Contacts of the helix formed by residues 37 - 43 (chain A) in PDB entry 3MOS
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 HIS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 3.8 5.6 - - - +
36A GLY* 1.4 81.4 - - - -
38A PRO* 1.3 68.8 - - - +
39A THR* 3.1 3.6 - - - -
40A SER* 3.0 21.3 + - - +
41A CYS* 3.1 15.9 + - - -
77A HIS* 3.5 40.3 + + + +
80A PRO* 5.2 1.4 - - - +
101A ARG* 4.0 19.2 + - - -
110A HIS* 4.7 6.7 + + - -
258A HIS* 3.5 28.3 + + - -
259A GLY* 3.3 30.4 - - - +
700A TPP 5.2 3.0 - - - -
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Residues in contact with PRO 38 (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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26A SER* 4.2 8.7 - - - +
27A ILE* 4.3 19.3 - - + -
30A THR* 3.5 27.4 - - + +
36A GLY 3.4 8.1 - - - +
37A HIS* 1.3 87.8 - - - +
39A THR* 1.3 64.3 + - + +
41A CYS* 3.2 12.9 + - + +
42A CYS* 3.0 26.5 + - - -
248A ILE* 4.9 2.0 - - + -
260A LYS 3.6 22.4 - - - +
261A PRO* 3.9 7.9 - - + -
262A LEU* 4.2 16.8 - - + +
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Residues in contact with THR 39 (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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37A HIS 3.1 0.6 - - - -
38A PRO* 1.3 82.9 - - + +
40A SER* 1.3 61.5 + - - +
42A CYS* 3.4 7.6 + - - -
43A SER* 3.5 5.0 + - - -
244A LYS* 3.7 24.5 - - - +
245A GLY* 2.9 39.0 + - - +
248A ILE* 4.3 7.0 - - + -
251A VAL* 3.4 32.8 - - + -
257A TRP* 3.3 36.8 + - + +
258A HIS* 4.2 1.7 - - - -
259A GLY 4.8 1.4 + - - -
262A LEU* 5.5 0.2 - - + -
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Residues in contact with SER 40 (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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37A HIS* 3.0 14.1 + - - +
39A THR* 1.3 75.7 + - - +
41A CYS* 1.3 65.1 + - - +
43A SER* 3.5 7.3 + - - -
44A ALA* 4.1 1.9 - - - +
75A LYS* 2.8 30.0 + - - +
77A HIS* 3.3 22.7 - - - -
78A ALA* 4.0 5.4 - - - +
244A LYS* 3.7 10.8 - - - +
258A HIS* 3.7 5.9 + - - -
259A GLY 5.2 0.3 + - - -
700A TPP 2.5 31.2 + - - -
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Residues in contact with CYS 41 (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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26A SER* 3.4 35.2 - - - +
37A HIS 3.1 16.9 + - - -
38A PRO* 3.4 9.6 - - - +
40A SER* 1.3 78.9 - - - +
42A CYS* 1.3 57.2 + - - +
44A ALA* 3.0 18.9 + - - +
45A ALA 3.3 8.3 + - - -
78A ALA* 3.8 14.1 - - - -
80A PRO* 3.9 16.2 - - - -
81A ILE* 3.3 38.4 - - + +
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Residues in contact with CYS 42 (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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23A ARG* 3.0 55.5 + - - +
26A SER* 5.4 0.7 - - - -
27A ILE* 4.5 7.9 - - - -
38A PRO* 3.0 19.6 + - - +
39A THR 3.4 0.6 + - - -
41A CYS* 1.3 75.3 - - - +
43A SER* 1.3 65.8 + - - +
44A ALA 3.2 0.3 + - - -
45A ALA* 3.4 6.5 + - - +
245A GLY* 3.8 7.9 - - - -
246A ARG* 3.3 31.9 - - - +
248A ILE* 3.9 22.0 - - - -
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Residues in contact with SER 43 (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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39A THR 3.5 6.4 + - - -
40A SER 3.5 9.2 + - - -
42A CYS* 1.3 77.3 - - - +
44A ALA* 1.3 57.5 + - - +
45A ALA 3.4 1.7 + - - -
47A ILE* 4.5 1.6 - - - +
183A ASP* 2.8 31.8 + - - +
185A ASN* 3.0 26.6 + - - -
218A GLY 4.6 1.2 - - - +
219A HIS* 3.3 19.5 + - - -
242A THR* 3.4 16.1 - - - +
243A PHE 3.3 24.8 + - - -
244A LYS* 4.0 2.0 - - - -
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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