Contacts of the helix formed by residues 1287 - 1299 (chain D) in PDB entry 2NQB
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 THR1287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844C GLY* 4.7 7.2 - - - +
846C GLY 6.1 0.2 - - - +
847C ALA* 3.9 8.3 - - - +
1285D THR* 3.7 24.7 - - + +
1286D ILE* 1.3 76.8 - - - +
1288D SER* 1.3 65.7 + - - +
1289D ARG* 3.2 14.3 + - - +
1290D GLU* 2.7 39.5 + - - +
1291D ILE* 3.1 14.6 + - - +
40I G 6.2 3.1 - - - -
257J A 6.1 0.2 - - - +
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Residues in contact with SER1288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C GLY* 3.9 23.4 - - - -
847C ALA* 3.9 12.6 - - - +
850C TYR* 4.0 20.4 - - - -
1287D THR* 1.3 76.7 + - - +
1289D ARG* 1.3 58.7 + - - +
1291D ILE* 3.4 6.5 + - - +
1292D GLN* 2.9 29.5 + - - +
1315D VAL* 4.3 14.2 - - - +
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Residues in contact with ARG1289 (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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74B GLU 3.3 15.6 + - - -
75B HIS* 2.9 53.4 + - + +
77B LYS* 3.7 30.7 - - - +
1287D THR* 3.0 12.2 + - - +
1288D SER* 1.3 80.8 + - - +
1290D GLU* 1.3 67.9 + - - +
1292D GLN* 3.4 9.8 + - + +
1293D THR* 3.1 27.8 + - - +
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Residues in contact with GLU1290 (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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75B HIS* 2.8 36.5 + - - -
1274D ALA* 4.1 25.6 - - + +
1277D LEU* 3.4 8.9 - - + +
1278D ALA* 4.7 10.7 - - + -
1283D ARG* 5.1 8.5 - - - +
1285D THR 4.0 8.0 - - - +
1286D ILE* 3.7 11.4 - - + -
1287D THR* 2.7 46.9 + - - +
1289D ARG* 1.3 79.6 + - - +
1291D ILE* 1.3 67.0 + - - +
1293D THR 3.3 0.7 + - - -
1294D ALA* 2.9 25.5 + - - +
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Residues in contact with ILE1291 (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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834C LEU* 5.1 5.4 - - + -
847C ALA* 3.8 25.1 - - + +
850C TYR* 3.6 22.7 - - + -
851C LEU* 4.1 26.0 - - + +
1270D ILE* 3.9 20.9 - - + -
1271D ALA* 5.3 1.8 - - - -
1274D ALA* 4.0 11.0 - - + -
1286D ILE* 3.9 19.1 - - + -
1287D THR 3.1 14.6 + - - +
1288D SER* 3.6 8.1 - - - +
1290D GLU* 1.3 77.9 - - - +
1292D GLN* 1.3 56.3 + - - +
1294D ALA* 3.4 5.8 + - - +
1295D VAL* 2.9 37.3 + - + +
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Residues in contact with GLN1292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850C TYR* 2.5 40.0 + - + +
1288D SER 2.9 17.5 + - - +
1289D ARG* 3.6 10.3 - - - +
1290D GLU 3.2 0.2 - - - -
1291D ILE* 1.3 75.5 - - - +
1293D THR* 1.3 65.5 + - - +
1295D VAL* 3.3 5.2 + - - +
1296D ARG* 3.1 51.7 + - - +
1308D VAL* 3.4 14.7 - - + +
1312D THR* 3.3 20.2 + - - -
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Residues in contact with THR1293 (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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71B THR* 3.7 23.8 - - + +
72B TYR* 5.5 0.2 - - - -
75B HIS* 2.8 36.1 + - + +
1277D LEU* 3.3 31.0 - - + -
1289D ARG* 3.1 9.6 + - - +
1290D GLU 3.3 0.2 + - - -
1292D GLN* 1.3 79.0 - - - +
1294D ALA* 1.3 63.4 + - - +
1296D ARG* 3.0 15.3 + - - +
