Contacts of the helix formed by residues 1134 - 1138 (chain B) in PDB entry 4E70
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 MET1134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A CYS* 3.6 20.2 - - - -
70A LEU* 6.0 1.3 - - + -
1130B PRO 3.3 4.0 + - - -
1131B TRP* 3.2 48.4 + - + +
1132B ARG 3.6 0.2 - - - -
1133B GLN* 1.3 77.5 - - - +
1135B SER* 1.3 57.5 + - - +
1137B TRP* 3.2 27.3 + - + +
1138B LEU* 2.8 39.9 + - + +
1151B ALA* 3.7 22.7 - - + -
1327B MET* 4.2 17.9 - - + +
1328B SER* 3.8 24.0 - - - -
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Residues in contact with SER1135 (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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31A CYS* 3.6 19.3 + - - +
34A GLU* 2.7 40.7 + - - +
35A LEU* 3.9 16.4 - - - +
1132B ARG 5.5 0.4 - - - -
1133B GLN* 3.4 0.6 - - - +
1134B MET* 1.3 77.6 - - - +
1136B ALA* 1.3 62.4 + - - +
1138B LEU* 3.3 11.6 + - - +
1139B ARG* 3.1 33.7 + - - +
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Residues in contact with ALA1136 (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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1133B GLN* 3.4 15.1 + - + +
1134B MET 3.3 0.4 - - - -
1135B SER* 1.3 79.8 - - - +
1137B TRP* 1.3 60.3 + - - +
1139B ARG* 3.3 9.2 + - - +
1140B THR* 2.7 25.9 + - - -
1154B PHE* 3.9 16.6 - - + -
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Residues in contact with TRP1137 (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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63A LYS* 2.7 51.0 + - + +
66A PHE* 3.7 40.4 - + + -
1133B GLN 2.9 17.2 + - - +
1134B MET* 3.6 25.8 - - + +
1136B ALA* 1.3 75.9 - - - +
1138B LEU* 1.3 92.7 + - + +
1140B THR* 3.0 9.3 + - - -
1147B ASP* 3.9 2.0 - - - -
1148B THR* 2.9 39.8 + - - -
1149B PRO 3.4 22.0 - - - -
1150B ASN* 3.6 14.3 - - + -
1151B ALA* 3.9 12.1 - - + -
1154B PHE* 3.8 22.4 - + + -
1327B MET* 5.0 7.9 - - + -
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Residues in contact with LEU1138 (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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31A CYS* 5.5 0.2 - - - -
35A LEU* 4.1 23.6 - - + -
59A ILE* 3.4 27.0 - - + +
60A PRO* 3.3 19.4 - - - +
63A LYS* 3.6 13.3 - - + +
66A PHE* 3.8 21.5 - - + -
67A LEU* 4.4 9.2 - - - +
70A LEU* 4.2 17.3 - - + -
1134B MET* 2.8 37.8 + - + +
1135B SER* 3.3 6.7 + - - +
1137B TRP* 1.3 99.8 - - + +
1139B ARG* 1.3 57.7 + - - +
1140B THR 3.3 1.0 + - - -
1327B MET* 5.2 3.1 - - + -
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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