Contacts of the helix formed by residues 1269 - 1283 (chain A) in PDB entry 1WUF
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 GLY1269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A ALA* 3.6 11.9 - - - +
1105A GLU* 3.2 11.7 - - - -
1106A LEU* 4.4 4.5 - - - -
1264A LEU* 3.1 26.5 + - - +
1267A VAL* 3.5 2.8 - - - +
1268A GLY* 1.3 79.8 - - - +
1270A MET* 1.3 61.3 + - - -
1271A SER 3.7 0.9 - - - -
1272A SER 4.3 1.6 - - - -
1273A ALA* 3.1 21.1 + - - +
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Residues in contact with MET1270 (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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1105A GLU* 2.8 10.4 + - - +
1106A LEU* 3.8 15.9 - - + +
1109A TRP* 3.6 43.7 - - + +
1120A LEU* 4.6 11.4 - - - -
1124A ILE* 3.9 20.4 - - + -
1264A LEU* 3.9 10.1 - - + -
1269A GLY* 1.3 69.1 - - - -
1271A SER* 1.3 67.2 + - - +
1272A SER 3.1 1.1 - - - -
1273A ALA* 3.0 2.8 + - + -
1274A LEU* 2.9 49.7 + - + +
1301A HIS* 5.6 0.9 - - - +
1305A LEU* 3.3 38.8 - - + -
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Residues in contact with SER1271 (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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1084A PRO 4.3 0.2 + - - -
1085A GLU* 3.3 36.7 + - - +
1088A GLN* 3.8 23.1 - - - +
1105A GLU* 3.1 16.3 + - - -
1109A TRP* 3.6 12.3 - - - -
1270A MET* 1.3 79.0 - - - +
1272A SER* 1.3 60.9 + - - +
1274A LEU* 3.4 5.2 + - - +
1275A LYS* 3.2 29.8 + - - +
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Residues in contact with SER1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A GLN* 3.5 25.7 + - - +
1105A GLU* 4.6 0.2 + - - -
1243A ARG 3.9 3.6 + - - -
1244A SER* 4.4 4.9 - - - -
1245A VAL* 4.5 1.0 + - - +
1267A VAL* 2.6 38.8 + - - +
1268A GLY 4.5 6.3 - - - -
1269A GLY 3.9 5.5 + - - -
1271A SER* 1.3 78.1 - - - +
1273A ALA* 1.3 65.1 + - - +
1275A LYS* 3.4 8.5 + - - +
1276A ILE* 3.1 26.7 + - - +
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Residues in contact with ALA1273 (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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1262A LEU* 3.5 22.2 - - + +
1264A LEU* 3.4 21.8 - - + -
1267A VAL* 4.0 12.3 - - + +
1269A GLY 3.1 20.2 + - - +
1270A MET 3.0 4.3 + - - +
1272A SER* 1.3 74.5 + - - +
1274A LEU* 1.3 58.3 + - - +
1276A ILE* 3.2 2.5 + - - -
1277A ALA* 2.9 25.4 + - - +
1305A LEU* 3.8 16.2 - - + -
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Residues in contact with LEU1274 (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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1109A TRP* 4.1 23.6 - - + -
1124A ILE* 4.1 16.6 - - + +
1270A MET* 2.9 43.7 + - + +
1271A SER* 3.8 4.5 - - - +
1273A ALA* 1.3 71.9 - - - +
1275A LYS* 1.3 66.8 + - + +
1277A ALA* 3.0 6.9 + - + +
1278A GLU* 2.9 40.5 + - - +
1305A LEU* 4.2 4.3 - - + -
1308A ARG* 3.9 42.6 - - + +
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Residues in contact with LYS1275 (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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1088A GLN* 3.3 28.3 + - - +
1245A VAL* 3.3 23.8 - - + +
1271A SER* 3.2 16.0 + - - +
1272A SER* 3.6 8.1 - - - +
1274A LEU* 1.3 78.5 - - + +
1276A ILE* 1.3 58.6 + - - +
1278A GLU* 3.6 11.4 + - - +
1279A TYR* 3.1 27.9 + - - +
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Residues in contact with ILE1276 (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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1242A ILE* 4.7 5.2 - - + -
