Contacts of the helix formed by residues 1269 - 1281 (chain A) in PDB entry 3CMT
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 ASN1269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1261A GLN* 2.7 51.0 + - + +
1263A LEU* 4.1 22.8 - - + +
1266A GLU* 5.4 3.8 - - - +
1267A GLY 3.5 2.3 + - - -
1268A ILE* 1.4 68.9 - - - +
1270A PHE* 1.3 63.0 + - - +
1271A TYR* 3.7 2.1 + - - +
1272A GLY* 2.9 32.1 + - - -
1273A GLU* 3.3 21.1 + - - +
1302A LYS* 5.0 4.0 - - - +
1306A THR* 3.7 15.4 + - - +
1310A LYS* 5.7 2.4 + - - -
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Residues in contact with PHE1270 (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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1041A SER* 5.6 4.0 - - - -
1043A GLY* 3.5 24.2 - - - +
1044A SER 4.6 0.9 - - - -
1045A LEU* 3.5 35.8 - - + +
1268A ILE* 2.9 13.3 + - - +
1269A ASN* 1.3 70.2 + - - +
1271A TYR* 1.3 92.0 + + + +
1273A GLU* 3.2 14.2 + - - +
1274A LEU* 3.0 33.0 + - + +
1317A LYS* 4.8 7.6 - - - -
1320A GLU* 3.7 36.3 - - + -
1324A ARG* 5.5 2.5 - - - -
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Residues in contact with TYR1271 (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 ASN* 3.7 1.2 + - - +
1270A PHE* 1.3 95.3 - + + +
1272A GLY* 1.3 59.7 + - - +
1274A LEU* 3.2 14.7 + - + +
1275A VAL* 3.0 32.9 + - - +
1306A THR* 3.6 24.9 - - + +
1309A LEU* 3.8 27.6 + - + +
1310A LYS* 3.5 38.6 + - + -
1313A PRO* 4.8 10.4 - - - +
1316A ALA* 3.7 23.9 - - + +
1317A LYS* 5.3 8.3 + - - -
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Residues in contact with GLY1272 (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 ASN* 2.9 29.5 + - - -
1271A TYR* 1.3 77.5 - - - +
1273A GLU* 1.3 60.4 + - - +
1275A VAL* 3.3 2.9 + - - +
1276A ASP* 3.2 14.2 + - - -
1302A LYS* 2.9 32.6 + - - -
1306A THR* 3.6 11.1 - - - +
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Residues in contact with GLU1273 (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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1044A SER* 2.6 31.0 + - - -
1045A LEU* 3.1 25.1 + - + -
1046A SER* 2.6 23.2 + - - +
1259A GLU 4.6 3.4 - - - +
1260A PHE* 3.5 22.2 - - + +
1268A ILE* 3.9 2.0 - - - +
1269A ASN 3.3 9.1 + - - +
1270A PHE* 3.2 23.2 + - - +
1272A GLY* 1.3 74.3 - - - +
1274A LEU* 1.3 54.7 + - - +
1276A ASP* 3.1 6.3 + - - +
1277A LEU* 2.8 50.4 + - + +
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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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1045A LEU* 3.8 22.2 - - + +
1270A PHE* 3.0 18.8 + - + +
1271A TYR* 3.2 19.7 + - + +
1273A GLU* 1.3 76.5 - - - +
1275A VAL* 1.3 57.1 + - - +
1277A LEU* 4.6 0.2 - - - -
1278A GLY* 2.8 27.9 + - - -
1284A ILE* 4.2 2.4 - - - +
1309A LEU* 4.0 17.3 - - + -
1316A ALA* 3.7 39.3 - - + +
1319A ILE* 4.3 12.2 - - + +
1320A GLU* 3.7 32.8 - - + +
1323A VAL* 4.6 4.7 - - + -
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Residues in contact with VAL1275 (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 TYR 3.0 18.6 + - - +
1272A GLY 3.5 7.9 - - - +
1273A GLU 3.2 0.2 - - - -
1274A LEU* 1.3 74.4 - - - +
1276A ASP* 1.3 65.2 + - - +
1278A GLY* 3.1 1.4 + - - -
1279A VAL* 2.9 31.1 + - + +
1284A ILE* 4.1 11.5 - - + +
1291A TYR* 3.7 34.3 - - + -
1298A ILE* 5.7 0.4 - - + -
1302A LYS* 4.2 11.2 - - + -
1305A ALA* 4.0 8.5 - - + -
1306A THR* 3.9 27.8 - - - +
1309A LEU* 3.7 17.7 - - + -
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Residues in contact with ASP1276 (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 GLY 3.2 2.0 + - - +
1273A GLU* 3.1 9.6 + - - +
1275A VAL* 1.3 79.5 - - - +
1277A LEU* 1.3 61.4 + - + +
1279A VAL* 3.9 4.9 - - - +
1280A LYS* 3.0 30.0 + - - +
1291A TYR* 5.2 2.1 + - - -
1302A LYS* 3.3 42.7 + - - +
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Residues in contact with LEU1277 (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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1045A LEU* 4.4 7.4 - - + -
1046A SER* 4.3 18.8 - - - -
1049A ILE* 4.2 18.4 - - + -
1273A GLU* 2.8 45.0 + - + +
1274A LEU 4.0 1.8 - - - +
1276A ASP* 1.3 75.3 - - + +
1278A GLY* 1.3 59.3 + - - +
1280A LYS* 3.5 17.6 + - + +
1281A GLU* 3.0 34.7 + - - +
1323A VAL* 4.0 16.6 - - + +
1327A LEU* 3.8 26.7 - - + -
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Residues in contact with GLY1278 (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 2.8 19.4 + - - -
1275A VAL 3.6 0.9 - - - -
1277A LEU* 1.3 74.0 - - - +
1279A VAL* 1.3 61.8 + - - +
1281A GLU 3.3 1.7 + - - -
1282A LYS 3.2 3.3 + - - -
1283A LEU* 2.9 36.3 + - - +
1284A ILE* 3.7 19.1 - - - -
1319A ILE* 4.6 2.0 - - - -
1323A VAL* 4.4 10.0 - - - +
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Residues in contact with VAL1279 (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 VAL* 2.9 20.5 + - + +
1276A ASP* 3.9 6.3 - - - +
1278A GLY* 1.3 74.6 - - - +
1280A LYS* 1.3 63.5 + - - +
1282A LYS* 3.1 20.1 + - - +
1284A ILE* 3.5 25.7 - - + +
1286A LYS* 4.2 24.5 - - + -
1291A TYR* 3.6 34.8 - - + -
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Residues in contact with LYS1280 (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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1276A ASP 3.0 18.3 + - - +
1277A LEU* 3.6 19.9 - - + +
1279A VAL* 1.3 79.0 - - - +
1281A GLU* 1.3 76.6 + - - +
1282A LYS* 3.3 14.1 + - - +
1327A LEU* 5.2 8.7 - - - +
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Residues in contact with GLU1281 (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 LEU 3.0 21.5 + - - +
1278A GLY 3.3 2.2 + - - +
1279A VAL 3.2 0.4 - - - -
1280A LYS* 1.3 94.5 - - + +
1282A LYS* 1.3 69.6 + - - +
1283A LEU* 3.2 16.9 + - + +
1323A VAL* 5.0 4.9 - - + -
1326A LEU* 3.9 35.4 - - + +
1327A LEU* 3.6 42.6 - - + +
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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