Contacts of the helix formed by residues 28 - 35 (chain B) in PDB entry 4M6W
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 SER 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B LYS 5.4 1.3 - - - -
25B TRP* 2.7 47.5 + - - -
26B ARG 3.2 2.7 + - - -
27B GLY* 1.3 78.4 - - - +
29B GLN* 1.3 53.6 + - - +
30B LEU 3.9 0.3 + - - -
31B ALA* 3.1 9.4 + - - +
32B GLN* 2.8 37.1 + - - +
122B GLN* 4.0 8.1 - - - -
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Residues in contact with GLN 29 (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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28B SER* 1.3 70.6 - - - +
30B LEU* 1.3 68.5 + - - +
32B GLN* 3.3 11.9 + - - +
33B GLU* 3.1 44.2 + - - +
122B GLN* 3.3 25.2 + - + +
123B MET* 3.6 30.0 - - + +
126B SER* 4.0 0.6 + - - -
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Residues in contact with LEU 30 (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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25B TRP* 3.7 40.8 - - + -
29B GLN* 1.3 80.1 - - - +
31B ALA* 1.3 61.3 + - - +
33B GLU 3.3 0.5 + - - -
34B MET* 3.2 44.6 + - + +
50B PHE* 4.1 12.3 - - + -
60B TYR* 3.9 10.1 - - + -
122B GLN* 3.0 35.6 + - + +
125B ALA* 3.8 16.6 - - + +
126B SER* 3.5 33.7 + - - +
129B VAL* 4.8 4.0 - - + -
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Residues in contact with ALA 31 (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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25B TRP* 3.5 26.7 - - + +
27B GLY* 4.4 3.6 - - - +
28B SER* 3.1 10.7 + - - +
30B LEU* 1.3 77.2 - - + +
32B GLN* 1.3 61.1 + - - +
34B MET* 4.2 2.9 - - + +
35B GLN* 2.9 32.9 + - - +
40B LEU* 3.9 25.1 - - + +
42B PHE* 4.2 10.1 - - + -
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Residues in contact with GLN 32 (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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27B GLY* 4.0 24.8 + - - +
28B SER 2.8 25.9 + - - +
29B GLN* 3.7 16.2 - - - +
30B LEU 3.3 0.2 - - - -
31B ALA* 1.3 75.5 - - - +
33B GLU* 1.3 60.8 + - - +
34B MET 3.7 0.2 + - - -
35B GLN* 3.5 33.5 + - - +
36B GLY 4.8 0.5 + - - -
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Residues in contact with GLU 33 (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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29B GLN* 3.1 29.3 + - - +
32B GLN* 1.3 76.0 - - - +
34B MET* 1.3 62.8 + - - +
36B GLY* 4.7 2.5 + - - -
37B LYS* 5.1 5.2 + - - +
123B MET* 3.7 18.6 - - + +
126B SER* 3.4 32.3 - - - +
127B CYS* 5.8 5.2 - - - -
130B ILE* 4.2 11.8 - - + +
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Residues in contact with MET 34 (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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19B ILE* 5.3 1.8 - - - -
30B LEU* 3.2 42.5 + - + +
31B ALA* 4.0 4.3 - - + +
33B GLU* 1.3 77.6 - - - +
35B GLN* 1.3 66.5 + - - +
36B GLY 2.7 5.9 + - - -
37B LYS 2.9 4.0 + - - -
38B ILE* 2.9 38.1 + - + +
40B LEU* 3.7 36.3 - - + -
50B PHE* 3.9 17.3 - - + -
126B SER* 4.4 6.3 - - - +
129B VAL* 3.9 28.7 - - - -
130B ILE* 4.3 20.4 - - + -
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Residues in contact with GLN 35 (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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31B ALA 2.9 19.4 + - - +
32B GLN* 3.5 27.3 + - - +
33B GLU 3.6 0.2 - - - -
34B MET* 1.3 75.1 - - - +
36B GLY* 1.3 80.2 + - - +
38B ILE 3.2 16.2 + - - +
39B LYS* 4.5 5.7 + - - +
40B LEU* 4.6 5.3 - - + +
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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