Contacts of the helix formed by residues 1270 - 1275 (chain B) in PDB entry 1M7N
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 GLY1270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1268B GLU* 3.1 6.2 - - - +
1269B PRO* 1.3 76.5 - - - +
1271B PHE* 1.3 54.5 + - - +
1272B ARG 3.0 3.1 - - - -
1273B GLU* 2.5 41.3 + - - +
1274B VAL* 3.3 10.6 + - - +
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Residues in contact with PHE1271 (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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1058B HIS* 3.9 23.6 - + - -
1111B GLN* 4.4 9.0 - - - +
1114B GLY 3.7 21.5 - - - -
1115B GLU* 4.7 0.2 - - + -
1118B ASP* 3.9 10.1 - - + -
1260B ILE* 3.8 26.5 - - + -
1264B LYS* 6.0 1.1 - - - -
1267B MET* 3.5 43.7 - - + -
1268B GLU* 3.1 19.6 + - - +
1270B GLY* 1.3 75.8 - - - +
1272B ARG* 1.3 57.1 + - - +
1274B VAL* 3.9 6.7 - - - -
1275B SER* 2.9 59.9 + - - -
1277B TYR* 4.2 0.9 - - + -
1278B TYR* 3.8 19.5 - + - -
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Residues in contact with ARG1272 (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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1268B GLU 4.4 0.4 + - - -
1269B PRO 3.5 13.5 + - - +
1270B GLY 2.8 1.2 + - - -
1271B PHE* 1.3 78.6 - - - +
1273B GLU* 1.3 87.4 + - - +
1274B VAL 3.8 0.2 + - - -
1275B SER* 4.5 1.9 + - - +
1278B TYR* 3.7 56.6 - - + +
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Residues in contact with GLU1273 (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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1269B PRO 4.5 6.2 - - - +
1270B GLY* 2.5 25.3 + - - +
1272B ARG* 1.3 100.7 + - - +
1274B VAL* 1.3 63.1 + - + +
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Residues in contact with VAL1274 (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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1056B CYS* 6.0 0.5 - - - -
1057B HIS* 3.3 60.6 + - + +
1058B HIS* 3.5 11.7 - - + +
1270B GLY 3.3 11.6 + - - +
1271B PHE* 3.8 11.7 - - - +
1273B GLU* 1.3 87.7 - - + +
1275B SER* 1.3 71.0 + - - +
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Residues in contact with SER1275 (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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1058B HIS* 4.1 3.1 - - - -
1118B ASP* 3.3 9.6 - - - -
1271B PHE* 2.9 52.0 + - - -
1272B ARG 4.6 1.4 - - - +
1273B GLU 4.0 0.2 - - - -
1274B VAL* 1.3 83.7 - - - +
1276B PHE* 1.3 62.0 + - - +
1277B TYR* 3.7 0.6 - - - +
1278B TYR* 3.1 30.5 + - - +
1279B SER* 3.3 18.7 + - - -
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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