Contacts of the strand formed by residues 1267 - 1276 (chain A) in PDB entry 5M5X
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 ILE1267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1263A LEU* 3.7 20.4 - - + +
1264A SER 3.6 8.6 + - - +
1266A VAL* 1.3 80.8 - - + +
1268A ASP* 1.3 60.9 + - - +
1269A LYS 3.8 5.8 - - - +
1270A VAL* 3.5 32.3 - - + -
1294A MET* 3.7 25.1 - - + -
1295A ARG 3.4 12.3 - - - +
1296A PHE* 4.5 1.1 - - + -
1297A PHE* 3.1 11.6 - - - -
1321A PHE* 5.7 0.2 - - + -
1489A VAL* 5.9 0.7 - - + -
1493A CYS* 3.6 31.6 - - + -
56I PHE* 3.6 36.9 - - + +
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Residues in contact with ASP1268 (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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1266A VAL 3.6 1.4 + - - -
1267A ILE* 1.3 74.2 - - - +
1269A LYS* 1.3 65.8 + - + +
1295A ARG* 2.9 9.5 + - + +
1296A PHE 3.6 22.4 - - - +
1297A PHE* 3.2 37.1 - - + -
53I ASP* 3.8 13.0 - - - +
56I PHE* 4.5 2.8 - - - -
61I ARG* 3.6 12.6 + - - +
64I LYS* 5.6 0.3 + - - -
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Residues in contact with LYS1269 (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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1267A ILE* 3.8 1.6 - - - +
1268A ASP* 1.3 85.5 - - + +
1270A VAL* 1.3 66.0 + - - +
1271A ILE* 3.7 29.6 - - + -
1293A HIS 4.0 0.2 - - - +
1294A MET* 3.5 1.2 - - - -
1295A ARG* 2.5 49.1 + - + +
50I THR* 3.2 27.7 - - + +
51I THR* 4.4 8.3 - - + -
53I ASP* 4.8 6.0 + - - +
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Residues in contact with VAL1270 (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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1267A ILE* 3.5 31.6 - - + -
1269A LYS* 1.3 74.5 - - - +
1271A ILE* 1.3 63.4 + - - +
1272A VAL* 3.7 30.7 + - + +
1292A ILE* 5.5 3.4 - - + -
1293A HIS 3.3 7.6 - - - +
1294A MET* 4.0 15.3 - - + -
1486A VAL* 6.0 3.4 - - + -
1489A VAL* 5.8 11.4 - - + -
1490A GLU* 5.0 4.0 - - - +
50I THR* 3.6 8.1 - - - +
51I THR* 3.2 43.5 + - - +
56I PHE* 4.8 3.4 - - + -
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Residues in contact with ILE1271 (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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1269A LYS* 3.7 42.0 - - + +
1270A VAL* 1.3 72.1 - - - +
1272A VAL* 1.3 59.3 + - - +
1273A THR* 3.6 19.3 + - - +
1291A VAL 3.8 1.6 - - - +
1293A HIS* 2.8 55.3 + - + +
1295A ARG* 4.2 16.4 - - + +
48I VAL* 5.5 4.9 - - + -
49I THR 3.7 11.0 - - - +
50I THR* 5.0 4.5 - - + +
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Residues in contact with VAL1272 (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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1270A VAL* 3.7 23.6 - - + +
1271A ILE* 1.3 71.2 - - - +
1273A THR* 1.3 61.4 + - - +
1274A GLU 3.8 1.9 + - - -
1290A TYR* 5.8 2.0 - - + -
1291A VAL 4.0 3.6 - - - -
1292A ILE* 3.8 34.3 - - + -
1485A MET* 3.7 37.8 - - + +
1486A VAL* 3.8 13.7 - - + -
1489A VAL* 5.7 2.7 - - + -
49I THR* 2.9 48.2 + - - +
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Residues in contact with THR1273 (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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1271A ILE* 3.6 19.5 + - - +
1272A VAL* 1.3 71.5 + - - +
1274A GLU* 1.3 60.9 + - - +
1275A THR* 3.5 7.4 + - - +
1290A TYR* 5.2 0.4 - - - -
1291A VAL* 3.5 35.8 + - - +
46I LYS* 3.3 36.1 - - + +
47I VAL 3.5 15.0 - - - +
48I VAL* 3.7 18.0 - - + +
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Residues in contact with GLU1274 (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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1272A VAL 3.8 3.6 + - - -
1273A THR* 1.3 71.8 - - - +
1275A THR* 1.3 64.5 + - - +
1276A THR* 4.7 0.4 - - - +
1288A ARG* 2.2 38.8 + - - +
1289A SER 3.3 19.5 - - - +
1290A TYR* 2.9 38.4 + - + +
1482A LYS* 5.5 0.9 + - - -
1483A LEU 4.6 0.9 + - - +
1485A MET* 3.3 26.7 - - + +
304B ASP* 5.5 0.5 - - - +
45I LEU* 4.5 1.7 - - + +
46I LYS* 3.9 0.9 - - - -
47I VAL* 3.0 50.7 + - + +
49I THR* 5.5 1.7 + - - +
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Residues in contact with THR1275 (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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1273A THR 3.5 9.1 + - - +
1274A GLU* 1.3 77.5 - - - +
1276A THR* 1.3 69.9 + - - +
1289A SER* 3.0 45.0 + - - +
1291A VAL* 4.4 13.8 - - + +
1473A LYS* 4.7 2.1 + - - -
45I LEU* 4.1 7.4 - - - -
46I LYS* 3.1 37.9 - - + +
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Residues in contact with THR1276 (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 GLU* 4.7 0.3 + - - -
1275A THR* 1.3 83.4 + - - +
1277A GLY* 1.3 61.8 + - - +
1287A ALA 3.6 22.9 - - - +
1288A ARG* 2.9 48.1 + - - +
1289A SER* 4.3 0.8 + - - -
1481A GLU* 4.5 2.7 - - - +
21I ASN* 4.9 8.1 - - - +
44I ASN* 4.4 2.4 - - - +
45I LEU* 3.3 50.1 + - + +
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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