Contacts of the helix formed by residues 1282 - 1293 (chain A) in PDB entry 1NF1
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 SER1282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1264A GLU* 3.4 9.0 + - - -
1275A PHE* 3.6 25.2 + - - -
1277A GLY 3.3 24.9 + - - -
1278A ASN* 4.6 0.9 - - - -
1279A SER* 3.0 20.9 + - - -
1281A ALA* 1.3 76.4 - - - +
1283A LYS* 1.3 53.2 + - - -
1285A MET* 3.5 8.3 - - - +
1286A THR* 2.5 42.7 + - - -
1391A ARG* 4.0 7.9 - - - -
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Residues in contact with LYS1283 (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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1236A TRP* 4.5 20.0 - - + +
1237A ASP* 4.8 12.1 - - - +
1240A ALA* 4.1 7.4 - - + +
1278A ASN* 4.6 14.9 - - + +
1279A SER 3.3 15.3 + - - +
1280A LEU* 4.6 6.1 - - + -
1281A ALA 3.3 0.2 - - - -
1282A SER* 1.3 76.2 - - - +
1284A ILE* 1.3 64.0 + - - +
1286A THR* 3.5 5.7 + - - -
1287A PHE* 3.1 23.2 + - - +
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Residues in contact with ILE1284 (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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1240A ALA* 3.9 22.1 - - + +
1243A LEU* 4.3 16.2 - - + -
1244A VAL* 3.9 14.2 - - + +
1256A LEU* 4.6 8.5 - - + -
1257A LEU* 3.6 30.3 - - + -
1260A MET* 3.5 41.1 - - + -
1261A PHE* 4.7 4.9 - - + -
1280A LEU* 4.4 12.6 - - + -
1281A ALA* 3.7 12.1 + - - +
1283A LYS* 1.3 73.7 - - - +
1285A MET* 1.3 69.7 + - - +
1287A PHE* 2.9 14.0 + - - +
1288A CYS* 3.0 12.4 + - - -
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Residues in contact with MET1285 (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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1261A PHE* 4.1 23.6 - - + -
1275A PHE* 4.1 21.8 - - + -
1281A ALA 2.8 23.2 + - - +
1282A SER* 3.5 7.4 - - - +
1284A ILE* 1.3 72.4 - - - +
1286A THR* 1.3 59.9 + - - +
1287A PHE 2.8 10.9 + - - -
1288A CYS* 2.9 22.8 + - - +
1289A PHE* 3.0 43.3 + - + +
1364A VAL* 5.5 6.0 - - + +
1368A LEU* 3.4 36.3 - - + -
1387A ALA* 4.0 14.6 - - + -
1391A ARG* 5.1 6.1 - - - -
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Residues in contact with THR1286 (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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1278A ASN* 5.9 0.2 - - - -
1282A SER 2.5 28.2 + - - -
1283A LYS* 3.9 6.3 - - - -
1284A ILE 3.4 0.4 - - - -
1285A MET* 1.3 75.1 - - - +
1287A PHE* 1.3 57.6 + - - +
1289A PHE* 3.5 10.3 - - - +
1290A LYS* 3.2 30.3 + - + +
1391A ARG* 2.7 47.1 + - + +
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Residues in contact with PHE1287 (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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1237A ASP 5.9 1.3 - - - -
1240A ALA* 4.1 7.0 - - + -
1241A ARG* 3.8 52.7 - - + -
1244A VAL* 3.9 26.9 - - + -
1245A THR* 5.2 2.7 - - - -
1283A LYS 3.1 12.8 + - - +
1284A ILE* 2.9 12.7 + - - +
1285A MET 2.8 1.2 + - - -
1286A THR* 1.3 74.5 - - - +
1288A CYS* 1.3 66.4 + - - +
1289A PHE 3.1 1.3 - - - -
1290A LYS* 3.0 18.4 + - + +
1291A VAL* 3.1 44.6 + - + +
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Residues in contact with CYS1288 (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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1244A VAL* 4.3 18.8 - - - -
1253A LEU* 5.2 2.0 - - - -
1257A LEU* 3.8 36.1 - - - -
1261A PHE* 5.7 0.7 - - - -
1284A ILE* 3.0 22.6 + - - -
1285A MET* 2.9 12.7 + - - +
1287A PHE* 1.3 70.5 - - - +
1289A PHE* 1.3 64.1 + - - +
1291A VAL* 5.0 2.0 - - - -
1292A TYR* 3.0 41.3 + - + +
1361A LEU* 5.5 1.6 - - - -
1364A VAL* 4.2 25.1 - - + -
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Residues in contact with PHE1289 (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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1285A MET* 3.0 45.8 + - + +
1286A THR* 3.5 12.3 - - - +
1288A CYS* 1.3 80.8 - - - +
1290A LYS* 1.3 64.1 + - + +
1293A GLY* 3.3 13.9 + - - -
1361A LEU* 3.6 34.6 - - + +
1364A VAL* 4.8 9.4 - - + -
1365A CYS* 4.4 13.9 - - - -
1368A LEU* 5.3 3.1 - - + -
1384A VAL* 5.4 2.0 - - + -
1387A ALA* 3.8 21.3 - - + -
1388A MET* 4.2 24.2 - - + -
1391A ARG* 3.6 23.6 - - + +
1392A PHE* 3.8 27.7 - + + -
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Residues in contact with LYS1290 (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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1286A THR* 3.2 15.7 + - + +
1287A PHE* 3.0 16.5 + - + +
1289A PHE* 1.3 76.9 - - + +
1291A VAL* 1.3 71.6 + - + +
1294A ALA* 3.1 39.2 + - + +
1297A LEU* 5.0 3.2 - - - +
1391A ARG 5.9 2.0 - - - +
1392A PHE* 3.5 41.4 + - + +
1395A PRO* 5.7 2.6 - - - +
1396A ALA* 4.9 5.9 - - - +
1402A GLU* 4.6 28.5 + - + +
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Residues in contact with VAL1291 (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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1241A ARG* 5.7 3.1 - - - +
1244A VAL* 6.2 1.3 - - + -
1287A PHE* 3.1 50.6 + - + +
1288A CYS* 5.0 0.4 - - - -
1290A LYS* 1.3 82.3 - - + +
1292A TYR* 1.3 88.6 + - + +
1293A GLY 3.2 0.5 + - - -
1294A ALA* 3.9 7.3 + - - +
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Residues in contact with TYR1292 (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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1244A VAL* 4.6 10.2 - - + +
1248A ASP* 3.4 27.6 + - - +
1253A LEU* 3.1 35.6 - - + +
1288A CYS* 3.0 26.0 + - + +
1291A VAL* 1.3 99.7 - - + +
1293A GLY* 1.3 56.1 + - - +
1294A ALA 3.8 0.4 - - - -
1295A THR* 4.6 4.9 + - - -
1358A PRO* 4.3 17.2 - - - +
1360A GLN* 3.8 50.6 - - + +
1361A LEU* 4.4 14.4 - - + -
1364A VAL* 4.0 17.3 - - + -
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Residues in contact with GLY1293 (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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1289A PHE 3.3 10.7 + - - -
1290A LYS 3.3 4.1 + - - -
1291A VAL 3.2 0.4 - - - -
1292A TYR* 1.3 80.7 - - - +
1294A ALA* 1.3 56.9 + - - +
1295A THR* 2.8 16.3 + - - -
1296A TYR* 3.6 1.9 + - - +
1297A LEU* 3.3 25.5 + - - +
1358A PRO* 4.8 6.7 - - - -
1361A LEU* 4.4 8.5 - - - -
1392A PHE* 3.6 15.8 - - - -
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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