Contacts of the helix formed by residues 1268 - 1275 (chain A) 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 GLU1268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107A SER* 4.5 10.0 + - - +
1108A LYS* 6.0 1.2 - - - +
1111A GLN* 3.2 40.8 + - - +
1266A GLU 3.8 0.9 + - - +
1267A MET* 1.3 74.8 - - - +
1269A PRO* 1.3 70.4 - - + +
1270A GLY* 3.2 4.0 - - - +
1271A PHE* 2.9 29.8 + - - +
1272A ARG* 4.0 0.9 + - - +
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Residues in contact with PRO1269 (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 MET 3.7 2.8 - - - +
1268A GLU* 1.3 88.1 - - + +
1270A GLY* 1.3 60.7 + - - +
1272A ARG* 2.9 40.0 + - + +
1273A GLU* 3.7 2.3 + - - +
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Residues in contact with GLY1270 (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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1268A GLU* 3.2 4.2 + - - +
1269A PRO* 1.3 81.1 - - - +
1271A PHE* 1.3 54.3 + - - +
1273A GLU* 2.7 30.6 + - - +
1274A VAL* 3.0 18.4 + - - +
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Residues in contact with PHE1271 (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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1058A HIS* 3.9 18.4 - + - -
1111A GLN* 4.6 3.6 - - - +
1114A GLY 3.9 9.4 - - - -
1115A GLU* 4.5 2.7 - - + -
1118A ASP* 3.5 28.0 - - + -
1260A ILE* 4.0 21.5 - - + -
1264A LYS* 5.9 0.2 - - + -
1267A MET* 3.5 45.1 - - + -
1268A GLU* 2.9 19.0 + - - +
1270A GLY* 1.3 76.0 - - - +
1272A ARG* 1.3 57.4 + - - +
1274A VAL* 4.0 7.0 - - - -
1275A SER* 2.8 64.0 + - - -
1277A TYR* 4.2 0.7 - - + -
1278A TYR* 3.9 21.1 - + - -
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Residues in contact with ARG1272 (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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1264A LYS* 5.3 7.3 + - - +
1265A GLU* 5.4 7.3 + - - -
1268A GLU 4.0 0.4 + - - -
1269A PRO* 2.9 23.1 + - + +
1271A PHE* 1.3 79.7 - - - +
1273A GLU* 1.3 59.3 + - - +
1275A SER* 4.6 1.6 + - - +
1278A TYR* 3.5 72.0 + - + +
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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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1269A PRO 4.6 1.3 - - - +
1270A GLY* 2.7 17.6 + - - +
1272A ARG* 1.3 81.4 - - - +
1274A VAL* 1.3 62.6 + - + +
1275A SER 5.3 0.4 - - - -
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Residues in contact with VAL1274 (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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1057A HIS* 3.4 62.6 + - + +
1058A HIS* 3.9 11.6 + - + +
1270A GLY 3.0 15.4 + - - +
1271A PHE* 4.0 7.0 - - - -
1273A GLU* 1.3 86.3 - - + +
1275A SER* 1.3 68.2 + - - +
1276A PHE 3.9 0.5 + - - -
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Residues in contact with SER1275 (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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1058A HIS* 4.2 3.1 - - - -
1118A ASP* 3.4 19.5 - - - -
1271A PHE* 2.8 41.3 + - - -
1272A ARG 4.6 1.2 - - - +
1273A GLU 3.8 0.9 - - - -
1274A VAL* 1.3 82.4 - - - +
1276A PHE* 1.3 63.2 + - - +
1277A TYR* 3.4 0.9 + - - +
1278A TYR* 3.1 30.1 + - - +
1279A SER* 3.2 19.8 + - - -
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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