Contacts of the helix formed by residues 1337 - 1349 (chain B) in PDB entry 1CM8
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 LEU1337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062B PHE* 4.8 10.8 - - + +
1064B SER* 5.1 14.6 - - - +
1065B GLU* 5.5 5.4 + - + +
1068B ALA* 5.2 0.6 - - - +
1336B THR* 1.3 73.7 - - - +
1338B ASP* 1.3 64.4 + - - +
1340B TRP* 3.5 9.8 + - - +
1341B LYS* 3.1 28.3 + - - +
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Residues in contact with ASP1338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099B LEU* 5.8 0.3 - - - +
1336B THR* 3.1 8.3 + - - +
1337B LEU* 1.3 83.7 - - - +
1339B GLU* 1.3 59.0 + - - +
1341B LYS* 3.9 19.8 + - - +
1342B ARG* 3.1 26.9 + - - +
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Residues in contact with GLU1339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335B ARG* 3.6 21.3 - - + +
1336B THR* 2.9 51.2 + - - +
1338B ASP* 1.3 75.8 - - - +
1340B TRP* 1.3 56.6 + - - +
1342B ARG* 3.8 3.4 - - - +
1343B VAL* 2.8 36.8 + - - +
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Residues in contact with TRP1340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B PHE* 4.2 0.9 - - - -
1065B GLU* 3.5 28.9 + - + +
1068B ALA* 3.4 26.7 - - + -
1069B LYS* 3.6 47.6 - - + -
1072B TYR* 3.8 42.2 - + + -
1073B ARG* 5.9 0.7 - - + -
1335B ARG* 3.7 28.4 + - + +
1336B THR 3.1 24.9 + - - -
1337B LEU* 3.8 5.8 - - - +
1339B GLU* 1.3 74.6 - - - +
1341B LYS* 1.3 54.7 + - - +
1343B VAL* 3.4 5.4 + - + +
1344B THR* 2.7 42.1 + - - -
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Residues in contact with LYS1341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B PHE* 3.6 34.3 - - + +
1099B LEU* 3.9 21.1 - - + -
1100B ASP 3.8 14.7 + - - -
1101B ASP* 5.2 1.0 - - - +
1102B PHE* 2.9 42.8 + - + -
1103B THR* 5.1 5.6 - - - +
1337B LEU 3.1 16.1 + - - +
1338B ASP* 3.9 19.6 + - - +
1340B TRP* 1.3 78.8 - - - +
1342B ARG* 1.3 55.6 + - - +
1344B THR* 3.6 0.2 - - - -
1345B TYR* 2.9 29.3 + - - +
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Residues in contact with ARG1342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099B LEU* 4.1 27.1 - - + +
1338B ASP 3.1 17.4 + - - +
1339B GLU* 3.8 5.2 - - - +
1341B LYS* 1.3 76.0 - - - +
1343B VAL* 1.3 65.7 + - - +
1344B THR 3.1 1.3 - - - -
1345B TYR* 3.3 2.3 + - - +
1346B LYS* 3.1 23.4 + - - +
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Residues in contact with VAL1343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072B TYR* 4.1 19.8 - - + -
1339B GLU 2.8 22.4 + - - +
1340B TRP* 3.8 8.3 - - + +
1342B ARG* 1.3 73.6 - - - +
1344B THR* 1.3 60.9 + - - +
1346B LYS* 3.6 6.5 - - - +
1347B GLU* 3.4 24.8 + - - +
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Residues in contact with THR1344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B PHE* 3.6 25.4 - - + -
1068B ALA 4.6 0.7 + - - -
1072B TYR* 3.5 32.3 + - - +
1075B LEU* 4.5 5.4 - - + -
1102B PHE* 4.1 2.2 - - + -
1105B PHE* 4.0 23.3 - - + -
1340B TRP 2.7 24.3 + - - -
1341B LYS 3.6 4.3 - - - -
1343B VAL* 1.3 73.8 - - - +
1345B TYR* 1.3 67.6 + - - +
1346B LYS 3.0 1.8 - - - -
1347B GLU* 2.8 17.3 + - - +
1348B VAL* 2.9 23.6 + - + +
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Residues in contact with TYR1345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B THR* 4.2 16.4 - - + -
1096B ASP 4.0 5.1 + - - -
1097B GLU 3.4 25.3 + - - -
1098B THR* 3.8 1.7 - - - -
1099B LEU* 3.7 38.6 - - + -
1102B PHE* 3.5 47.5 - + + -
1341B LYS 2.9 18.7 + - - +
1342B ARG 3.6 5.2 - - - +
1344B THR* 1.3 75.2 - - - +
1346B LYS* 1.3 62.4 + - - +
1348B VAL* 3.2 4.4 + - + +
1349B LEU* 3.1 60.5 + - + +
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Residues in contact with LYS1346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342B ARG 3.1 11.6 + - - +
1343B VAL* 3.6 12.1 - - - +
1344B THR 3.0 0.4 - - - -
1345B TYR* 1.3 78.9 - - - +
1347B GLU* 1.3 58.9 + - + +
1348B VAL 3.2 0.2 + - - -
1349B LEU* 3.4 6.6 + - - +
1350B SER* 3.0 31.7 + - - -
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Residues in contact with GLU1347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072B TYR* 4.0 12.5 + - + -
1075B LEU* 3.8 17.7 - - + +
1076B ARG* 3.3 44.6 + - + -
1079B LYS* 2.7 57.7 + - - +
1343B VAL 3.4 12.3 + - - +
1344B THR* 2.8 13.2 + - - +
1346B LYS* 1.3 76.2 - - + +
1348B VAL* 1.3 61.1 + - - +
1350B SER* 3.5 7.9 + - - -
1351B PHE* 4.0 1.9 + - - +
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Residues in contact with VAL1348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B LEU* 3.6 18.4 - - + -
1092B VAL* 4.0 23.6 - - + +
1093B PHE* 4.4 12.3 - - - -
1094B THR* 4.2 23.1 - - + -
1102B PHE* 4.3 7.0 - - + -
1105B PHE* 4.2 13.0 - - + -
1344B THR* 2.9 30.2 + - + +
1345B TYR* 3.5 10.5 - - + +
1346B LYS 3.1 0.2 - - - -
1347B GLU* 1.3 79.5 - - - +
1349B LEU* 1.3 65.7 + - + +
1351B PHE* 3.4 18.9 + - - +
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Residues in contact with LEU1349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B THR* 4.8 6.3 - - + -
1345B TYR* 3.1 61.7 + - + +
1346B LYS* 4.1 5.2 - - - +
1348B VAL* 1.3 80.5 - - + +
1350B SER* 1.3 58.9 + - - +
1351B PHE 3.1 12.0 + - - +
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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