Contacts of the helix formed by residues 1313 - 1329 (chain B) in PDB entry 4E70
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 SER1313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A HIS* 3.4 22.9 + - - -
1311B ASN 3.8 1.3 + - - -
1312B ASP* 1.3 72.7 - - - +
1314B ASN* 1.3 68.3 + - - +
1316B MET* 4.5 2.7 - - - -
1317B GLY* 2.9 24.6 + - - -
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Residues in contact with ASN1314 (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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18A HIS* 4.7 2.8 + - - -
402A GOL 5.4 4.3 + - - -
1312B ASP* 3.3 9.9 + - - +
1313B SER* 1.3 90.3 + - - +
1315B SER* 1.3 63.4 + - - +
1317B GLY* 3.3 2.7 + - - -
1318B THR* 3.1 26.2 + - - -
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Residues in contact with SER1315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 6.3 0.2 - - - -
1310B CYS* 3.3 19.5 - - - -
1312B ASP* 2.6 32.7 + - - -
1314B ASN* 1.3 76.4 - - - +
1316B MET* 1.3 59.5 + - - +
1318B THR* 3.2 4.2 + - - -
1319B SER* 2.9 31.7 + - - -
1360B LEU* 3.7 19.1 - - - +
1401B GOL 3.5 20.4 - - - -
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Residues in contact with MET1316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 6.3 0.2 - - - -
76A HIS* 4.0 18.4 - - + +
1305B LEU* 3.4 42.2 - - + +
1306B ASP* 4.7 6.5 - - + -
1310B CYS 3.8 9.1 + - - +
1311B ASN* 4.7 11.7 - - + +
1312B ASP 2.9 17.8 + - - +
1313B SER* 3.8 4.5 - - - +
1315B SER* 1.3 76.6 - - - +
1317B GLY* 1.3 58.8 + - - +
1319B SER* 3.2 3.8 + - - -
1320B LEU* 2.9 50.6 + - + +
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Residues in contact with GLY1317 (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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18A HIS* 4.3 12.3 - - - -
73A MET* 5.0 0.9 - - - +
76A HIS* 3.3 29.1 + - - -
402A GOL 4.9 1.3 - - - -
1313B SER 2.9 13.5 + - - -
1314B ASN 3.3 2.2 + - - -
1315B SER 3.2 0.2 - - - -
1316B MET* 1.3 76.7 - - - +
1318B THR* 1.3 56.6 + - - +
1320B LEU* 3.4 3.3 + - - +
1321B ILE* 3.0 31.7 + - - +
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Residues in contact with THR1318 (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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14A PRO* 3.7 25.8 + - + +
17A TRP* 4.3 15.7 - - + -
18A HIS* 2.9 31.4 + - + +
21A LEU* 6.0 0.2 - - + -
1314B ASN 3.1 13.3 + - - -
1315B SER* 3.2 7.6 + - - -
1317B GLY* 1.3 74.1 - - - +
1319B SER* 1.3 66.0 + - - +
1321B ILE* 3.2 7.6 + - + +
1322B LEU* 2.9 25.4 + - + +
1360B LEU* 3.8 19.3 - - + -
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Residues in contact with SER1319 (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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1303B HIS* 4.8 0.7 + - - -
1305B LEU* 3.5 26.9 + - - +
1310B CYS* 5.0 9.7 + - - -
1315B SER 2.9 18.1 + - - -
1316B MET* 3.2 9.7 + - - -
1318B THR* 1.3 77.2 - - - +
1320B LEU* 1.3 56.8 + - - +
1322B LEU* 3.2 2.7 + - - +
1323B ASP* 2.9 25.1 + - - +
1334B LEU* 3.4 22.6 - - - +
1360B LEU* 3.9 22.1 + - - +
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Residues in contact with LEU1320 (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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69A ARG 5.9 0.2 - - - +
72A ARG* 3.6 49.6 - - + +
73A MET* 3.9 19.1 - - + +
76A HIS* 3.5 36.3 - - + -
1305B LEU* 4.2 11.7 - - + -
1316B MET* 2.9 39.9 + - + +
1317B GLY* 3.9 3.6 - - - +
1319B SER* 1.3 73.6 - - - +
1321B ILE* 1.3 62.0 + - - +
1323B ASP* 3.2 8.1 + - + +
1324B MET* 2.9 31.7 + - - +
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Residues in contact with ILE1321 (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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17A TRP 5.3 0.2 - - - +
18A HIS* 3.6 41.3 - - + +
21A LEU* 3.5 48.5 - - + +
22A GLY* 5.4 0.2 - - - -
24A ILE* 4.1 11.5 - - + +
25A ASN* 3.8 17.5 - - - +
73A MET* 3.5 23.3 - - + -
402A GOL 5.8 0.4 - - - -
1317B GLY 3.0 13.1 + - - +
1318B THR* 3.2 12.1 + - + +
1320B LEU* 1.3 76.8 - - - +
1322B LEU* 1.3 56.8 + - - +
1324B MET* 3.2 3.5 + - - +
1325B LEU* 2.9 26.9 + - - +
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Residues in contact with LEU1322 (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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17A TRP* 4.0 26.9 - - + -
