Contacts of the strand formed by residues 1292 - 1302 (chain A) in PDB entry 2NLK
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 GLN1292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1284A ARG* 4.9 5.4 - - + -
1285A LEU 3.4 8.7 - - - +
1286A CYS* 5.4 4.5 - - - -
1287A LEU* 6.1 0.2 - - - -
1290A GLU 4.2 1.1 + - - +
1291A GLU* 1.3 75.3 - - - +
1293A ILE* 1.3 62.6 + - - +
1294A ILE* 4.0 18.0 + - + +
1315A GLN 4.0 2.1 - - - +
1316A CYS 4.4 0.2 - - - -
1317A PRO* 3.2 25.4 - - - +
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Residues in contact with ILE1293 (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 ARG* 3.1 6.1 - - - +
1285A LEU* 2.9 47.7 + - + +
1286A CYS 6.0 1.3 - - - +
1287A LEU* 6.0 7.0 - - + -
1292A GLN* 1.3 73.7 - - - +
1294A ILE* 1.3 64.8 + - - +
1295A ILE* 3.7 6.2 + - + +
1314A PHE* 3.6 36.3 - - + -
1315A GLN 3.4 12.8 - - - +
1316A CYS* 4.6 1.6 - - - -
1317A PRO* 4.3 12.6 - - + -
1332A LEU* 4.1 19.3 - - + -
1335A VAL* 3.8 32.5 - - + -
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Residues in contact with ILE1294 (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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1282A LYS* 5.8 1.3 - - + -
1283A ASP 3.6 7.2 - - - +
1284A ARG* 4.0 16.2 - - + -
1292A GLN* 4.5 12.8 - - + +
1293A ILE* 1.3 73.3 - - - +
1295A ILE* 1.3 62.8 + - - +
1296A HIS* 3.4 32.5 + - + -
1313A HIS* 3.4 2.6 + - - +
1314A PHE* 3.5 0.9 - - - -
1315A GLN* 2.7 57.4 + - + +
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Residues in contact with ILE1295 (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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1282A LYS* 3.2 3.8 - - - +
1283A ASP* 2.7 58.3 + - + +
1284A ARG 4.2 0.7 - - - +
1285A LEU* 3.6 28.7 - - + -
1293A ILE* 3.7 11.0 - - + +
1294A ILE* 1.3 72.7 - - - +
1296A HIS* 1.3 70.9 + - - +
1297A ASP* 4.3 4.5 - - - +
1312A ARG* 3.4 41.7 - - + +
1313A HIS 3.2 2.2 - - - -
1314A PHE* 3.1 40.6 - - + -
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Residues in contact with HIS1296 (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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1263A TRP* 4.0 25.2 + + - -
1279A LEU* 3.9 20.6 - - + -
1281A SER 3.4 4.9 - - - -
1282A LYS* 4.0 20.2 - - + +
1294A ILE* 3.4 29.7 + - + +
1295A ILE* 1.3 73.8 - - - +
1297A ASP* 1.3 62.5 + - - +
1298A PHE* 3.4 25.5 - + + -
1312A ARG* 3.8 0.9 - - - -
1313A HIS* 2.9 44.3 + - + +
1315A GLN* 4.0 14.3 + - - -
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Residues in contact with ASP1297 (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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1279A LEU* 3.2 5.4 - - - +
1280A ILE* 2.7 48.1 + - + +
1281A SER* 2.8 26.9 + - - +
1283A ASP* 6.1 0.9 - - - +
1295A ILE* 4.3 4.0 - - - +
1296A HIS* 1.3 73.6 - - - +
1298A PHE* 1.3 57.5 + - - +
1311A VAL 3.7 2.7 - - - +
1312A ARG* 2.9 58.1 + - - +
1343A ARG* 4.0 6.4 + - - -
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Residues in contact with PHE1298 (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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1235A TRP* 4.2 12.8 - + + -
1263A TRP* 3.5 30.1 - + + -
1264A PRO* 3.5 37.9 - - + -
1277A VAL* 3.8 16.8 - - + -
1278A THR 3.1 6.1 - - - +
1279A LEU* 3.6 27.1 - - + -
1280A ILE* 4.4 1.8 - - - +
1296A HIS* 3.4 38.8 - + + -
1297A ASP* 1.3 72.9 - - - +
1299A ILE* 1.3 64.4 + - - +
1300A LEU* 4.2 7.4 - - + -
1310A GLU* 3.6 4.9 - - - +
1311A VAL* 2.9 39.4 + - + +
1313A HIS* 3.9 15.3 - + + -
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Residues in contact with ILE1299 (chain A).
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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1276A THR 3.2 3.5 - - - +
1277A VAL* 3.6 0.3 - - - -
1278A THR* 2.8 45.3 + - + -
1280A ILE* 3.8 32.1 - - + +
1298A PHE* 1.3 77.9 - - - +
1300A LEU* 1.3 62.4 + - - +
1301A GLU* 3.8 25.6 + - + +
1308A VAL* 3.6 24.5 - - + -
1309A LEU 3.3 2.9 - - - -
1310A GLU* 4.1 18.8 - - + +
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Residues in contact with LEU1300 (chain A).
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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1235A TRP* 4.0 16.4 - - + +
1238A ILE* 3.9 24.7 - - + -
1239A TRP* 3.4 28.5 - - + -
1275A PHE* 3.6 31.2 - - + -
1276A THR 3.0 5.4 - - - +
1277A VAL* 3.7 27.6 - - + -
1298A PHE* 4.3 4.7 - - + -
1299A ILE* 1.3 75.7 - - - +
1301A GLU* 1.3 60.8 + - - +
1308A VAL* 3.2 3.9 - - - -
1309A LEU* 2.8 42.5 + - + +
1311A VAL* 4.0 17.9 - - + -
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Residues in contact with GLU1301 (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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1275A PHE* 3.1 3.9 - - - -
1276A THR* 2.9 41.0 + - - +
1278A THR* 3.8 20.1 + - - +
1299A ILE* 3.8 24.5 - - + +
1300A LEU* 1.3 76.1 - - - +
1302A ALA* 1.3 67.3 + - - +
1303A THR* 4.3 0.7 - - - +
1306A ASP 6.3 0.2 - - - -
1307A TYR 3.5 5.8 - - - +
1308A VAL* 3.9 20.4 - - + +
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Residues in contact with ALA1302 (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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1239A TRP* 3.6 24.1 - - + -
1274A ALA 3.4 9.0 - - - +
1301A GLU* 1.3 77.7 - - - +
1303A THR* 1.3 60.6 + - - +
1304A GLN 4.4 0.7 - - - +
1305A ASP* 2.9 48.7 - - + +
1306A ASP* 5.1 0.5 - - - -
1307A TYR 2.9 16.5 + - - +
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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