Contacts of the helix formed by residues 1276 - 1294 (chain A) in PDB entry 5EPG
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 GLY1276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208A PHE* 3.6 17.2 - - - -
1212A MET* 3.6 27.3 - - - -
1215A TYR* 3.4 9.8 - - - +
1272A GLY 3.8 1.2 + - - -
1273A VAL 3.1 11.2 + - - -
1275A LEU* 1.3 78.8 - - - +
1277A CYS* 1.3 54.8 + - - +
1279A VAL* 3.2 27.8 + - - +
1280A PHE 3.8 1.2 + - - -
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Residues in contact with CYS1277 (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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930A LEU* 4.2 4.9 - - + -
1010A VAL* 4.2 5.2 - - - -
1215A TYR* 3.2 32.1 - - + -
1274A PHE* 3.0 52.6 + - - -
1276A GLY* 1.3 71.2 - - - +
1278A SER* 1.3 66.9 + - - +
1279A VAL 3.1 1.6 - - - -
1280A PHE* 3.0 8.0 + - + -
1281A PHE* 2.9 50.8 + - + -
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Residues in contact with SER1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A ALA* 3.5 11.1 - - - +
1010A VAL* 4.0 16.7 - - - +
1167A ALA* 3.6 28.1 - - - +
1168A CYS 4.1 1.4 - - - -
1169A SER* 2.7 34.3 + - - -
1185A THR* 4.4 0.2 - - - +
1208A PHE* 4.1 5.4 - - - -
1275A LEU 3.0 19.2 + - - -
1277A CYS* 1.3 79.6 - - - +
1279A VAL* 1.3 55.3 + - - +
1282A ALA* 3.0 29.3 + - - +
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Residues in contact with VAL1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1169A SER* 3.3 23.3 - - - +
1171A VAL* 4.2 4.0 - - + -
1182A ASN* 3.7 32.5 - - + +
1185A THR* 4.7 1.8 - - - +
1208A PHE* 3.9 12.3 - - + -
1212A MET* 3.9 17.5 - - + -
1216A THR* 3.8 23.8 - - + -
1276A GLY 3.2 13.1 + - - +
1277A CYS 3.1 0.4 - - - -
1278A SER* 1.3 74.1 + - - +
1280A PHE* 1.3 64.2 + - - +
1282A ALA* 3.3 3.9 + - - +
1283A ILE* 3.0 30.4 + - + +
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Residues in contact with PHE1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A ILE* 4.5 6.7 - - + -
930A LEU* 3.9 15.0 - - + -
934A SER* 6.1 0.2 - - - -
1215A TYR* 3.6 32.3 - + + -
1216A THR* 5.0 1.7 - - - +
1276A GLY 3.8 1.6 + - - -
1277A CYS* 3.0 19.6 + - - +
1279A VAL* 1.3 78.2 - - - +
1281A PHE* 1.3 92.2 + + - +
1283A ILE* 3.3 4.0 + - - -
1284A HIS* 2.9 33.4 + + - +
1302A LEU* 3.4 26.9 - - + -
1303A ASN 3.8 19.7 - - - -
1304A SER* 3.9 14.4 - - - -
1306A LEU* 3.5 28.4 - - + +
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Residues in contact with PHE1281 (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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930A LEU* 3.7 17.3 - - + -
933A GLU* 3.3 37.0 - - + -
934A SER* 4.0 9.0 - - - -
937A THR* 4.0 25.4 - - + -
951A ARG* 4.0 9.4 - - - +
1008A ALA* 3.5 19.5 - - + +
1010A VAL* 3.8 15.0 - - + -
1277A CYS* 2.9 44.2 + - + +
1280A PHE* 1.3 94.2 - + - +
1282A ALA* 1.3 60.5 + - - +
1284A HIS* 3.5 13.2 + + + +
1285A ASP* 2.9 27.7 + - - +
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Residues in contact with ALA1282 (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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1006A GLY* 3.3 19.1 - - - +
