Contacts of the helix formed by residues 1257 - 1276 (chain B) in PDB entry 3KHR
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 ASN1257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255B SER* 2.8 10.8 + - - +
1256B ARG* 1.3 77.1 - - - +
1258B LEU* 1.3 65.7 + - - +
1259B GLU* 3.5 10.4 + - - +
1260B GLU* 3.1 38.1 + - + +
1261B ILE* 3.1 23.9 + - - +
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Residues in contact with LEU1258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256B ARG 3.8 3.2 + - - -
1257B ASN* 1.3 76.5 - - - +
1259B GLU* 1.3 62.8 + - + +
1261B ILE* 3.8 3.5 - - - -
1262B LYS* 2.9 54.9 + - + +
1316B VAL* 4.1 17.5 - - + -
1319B LEU* 3.6 30.3 - - + -
1320B GLN* 3.7 31.2 - - + +
1323B LEU* 4.5 15.2 - - + +
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Residues in contact with GLU1259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257B ASN* 3.5 10.4 + - - +
1258B LEU* 1.3 80.9 - - + +
1260B GLU* 1.3 57.1 + - - +
1262B LYS* 3.0 41.2 + - - +
1263B PRO* 3.2 22.7 - - - +
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Residues in contact with GLU1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251B MET* 5.9 0.4 - - + -
1253B ARG* 3.0 56.2 + - - +
1255B SER* 3.8 22.4 + - - +
1257B ASN* 3.1 28.8 + - - +
1258B LEU 3.1 0.6 - - - -
1259B GLU* 1.3 78.3 - - - +
1261B ILE* 1.3 61.5 + - + +
1263B PRO* 3.3 11.4 - - - +
1264B TYR* 3.5 21.5 - - + -
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Residues in contact with ILE1261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251B MET* 3.8 25.1 - - + -
1255B SER* 4.1 19.7 - - - +
1256B ARG 4.4 2.9 - - - -
1257B ASN 3.1 21.8 + - - +
1258B LEU* 4.0 4.0 - - - +
1260B GLU* 1.3 75.9 - - - +
1262B LYS* 1.3 65.0 + - - +
1264B TYR* 2.9 17.2 + - - +
1265B LEU* 3.2 7.3 + - + -
1319B LEU* 3.6 28.7 - - + -
1323B LEU* 4.6 3.4 - - + -
1330B ILE* 3.7 30.1 - - + -
1333B ILE* 4.0 26.9 - - + -
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Residues in contact with LYS1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B LEU* 2.9 44.0 + - + +
1259B GLU* 3.0 34.9 + - - +
1261B ILE* 1.3 76.0 - - - +
1263B PRO* 1.3 63.2 - - + +
1265B LEU* 3.4 6.5 + - + -
1266B PHE* 2.9 70.3 + - + -
1316B VAL* 4.3 17.4 - - + +
1319B LEU* 5.0 2.5 - - + -
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Residues in contact with PRO1263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259B GLU 3.2 20.6 - - - +
1260B GLU 3.3 13.5 - - - +
1261B ILE 3.5 0.2 - - - -
1262B LYS* 1.3 92.3 - - + +
1264B TYR* 1.3 61.8 + - + +
1266B PHE* 4.1 7.1 - - + +
1267B ARG* 3.3 22.7 + - - +
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Residues in contact with TYR1264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249B VAL* 4.0 17.9 - - + +
1250B THR 3.8 9.0 - - - -
1251B MET* 3.3 40.8 - - + +
1252B LYS* 2.8 49.9 + - + +
1253B ARG* 4.3 2.5 + - - +
1260B GLU* 3.5 28.9 - - + -
1261B ILE 2.9 8.3 + - - +
1263B PRO* 1.3 78.0 - - + +
1265B LEU* 1.3 66.1 + - - +
1267B ARG* 3.4 23.0 + - - +
1268B ALA* 3.1 22.3 + - - +
1333B ILE* 3.5 18.6 - - + -
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Residues in contact with LEU1265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261B ILE* 3.2 8.5 + - + +
1262B LYS* 3.7 9.2 - - - +
1264B TYR* 1.3 79.7 - - - +
1266B PHE* 1.3 63.8 + - + +
1268B ALA* 3.3 7.1 + - - +
1269B ILE* 3.0 32.4 + - + +
1286B VAL* 3.8 24.5 - - + -
1315B SER* 3.3 47.8 - - - +
1316B VAL* 4.3 3.6 - - + +
1319B LEU* 3.9 22.2 - - + -
1333B ILE* 3.8 19.9 - - + +
1334B GLY 4.2 11.4 - - - +
1335B VAL* 4.6 5.2 - - + -
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Residues in contact with PHE1266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262B LYS* 2.9 57.4 + - + +
1263B PRO* 4.1 6.7 - - + +
1264B TYR 3.2 0.4 - - - -
1265B LEU* 1.3 83.6 - - + +
1267B ARG* 1.3 56.2 + - - +
1269B ILE* 3.4 8.3 + - + +
1270B GLU* 2.9 31.8 + - - +
1312B TYR* 3.4 45.6 - + + -
1315B SER* 3.8 16.4 - - - -
1316B VAL* 3.8 14.1 - - + -
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Residues in contact with ARG1267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247B ARG* 4.4 9.5 - - - +