1244A SER* 3.7 18.8 - - - +
1245A VAL* 3.6 23.3 - - + +
1248A VAL* 3.8 22.0 - - + -
1260A ILE* 4.6 8.7 - - + -
1262A LEU* 4.1 17.5 - - + -
1267A VAL* 3.0 36.6 - - + -
1272A SER 3.1 10.7 + - - +
1273A ALA 3.5 6.7 - - - +
1274A LEU 3.1 0.4 - - - -
1275A LYS* 1.3 75.0 - - - +
1277A ALA* 1.3 60.2 + - - +
1279A TYR* 3.2 5.0 + - - +
1280A CYS* 2.9 37.5 + - - -
1287A VAL* 5.0 0.4 - - + -
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Residues in contact with ALA1277 (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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1262A LEU* 4.4 0.4 - - + +
1273A ALA 2.9 12.9 + - - +
1274A LEU* 3.0 12.3 + - + +
1276A ILE* 1.3 76.4 - - - +
1278A GLU* 1.3 64.9 + - - +
1280A CYS* 3.3 2.8 + - - +
1281A ALA 3.0 18.0 + - - -
1287A VAL* 4.5 12.8 - - - -
1308A ARG* 5.2 2.0 - - - +
1310A GLU* 3.4 27.4 - - + +
1311A PHE* 3.7 30.3 - - + -
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Residues in contact with GLU1278 (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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1274A LEU* 2.9 24.9 + - - +
1275A LYS* 3.8 9.9 - - - +
1277A ALA* 1.3 77.5 - - - +
1279A TYR* 1.3 60.9 + - - +
1281A ALA* 3.3 6.9 + - - +
1282A LEU* 3.1 29.1 + - + +
1308A ARG* 3.3 24.3 + - - +
1310A GLU* 3.8 19.1 - - - +
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Residues in contact with TYR1279 (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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1245A VAL* 3.7 22.0 - - + -
1248A VAL* 3.7 28.3 - - + -
1249A GLU* 3.4 39.4 + - + +
1252A HIS* 3.0 22.8 + - - +
1275A LYS 3.1 18.1 + - - +
1276A ILE* 3.2 6.0 + - - +
1278A GLU* 1.3 75.5 - - - +
1280A CYS* 1.3 69.2 + - - +
1282A LEU* 3.2 8.6 + - + +
1283A ASN* 3.0 38.0 + - - +
1285A ILE* 3.9 13.7 - - + -
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Residues in contact with CYS1280 (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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1248A VAL* 4.3 8.7 - - - -
1260A ILE* 4.2 12.6 - - - -
1276A ILE* 2.9 33.1 + - - +
1277A ALA 3.8 3.8 - - - +
1279A TYR* 1.3 78.3 - - - +
1281A ALA* 1.3 63.5 + - - +
1283A ASN 3.2 5.4 + - - -
1284A GLU* 3.2 1.2 + - - -
1285A ILE* 2.9 68.5 + - + +
1287A VAL* 3.9 21.8 - - + -
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Residues in contact with ALA1281 (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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1277A ALA 3.0 13.9 + - - +
1278A GLU* 3.3 11.0 - - - +
1280A CYS* 1.3 78.7 - - - +
1282A LEU* 1.3 63.3 + - + +
1283A ASN 3.4 0.5 + - - -
1284A GLU* 3.9 9.2 + - - +
1285A ILE 5.0 0.4 - - - -
1287A VAL* 5.4 0.8 - - - +
1310A GLU* 3.7 22.4 - - + +
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Residues in contact with LEU1282 (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 GLU* 3.1 19.7 + - + +
1279A TYR* 3.2 6.5 + - + +
1281A ALA* 1.3 79.4 - - + +
1283A ASN* 1.3 72.2 + - - +
1284A GLU 3.6 1.1 + - - -
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Residues in contact with ASN1283 (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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1252A HIS* 3.1 40.1 + - + +
1279A TYR* 3.0 44.2 + - + +
1280A CYS 3.2 0.4 + - - -
1282A LEU* 1.3 91.6 + - - +
1284A GLU* 1.3 61.8 + - - +
1285A ILE* 2.9 22.7 + - + +
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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