21A LEU* 3.8 23.8 - - + -
1268B TRP* 5.2 1.3 - - + -
1303B HIS* 3.7 32.3 - - + +
1318B THR* 2.9 19.1 + - + +
1319B SER 3.5 6.5 - - - +
1321B ILE* 1.3 73.6 - - - +
1323B ASP* 1.3 61.0 + - - +
1325B LEU* 3.2 7.3 + - + +
1326B PHE* 2.8 41.2 + - + -
1334B LEU* 4.1 13.5 - - + -
1360B LEU* 4.1 6.5 - - + -
1402B N7I 3.8 26.2 - - + -
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Residues in contact with ASP1323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 2.9 50.9 + - - +
72A ARG* 3.1 24.3 + - - +
1305B LEU* 5.9 0.2 - - + -
1319B SER 2.9 13.5 + - - +
1320B LEU* 3.2 15.8 + - + +
1322B LEU* 1.3 76.6 - - - +
1324B MET* 1.3 61.0 + - + +
1326B PHE* 3.5 1.2 + - - -
1327B MET* 2.9 23.6 + - - +
1333B SER* 3.4 3.8 - - - -
1334B LEU* 2.9 38.5 + - + +
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Residues in contact with MET1324 (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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24A ILE* 3.6 16.6 - - + -
28A THR* 3.9 18.2 - - + -
69A ARG* 3.4 42.0 - - + +
70A LEU* 3.7 16.4 - - - +
73A MET* 3.8 24.0 - - + -
1131B TRP* 3.4 16.1 - - + -
1320B LEU 2.9 16.3 + - - +
1321B ILE 3.5 7.0 - - - +
1322B LEU 3.2 0.2 - - - -
1323B ASP* 1.3 80.4 - - + +
1325B LEU* 1.3 66.9 + - - +
1327B MET* 3.2 27.4 + - + +
1328B SER 3.0 17.7 + - - -
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Residues in contact with LEU1325 (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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21A LEU* 4.1 20.4 - - + -
23A TYR* 3.9 21.3 - - - +
24A ILE* 4.2 12.4 - - + +
1122B SER 5.4 0.2 - - - +
1127B LEU* 4.6 12.8 - - + +
1131B TRP* 5.5 0.4 - - - +
1321B ILE 2.9 17.2 + - - +
1322B LEU* 3.5 7.6 - - + +
1324B MET* 1.3 72.4 - - - +
1326B PHE* 1.3 75.3 + - + +
1328B SER* 2.8 26.9 + - - +
1329B PHE* 3.2 29.5 + - + -
1402B N7I 3.6 42.0 - - + +
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Residues in contact with PHE1326 (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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1268B TRP* 4.6 6.1 - + - -
1271B CYS* 3.9 36.6 - - + -
1303B HIS* 4.9 4.0 - + - -
1322B LEU* 2.8 28.9 + - + +
1323B ASP 3.8 4.3 - - - +
1325B LEU* 1.3 86.6 - - + +
1327B MET* 1.3 62.8 + - - +
1329B PHE* 4.5 0.7 - + - -
1330B LEU* 2.9 50.5 + - + +
1332B GLY 4.0 15.3 - - - +
1333B SER* 4.4 2.9 - - - +
1334B LEU* 3.5 29.8 - - + -
1402B N7I 3.7 50.3 - + + -
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Residues in contact with MET1327 (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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66A PHE* 3.7 59.3 - - + +
69A ARG* 3.4 25.3 - - - +
70A LEU* 4.7 8.3 - - + -
1131B TRP* 4.8 2.9 - - + -
1134B MET* 4.2 28.5 - - + +
1137B TRP* 5.0 7.9 - - + -
1138B LEU* 5.2 3.4 - - + -
1150B ASN* 3.7 15.6 - - - +
1151B ALA 4.8 0.7 + - - -
1323B ASP 2.9 12.7 + - - +
1324B MET* 3.2 34.9 + - + +
1326B PHE* 1.3 79.9 - - - +
1328B SER* 1.3 60.1 + - - +
1329B PHE 3.7 0.2 + - - -
1330B LEU 4.0 2.3 - - - +
1331B GLU 6.4 0.2 - - - -
1332B GLY 4.4 1.6 - - - -
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Residues in contact with SER1328 (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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1127B LEU* 4.8 4.6 + - - +
1130B PRO* 5.6 2.9 - - - -
1131B TRP* 3.5 36.6 + - - -
1134B MET* 3.8 15.9 - - - -
1150B ASN* 3.4 7.5 - - - +
1151B ALA* 4.6 4.5 - - - -
1152B PHE* 2.9 28.9 + - - +
1324B MET 3.0 9.9 + - - -
1325B LEU* 2.8 21.5 + - - +
1327B MET* 1.3 79.3 - - - +
1329B PHE* 1.3 63.4 + - - +
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Residues in contact with PHE1329 (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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1127B LEU* 3.5 30.1 - - + -
1150B ASN* 3.5 9.6 + - - -
1152B PHE* 3.7 16.9 - - + +
1161B VAL* 3.8 31.7 + - + +
1171B PHE* 5.9 0.4 - + - -
1175B PHE* 3.6 35.9 - + - -
1325B LEU* 3.2 56.8 + - + -
1326B PHE* 4.5 0.2 - + - -
1328B SER* 1.3 81.8 + - - +
1330B LEU* 1.3 94.6 + - + +
1402B N7I 3.9 15.0 - + - -
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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