 0.9 - - - +
1136D GLY* 5.6 8.3 - - - +
1239D ASP 2.9 18.1 + - - +
1240D VAL* 3.4 9.4 + - - +
1242D ARG* 1.3 78.3 - - - +
1244D GLN* 1.3 61.1 + - - +
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Residues in contact with GLN1244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929D GLN* 3.4 27.0 + - + +
930D LEU* 3.8 25.2 - - + +
931D THR* 3.5 30.5 - - - +
1240D VAL 3.8 3.9 + - - +
1241D TYR 3.8 6.0 + - - +
1242D ARG 3.2 0.4 - - - -
1243D LEU* 1.3 81.7 + - - +
1245D GLY* 1.3 58.4 + - - +
1246D VAL* 4.5 10.3 - - + -
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Residues in contact with GLY1245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241D TYR 3.4 3.4 + - - -
1242D ARG* 3.6 11.8 + - - -
1244D GLN* 1.3 79.3 - - - +
1246D VAL* 1.3 65.2 + - - +
1247D LYS 4.2 0.7 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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