1007A LEU 4.0 5.8 - - - -
1008A ALA* 3.3 6.7 - - - +
1169A SER 3.2 26.9 - - - +
1171A VAL* 3.6 21.2 - - + +
1278A SER 3.0 16.3 + - - +
1279A VAL* 3.5 5.6 - - - +
1281A PHE* 1.3 76.7 - - - +
1283A ILE* 1.3 57.9 + - - +
1285A ASP* 3.3 1.4 + - - +
1286A ALA 3.1 21.1 + - - -
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Residues in contact with ILE1283 (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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1171A VAL* 3.6 22.7 - - + -
1173A ILE* 4.4 9.2 - - + -
1180A HIS* 3.7 34.8 - - + +
1216A THR* 4.0 11.4 - - + -
1279A VAL* 3.0 24.4 + - + +
1280A PHE 3.6 1.6 - - - +
1282A ALA* 1.3 71.3 - - - +
1284A HIS* 1.3 60.3 + - - +
1286A ALA* 3.2 3.9 + - - +
1287A VAL* 2.9 33.5 + - + +
1306A LEU* 3.3 29.4 - - + +
1311A ILE* 3.9 25.4 - - + -
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Residues in contact with HIS1284 (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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937A THR* 4.3 25.0 + - - +
938A GLU* 6.5 1.1 - - + -
1280A PHE* 2.9 25.5 + + + +
1281A PHE* 3.5 19.2 + + + +
1283A ILE* 1.3 77.1 - - - +
1285A ASP* 1.3 63.8 + - - +
1287A VAL* 3.6 2.3 + - - +
1288A SER* 3.1 33.0 + - - -
1300A LEU* 3.7 28.6 + - + +
1301A THR* 4.9 1.2 - - - +
1302A LEU* 3.8 41.4 + - + -
1306A LEU* 4.1 1.8 - - + +
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Residues in contact with ASP1285 (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 LYS* 3.1 25.0 + - - -
993A VAL* 4.6 2.3 - - - +
997A ASN* 6.0 0.7 - - - -
1005A LYS 5.0 0.9 - - - -
1006A GLY* 3.4 4.4 - - - -
1007A LEU 3.0 31.4 + - - +
1281A PHE 2.9 14.9 + - - +
1282A ALA 3.4 9.2 - - - +
1284A HIS* 1.3 75.6 + - - +
1286A ALA* 1.3 65.0 + - - +
1288A SER* 3.2 8.7 + - - -
1289A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA1286 (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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1004A LYS* 3.5 16.3 - - - +
1005A LYS 3.5 32.8 - - - +
1006A GLY* 3.6 3.3 - - - +
1171A VAL* 4.6 0.9 - - + -
1173A ILE* 3.8 30.0 - - + +
1282A ALA 3.1 9.3 + - - +
1283A ILE* 3.2 7.4 + - - +
1285A ASP* 1.3 74.9 - - - +
1287A VAL* 1.3 61.8 + - - +
1289A ALA* 3.4 2.6 + - - +
1290A ALA* 3.3 16.8 + - - +
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Residues in contact with VAL1287 (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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1173A ILE* 3.7 20.6 - - + -
1283A ILE* 2.9 23.3 + - + +
1284A HIS 3.9 4.0 - - - +
1286A ALA* 1.3 75.3 - - - +
1288A SER* 1.3 57.7 + - - +
1290A ALA* 3.2 4.3 + - - +
1291A ARG* 3.0 38.7 + - - +
1300A LEU* 4.1 7.2 - - + -
1302A LEU* 4.2 14.1 - - + -
1311A ILE* 4.2 17.0 - - + +
1314A ALA* 3.5 32.5 - - + -
1315A CYS* 4.1 10.8 - - - -
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Residues in contact with SER1288 (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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1284A HIS* 3.1 21.2 + - - -
1285A ASP* 3.2 13.0 + - - -
1287A VAL* 1.3 76.9 - - - +
1289A ALA* 1.3 51.9 + - - +
