Contacts of the helix formed by residues 1282 - 1291 (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 PRO1282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PRO* 3.5 45.8 - - + +
283A LEU* 4.4 10.1 - - + +
286A ASN* 4.8 8.7 - - + +
1280B ALA 4.6 1.1 - - - +
1281B SER* 1.3 87.7 - - - +
1283B LEU* 1.3 68.2 + - + +
1285B VAL* 3.2 9.8 + - + +
1286B ASN* 2.9 26.2 + - - +
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Residues in contact with LEU1283 (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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283A LEU* 4.9 3.6 - - + -
286A ASN* 3.3 45.1 - - + +
290A LYS* 4.0 5.4 - - - +
308A HIS* 4.3 6.3 - - + +
309A PRO* 4.7 7.0 - - + -
1281B SER* 3.5 5.8 + - - +
1282B PRO* 1.3 80.6 - - + +
1284B ALA* 1.3 59.6 + - - +
1286B ASN* 3.2 4.1 + - - -
1287B LEU* 2.9 25.6 + - - +
1308B HIS* 3.4 16.0 - - + -
1309B PRO* 3.6 38.6 - - + +
1310B TYR* 4.2 18.3 - - + +
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Residues in contact with ALA1284 (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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1216B MET* 4.1 14.2 - - + +
1220B ILE* 4.5 12.1 - - + -
1280B ALA* 4.8 1.1 - - + -
1281B SER* 3.1 31.6 + - - +
1283B LEU* 1.3 73.4 - - - +
1285B VAL* 1.3 66.8 + - - +
1287B LEU* 3.4 2.9 + - - +
1288B LEU* 3.0 30.4 + - - +
1310B TYR* 3.9 24.3 - - + +
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Residues in contact with VAL1285 (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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1272B ASP* 5.2 0.4 - - - +
1273B PHE* 3.8 13.1 - - + -
1274B ALA* 3.7 39.0 - - + +
1277B LEU* 3.7 25.4 - - + +
1280B ALA* 4.1 11.7 - - + +
1281B SER 3.0 16.4 + - - +
1282B PRO* 3.2 10.1 + - + +
1284B ALA* 1.3 74.5 - - - +
1286B ASN* 1.3 65.6 + - - +
1288B LEU* 3.3 2.3 + - - +
1289B GLU* 2.9 30.9 + - - +
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Residues in contact with ASN1286 (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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283A LEU* 4.1 19.3 - - + +
309A PRO* 3.3 24.1 - - - +
312A GLU* 3.8 9.2 - - - +
1282B PRO 2.9 14.1 + - - +
1283B LEU* 3.2 8.9 + - - +
1285B VAL* 1.3 77.0 - - - +
1287B LEU* 1.3 61.8 + - - +
1289B GLU* 3.0 12.4 + - - +
1290B LYS* 3.0 48.6 + - - +
1308B HIS* 2.6 30.7 + - + +
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Residues in contact with LEU1287 (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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1138B LEU* 5.1 0.2 - - + -
1216B MET* 4.1 6.1 - - - -
1283B LEU 2.9 16.4 + - - +
1284B ALA* 3.7 4.9 - - - +
1286B ASN* 1.3 76.2 - - - +
1288B LEU* 1.3 57.1 + - - +
1290B LYS* 3.0 8.5 + - + +
1291B MET* 2.8 63.3 + - + +
1300B VAL* 4.8 4.0 - - + -
1305B ALA* 4.1 16.4 - - - +
1308B HIS* 3.9 33.7 - - + -
1310B TYR* 3.7 15.7 - - + -
1311B PHE* 3.5 33.9 - - + -
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Residues in contact with LEU1288 (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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1213B GLY* 3.3 30.3 - - - +
1216B MET* 3.8 21.8 - - + -
1217B ALA* 4.1 13.5 - - + -
1220B ILE* 3.9 21.3 - - + -
1273B PHE* 3.9 14.1 - - + -
1277B LEU* 3.3 29.4 - - + -
1284B ALA 3.0 19.1 + - - +
1285B VAL* 3.6 4.3 - - - +
1287B LEU* 1.3 75.6 - - - +
1289B GLU* 1.3 54.6 + - - +
1291B MET* 3.0 12.2 + - + +
1292B LEU* 2.7 42.7 + - + +
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Residues in contact with GLU1289 (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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312A GLU* 5.7 4.0 - - - +
1270B LYS* 2.7 32.0 + - - +
1272B ASP* 4.5 4.8 - - - +
1273B PHE* 3.1 47.2 + - + +
1285B VAL* 2.9 20.3 + - - +
1286B ASN* 3.0 15.9 + - - +
1288B LEU* 1.3 77.6 - - - +
1290B LYS* 1.3 59.1 + - + +
1292B LEU 3.7 1.2 + - - -
1293B VAL* 3.1 28.5 + - + +
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Residues in contact with LYS1290 (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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309A PRO* 4.5 8.0 - - - +
312A GLU* 2.6 44.3 + - - +
1286B ASN* 3.0 36.5 + - - +
1287B LEU* 3.0 11.1 + - + +
1289B GLU* 1.3 79.4 - - + +
1291B MET* 1.3 58.6 + - - +
1293B VAL* 4.2 8.9 - - - +
1298B GLN 4.5 1.1 - - - +
1299B ARG* 3.8 6.4 - - - +
1300B VAL* 3.1 44.3 + - + +
1308B HIS* 3.9 17.5 - - + +
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Residues in contact with MET1291 (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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1134B VAL* 5.0 1.8 - - + -
1138B LEU* 4.8 8.7 - - - -
1209B ILE* 3.8 29.0 - - + +
1210B TRP* 4.2 2.8 - - - -
1212B VAL* 4.1 22.9 - - + -
1213B GLY* 4.2 12.1 - - - -
1216B MET* 3.7 26.2 - - + -
1287B LEU* 2.8 45.3 + - + +
1288B LEU* 3.7 15.7 - - + +
1290B LYS* 1.3 78.4 - - - +
1292B LEU* 1.3 61.9 + - - +
1293B VAL 3.4 2.5 - - - -
1299B ARG* 2.8 25.9 - - - +
1300B VAL* 3.8 18.4 - - + -
1305B ALA* 5.0 1.6 - - - -
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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