1249B VAL* 3.8 28.3 - - - +
1250B THR 5.3 1.4 + - - -
1263B PRO 3.3 17.1 + - - +
1264B TYR* 3.9 30.2 - - - +
1266B PHE* 1.3 72.5 - - - +
1268B ALA* 1.3 67.1 + - - +
1270B GLU* 3.2 8.1 + - + +
1271B GLU* 3.0 49.1 + - + +
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Residues in contact with ALA1268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247B ARG* 3.6 31.6 - - + +
1249B VAL* 5.0 7.5 - - + +
1264B TYR 3.1 13.4 + - - +
1265B LEU* 3.3 12.3 + - - +
1267B ARG* 1.3 76.6 - - - +
1269B ILE* 1.3 55.7 + - - +
1272B SER* 2.8 33.8 + - - -
1333B ILE 4.6 3.6 - - - +
1334B GLY* 4.4 9.4 - - - -
1335B VAL* 3.6 15.7 - - + -
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Residues in contact with ILE1269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265B LEU* 3.0 19.8 + - + +
1266B PHE* 3.6 16.4 - - + +
1268B ALA* 1.3 74.5 - - - +
1270B GLU* 1.3 59.8 + - - +
1272B SER* 3.2 2.3 + - - -
1273B TYR* 2.8 31.3 + - + +
1308B LYS* 4.5 12.1 - - + -
1311B ALA* 3.8 31.0 - - + +
1312B TYR* 3.9 21.1 - - + -
1315B SER* 3.3 34.1 - - - +
1335B VAL* 3.7 26.7 - - + -
1337B PHE* 4.2 7.1 - - + -
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Residues in contact with GLU1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B PHE 2.9 14.9 + - - +
1267B ARG* 3.2 13.7 + - + +
1269B ILE* 1.3 77.9 - - - +
1271B GLU* 1.3 60.1 + - + +
1273B TYR* 3.4 2.3 + - - +
1274B TYR* 3.1 27.3 + - - +
1308B LYS* 2.7 36.2 + - - +
1312B TYR* 2.5 28.7 + - - +
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Residues in contact with GLU1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247B ARG* 2.8 48.7 + - - +
1267B ARG* 3.0 44.5 + - + +
1268B ALA 4.2 1.8 - - - +
1270B GLU* 1.3 75.5 - - + +
1272B SER* 1.3 65.4 + - - +
1274B TYR* 3.4 9.3 + - - +
1275B LYS* 3.2 32.2 + - - +
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Residues in contact with SER1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245B ILE* 3.7 8.8 - - - +
1246B GLY* 3.2 11.2 - - - -
1247B ARG* 3.1 30.8 + - - +
1268B ALA 2.8 18.4 + - - -
1269B ILE 3.5 3.4 - - - -
1271B GLU* 1.3 77.1 - - - +
1273B TYR* 1.3 62.7 + - - +
1275B LYS* 3.1 18.7 + - - +
1276B LEU* 3.3 11.2 + - - +
1335B VAL* 3.6 5.7 + - - -
1337B PHE* 3.6 23.8 - - - -
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Residues in contact with TYR1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B ILE* 2.8 19.6 + - + +
1270B GLU 3.9 0.7 - - - +
1272B SER* 1.3 69.4 - - - +
1274B TYR* 1.3 67.2 + - - +
1276B LEU* 3.2 41.8 + - + +
1277B ASP 4.4 0.9 + - - -
1279B ARG 5.5 2.2 - - - -
1280B ILE* 4.9 10.4 - - + +
1281B PRO* 4.2 10.0 - - + +
1306B ILE 2.4 30.1 + - - -
1307B SER* 3.4 10.2 - - - -
1308B LYS* 3.6 54.1 - - + -
1311B ALA* 4.9 0.7 - - + -
1337B PHE* 4.1 20.6 - + - -
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Residues in contact with TYR1274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B GLU 3.1 14.4 + - - +
1271B GLU* 3.5 14.1 - - - +
1273B TYR* 1.3 76.7 - - - +
1275B LYS* 1.3 68.6 + - + +
1276B LEU 3.4 0.7 + - - -
1277B ASP* 3.6 10.2 + - - +
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Residues in contact with LYS1275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245B ILE* 3.6 26.3 - - + +
1246B GLY 4.0 11.8 + - - +
1247B ARG* 3.8 17.1 - - - +
1271B GLU* 3.2 18.0 + - - +
1272B SER* 3.1 10.1 + - - +
1274B TYR* 1.3 83.1 - - + +
1276B LEU* 1.3 64.4 + - - +
1277B ASP* 3.1 12.5 + - - +
1279B ARG* 4.8 6.4 + - - -
1906J G 3.1 32.9 + - - -
1907J C 5.5 4.2 + - - +
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Residues in contact with LEU1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245B ILE* 4.1 18.8 - - + -
1272B SER 3.3 8.1 + - - +
1273B TYR* 3.2 55.5 + - + +
1275B LYS* 1.3 76.0 - - - +
1277B ASP* 1.3 67.8 + - - +
1278B LYS 3.4 1.1 - - - +
1279B ARG* 3.1 44.4 + - + +
1281B PRO* 3.9 17.9 - - + -
1337B PHE* 4.1 11.7 - - + -
1340B PHE* 3.6 31.6 - - + -
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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
------------------------------------------------------------
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