Contacts of the helix formed by residues 1264 - 1278 (chain D) in PDB entry 5TJ4
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 THR1264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1263D LEU* 1.3 78.6 - - - +
1265D GLU* 1.3 58.7 + - + +
1266D GLU* 3.2 26.5 - - + +
1267D LYS* 2.9 31.0 + - + +
1268D ARG* 2.8 32.8 + - - +
309J GLU* 5.2 10.4 - - + +
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Residues in contact with GLU1265 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1318C ALA 4.4 7.2 - - - +
1263D LEU 3.6 4.6 + - - +
1264D THR* 1.3 73.8 - - + +
1266D GLU* 1.3 60.9 + - - +
1268D ARG* 3.2 43.9 + - - +
1269D LYS* 3.1 24.3 + - - +
1402D LEU 5.6 0.7 - - - +
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Residues in contact with GLU1266 (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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1317C ALA 4.5 5.2 - - - +
1318C ALA* 3.9 32.8 + - + +
1264D THR* 3.1 15.6 - - + +
1265D GLU* 1.3 79.0 - - - +
1267D LYS* 1.3 58.7 + - + +
1269D LYS* 3.7 3.7 + - - +
1270D ASP* 3.2 31.5 + - - +
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Residues in contact with LYS1267 (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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1263D LEU* 3.9 9.9 - - + -
1264D THR* 2.9 31.8 + - + +
1266D GLU* 1.3 76.4 - - + +
1268D ARG* 1.3 54.9 + - - +
1270D ASP* 2.9 12.8 + - - +
1271D VAL* 2.8 39.7 + - - +
1312D SER* 4.4 5.4 + - - +
1313D SER* 3.6 34.0 - - - +
1315D PHE 2.6 26.6 + - - -
1316D ASN* 3.6 19.6 + - - +
1317D ALA* 4.0 5.4 - - - +
1325D ARG* 4.0 8.6 - - - +
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Residues in contact with ARG1268 (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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1260D LEU 3.5 19.7 + - - +
1261D LYS* 4.2 22.9 + - - +
1263D LEU* 4.2 17.3 + - + +
1264D THR 2.8 16.3 + - - +
1265D GLU* 3.2 38.0 + - - +
1267D LYS* 1.3 70.1 - - - +
1269D LYS* 1.3 63.2 + - - +
1271D VAL* 3.1 8.2 + - - +
1272D LEU* 3.0 24.3 + - - +
1401D GLU* 3.5 30.6 + - - +
1402D LEU* 3.9 35.6 + - + +
1404D GLU* 3.8 17.2 - - - +
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Residues in contact with LYS1269 (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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1319C GLY* 4.5 22.4 - - - +
1265D GLU 3.1 14.8 + - - +
1266D GLU* 3.8 5.6 - - - +
1267D LYS 3.3 0.2 - - - -
1268D ARG* 1.3 78.9 - - - +
1270D ASP* 1.3 62.1 + - - +
1272D LEU* 3.6 8.3 + - - +
1273D ASN* 3.1 37.5 + - - +
1402D LEU 5.9 0.4 - - - -
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Residues in contact with ASP1270 (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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1266D GLU* 3.2 19.4 + - - +
1267D LYS* 2.9 14.1 + - - +
1269D LYS* 1.3 75.5 - - - +
1271D VAL* 1.3 64.4 + - + +
1273D ASN* 3.7 7.8 + - - +
1274D SER* 3.3 25.1 + - - -
1309D PRO* 4.6 30.5 - - + +
1310D LEU* 4.5 4.4 + - - -
1312D SER* 5.9 1.6 - - - -
1313D SER* 5.3 2.0 - - - -
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Residues in contact with VAL1271 (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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1260D LEU* 5.5 3.8 - - + -
1263D LEU* 5.0 8.1 - - + -
1267D LYS 2.8 22.6 + - - +
1268D ARG* 3.5 8.1 - - - +
1270D ASP* 1.3 70.1 - - - +
1272D LEU* 1.3 61.9 + - - +
1274D SER* 3.0 4.5 + - - -
1275D LEU* 2.8 39.2 + - + +
1310D LEU* 3.6 26.2 - - + +
1313D SER* 3.7 25.8 - - - +
1329D ILE* 3.9 14.6 - - + -
1402D LEU* 3.7 23.1 - - + -