1291A ARG* 3.1 7.8 + - - +
1292A GLN* 2.8 38.1 + - - +
1300A LEU* 3.5 21.0 - - - +
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Residues in contact with ALA1289 (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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997A ASN* 3.6 33.9 - - + +
1004A LYS* 3.3 14.8 + - + -
1285A ASP* 3.1 15.9 + - - +
1286A ALA 3.7 8.5 - - - +
1287A VAL 3.3 0.2 - - - -
1288A SER* 1.3 75.7 - - - +
1290A ALA* 1.3 60.3 + - - +
1292A GLN* 3.3 35.9 + - - +
1293A GLU* 3.4 5.0 + - - +
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Residues in contact with ALA1290 (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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1004A LYS* 3.8 27.3 - - + +
1175A CYS* 4.1 16.4 - - - -
1286A ALA 3.3 5.1 + - - +
1287A VAL 3.2 8.8 + - - +
1289A ALA* 1.3 77.7 - - - +
1291A ARG* 1.3 60.9 + - - +
1293A GLU* 4.2 1.2 - - - +
1294A ARG* 3.1 47.2 + - - +
1315A CYS* 4.1 12.6 - - + -
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Residues in contact with ARG1291 (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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1287A VAL* 3.0 17.7 + - + +
1288A SER* 3.1 6.3 + - - +
1290A ALA* 1.3 76.1 - - - +
1292A GLN* 1.3 58.1 + - - +
1293A GLU 3.5 0.2 - - - -
1295A GLY 3.1 5.0 + - - -
1296A LEU* 2.8 73.5 + - + +
1297A HIS 5.3 2.4 + - - -
1299A PRO* 4.8 10.5 + - - +
1300A LEU* 3.8 43.7 - - - +
1314A ALA* 2.4 48.3 + - - +
1315A CYS* 5.2 1.8 - - - -
1316A GLU* 3.6 29.9 + - - +
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Residues in contact with GLN1292 (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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997A ASN* 5.6 3.0 - - - +
1004A LYS* 5.6 0.6 - - - +
1288A SER 2.8 14.6 + - - +
1289A ALA* 3.3 33.1 + - - +
1291A ARG* 1.3 72.3 - - - +
1293A GLU* 1.3 71.3 + - + +
1294A ARG 3.2 0.2 - - - -
1295A GLY* 3.2 12.5 + - - -
1297A HIS* 4.2 21.5 + - + +
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Residues in contact with GLU1293 (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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548A LYS* 3.2 28.4 - - - -
997A ASN 4.0 7.4 - - - +
998A ALA* 4.4 4.8 - - - +
1000A ASN 4.6 0.2 - - - +
1001A TYR* 3.2 34.1 - - + +
1004A LYS* 2.8 33.1 + - - +
1289A ALA 3.4 12.7 + - - +
1290A ALA* 4.2 3.4 - - - +
1291A ARG 3.5 0.2 - - - -
1292A GLN* 1.3 86.2 - - + +
1294A ARG* 1.3 60.2 + - + +
1295A GLY* 4.8 0.2 - - - -
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Residues in contact with ARG1294 (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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1001A TYR* 3.0 62.4 + - + +
1002A TRP* 3.6 15.1 - - - -
1175A CYS* 3.5 24.9 - - - +
1290A ALA* 3.1 30.2 + - - +
1292A GLN 3.2 0.2 - - - -
1293A GLU* 1.3 77.0 + - + +
1295A GLY* 1.3 59.9 - - - +
1296A LEU* 3.6 16.5 + - + +
1315A CYS* 3.3 21.1 + - - +
1316A GLU 2.7 38.4 + - - +
1317A ASP* 3.5 14.3 + - - +
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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