1297D LEU* 3.0 25.1 + - + +
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Residues in contact with ALA1294 (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 ILE* 3.7 19.1 - - + +
1273D GLU* 3.7 35.7 - - + -
1274D ALA* 3.9 5.8 - - - +
1277D LEU* 3.8 0.6 - - + +
1290D GLU 2.9 16.9 + - - +
1291D ILE* 3.5 5.8 - - - +
1293D THR* 1.3 77.7 - - - +
1295D VAL* 1.3 57.5 + - - +
1297D LEU* 3.1 3.3 + - - +
1298D LEU* 2.9 36.5 + - + +
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Residues in contact with VAL1295 (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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850C TYR* 4.4 3.4 - - + -
854C VAL* 4.0 22.4 - - + -
1270D ILE* 4.2 20.9 - - + -
1291D ILE* 2.9 26.6 + - + +
1292D GLN* 3.5 9.6 - - - +
1294D ALA* 1.3 75.1 - - - +
1296D ARG* 1.3 58.1 + - - +
1298D LEU* 4.5 4.5 - - - +
1299D LEU* 3.0 40.1 + - + +
1304D ALA* 4.3 9.9 - - - +
1307D ALA* 3.7 27.8 - - + -
1308D VAL* 4.4 8.5 - - + +
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Residues in contact with ARG1296 (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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67B ARG* 6.0 1.7 - - - -
68B ASP* 5.4 0.7 - - - +
71B THR* 4.6 15.5 - - + +
1292D GLN* 3.1 43.2 + - - +
1293D THR* 3.0 17.4 + - - +
1295D VAL* 1.3 79.8 - - - +
1297D LEU* 1.3 58.7 + - - +
1299D LEU 3.8 11.4 - - - +
1304D ALA* 4.6 11.7 - - + +
1308D VAL* 4.1 31.8 - - + +
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Residues in contact with LEU1297 (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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68B ASP* 3.8 38.1 - - - +
71B THR* 3.7 25.6 - - + -
72B TYR* 3.9 23.6 - - + +
92B ARG* 3.0 37.8 + - - +
1273D GLU* 2.9 28.5 - - - +
1277D LEU* 4.7 1.6 - - + -
1293D THR* 3.0 28.5 + - + +
1294D ALA* 3.7 5.6 - - - +
1296D ARG* 1.3 76.2 - - - +
1298D LEU* 1.3 60.5 + - - +
1299D LEU 4.9 0.7 - - - +
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Residues in contact with LEU1298 (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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92B ARG* 3.0 24.5 - - - +
896C LEU* 3.8 16.7 - - + +
1269D ARG* 3.4 43.1 - - + +
1270D ILE* 3.8 13.7 - - + +
1273D GLU* 3.4 26.5 - - + -
1294D ALA 2.9 23.0 + - - +
1295D VAL* 4.1 2.9 - - - +
1297D LEU* 1.3 79.0 - - - +
1299D LEU* 1.3 71.7 + - + +
1300D PRO* 4.0 2.6 - - - +
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Residues in contact with LEU1299 (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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854C VAL* 4.6 2.2 - - + -
858C LEU* 4.1 24.0 - - + -
896C LEU* 3.7 33.4 - - + -
1266D ILE* 5.4 2.2 - - + -
1270D ILE* 5.7 4.9 - - + -
1295D VAL* 3.0 27.6 + - + +
1296D ARG 3.8 13.2 - - - +
1297D LEU 4.9 0.5 - - - -
1298D LEU* 1.3 81.3 - - + +
1300D PRO* 1.3 70.1 - - + +
1301D GLY 3.8 1.0 + - - -
1303D LEU* 3.9 15.0 - - + +
1304D ALA* 3.8 17.1 - - - +
1307D ALA* 3.6 30.7 - - + -
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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
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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