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Residues in contact with LEU1272 (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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1302C HIS* 3.6 27.6 - - - +
1268D ARG 3.0 14.5 + - - +
1269D LYS* 3.8 8.3 - - - +
1271D VAL* 1.3 77.6 - - - +
1273D ASN* 1.3 53.1 + - - +
1275D LEU* 3.3 1.7 + - - -
1276D ALA* 2.8 37.1 + - - +
1350D LEU* 4.0 15.0 - - + -
1399D LEU* 3.5 31.0 - - + +
1402D LEU* 3.8 45.3 - - + +
1403D ALA* 3.9 13.2 - - + +
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Residues in contact with ASN1273 (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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1301C LEU* 5.8 1.0 - - - +
1302C HIS 3.6 9.1 - - - +
1303C MET 3.7 0.5 - - - -
1304C GLU* 2.7 48.6 + - + +
1269D LYS* 3.1 26.7 + - - +
1270D ASP* 4.1 8.7 + - - +
1272D LEU* 1.3 78.5 - - - +
1274D SER* 1.3 61.8 + - - +
1276D ALA* 3.7 4.2 + - - +
1277D LYS* 3.4 26.7 + - - +
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Residues in contact with SER1274 (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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1270D ASP 3.3 9.0 + - - -
1271D VAL 3.0 6.1 + - - -
1273D ASN* 1.3 76.3 - - - +
1275D LEU* 1.3 63.8 + - - +
1277D LYS* 3.6 15.4 + - - +
1278D CYS* 3.5 15.2 - - - -
1284D ILE* 5.2 0.9 - - - +
1288D LEU* 4.1 7.1 - - - +
1309D PRO* 3.6 26.2 - - - +
1310D LEU* 3.6 29.5 - - - +
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Residues in contact with LEU1275 (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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1260D LEU* 5.9 0.2 - - + -
1271D VAL* 2.8 29.5 + - + +
1272D LEU* 3.8 4.3 - - - +
1274D SER* 1.3 69.9 - - - +
1276D ALA* 1.3 64.7 + - - +
1278D CYS* 3.1 21.0 + - - +
1279D LEU* 3.8 8.5 + - - +
1288D LEU* 4.5 7.2 - - + -
1310D LEU* 4.7 2.9 - - + -
1329D ILE* 4.2 23.6 - - + -
1332D PHE* 3.7 52.2 - - + -
1333D LEU* 4.1 15.3 - - + -
1398D ILE* 4.6 2.9 - - + -
1399D LEU* 4.6 7.0 - - + -
1402D LEU* 3.9 25.8 - - + -
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Residues in contact with ALA1276 (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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1303C MET* 3.8 33.0 - - + -
1304C GLU 4.4 6.1 - - - +
1272D LEU* 2.8 23.4 + - + +
1273D ASN 3.9 5.4 - - - +
1275D LEU* 1.3 73.9 - - - +
1277D LYS* 1.3 62.4 + - - +
1279D LEU* 3.1 31.5 + - + +
1347D ALA* 5.7 0.3 - - - +
1350D LEU* 3.8 11.7 - - + -
1399D LEU* 5.0 2.2 - - - +
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Residues in contact with LYS1277 (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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1304C GLU* 4.3 18.8 + - + +
1306C PRO* 4.1 27.6 - - + -
1273D ASN 3.4 14.8 + - - +
1274D SER* 3.8 11.9 - - - +
1275D LEU 3.3 0.8 - - - -
1276D ALA* 1.3 76.9 - - - +
1278D CYS* 1.3 60.4 + - - +
1279D LEU 3.5 3.5 + - - +
1281D LYS* 4.1 6.4 - - - +
1284D ILE* 3.8 34.5 - - + +
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Residues in contact with CYS1278 (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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1274D SER 3.5 10.1 - - - -
1275D LEU* 3.1 13.6 + - - +
1277D LYS* 1.3 75.1 - - - +
1279D LEU* 1.3 63.7 + - - +
1280D GLY 3.0 4.7 + - - -
1281D LYS 3.2 18.0 + - - +
1284D ILE* 4.0 12.8 - - - -
1285D ARG* 4.0 23.6 - - + +
1288D LEU* 3.4 32.5 - - - -
1333D LEU* 4.1 7.0 - - - -
1336D LEU* 3.8 18.9 - - + +
1343D GLN* 3.4 6.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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