Contacts of the helix formed by residues 37 - 45 (chain C) in PDB entry 4U9W
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 ASP 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C LEU* 4.5 3.0 - - - +
36C GLY* 1.3 78.0 - - - +
38C PRO* 1.3 61.0 - - - +
39C LEU* 2.9 21.5 + - - +
40C GLU* 2.9 42.5 + - + +
41C ALA 4.5 0.2 + - - -
46C LYS* 3.0 32.2 + - - -
59C CYS* 3.4 24.5 + - - +
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Residues in contact with PRO 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 4.2 28.7 - - + -
36C GLY 4.1 0.4 - - - -
37C ASP* 1.3 87.2 - - - +
39C LEU* 1.3 56.6 + - - +
40C GLU 3.1 1.1 + - - -
41C ALA* 3.6 10.8 + - + +
42C PHE* 3.5 18.5 - - - -
59C CYS* 3.7 9.0 - - - -
107C TRP* 3.4 41.1 - - + -
124C PHE* 5.3 0.2 - - + -
126C PHE* 4.4 13.9 - - + -
162C MET* 3.7 26.1 - - + +
165C SER* 5.6 0.2 + - - -
166C THR* 5.6 1.3 - - + -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 2.9 14.2 + - - +
38C PRO* 1.3 74.3 - - - +
40C GLU* 1.3 63.2 + - - +
41C ALA 3.0 3.8 + - - -
42C PHE* 3.2 47.2 + - + +
43C PRO* 3.5 5.0 - - - +
45C PHE* 4.0 18.8 - - + +
46C LYS* 3.8 19.9 - - + -
57C ILE* 3.6 42.0 - - + +
58C GLU 4.4 0.2 - - - -
59C CYS* 4.0 13.9 - - + +
109C LEU* 4.8 1.3 - - + -
158C ILE* 4.0 13.9 - - + -
162C MET* 3.7 14.6 - - + +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 5.6 1.0 + - - -
37C ASP* 2.9 38.9 + - + +
39C LEU* 1.3 78.4 - - - +
41C ALA* 1.3 57.3 + - - +
43C PRO* 3.1 22.0 - - - +
46C LYS* 4.3 9.2 - - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP 4.5 0.2 + - - -
38C PRO 3.6 11.6 + - - +
39C LEU 3.0 1.0 - - - -
40C GLU* 1.3 80.1 - - - +
42C PHE* 1.3 73.6 + - + +
43C PRO* 3.6 3.2 - - - +
165C SER* 4.3 8.1 - - - +
41D ALA* 3.6 30.7 - - + +
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PRO 3.5 20.4 - - - -
39C LEU* 3.2 24.4 + - + +
41C ALA* 1.3 89.3 - - + +
43C PRO* 1.3 60.9 - - - +
44C VAL* 3.1 4.5 - - - -
45C PHE* 2.9 40.4 + - + +
158C ILE* 4.5 2.9 - - + -
161C LEU* 3.6 41.7 - - + -
162C MET* 3.6 23.6 - - + -
165C SER* 3.9 11.9 - - - -
41D ALA* 4.3 0.7 - - + -
42D PHE* 3.8 33.9 - + - -
165D SER* 4.7 12.8 - - - +
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Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 3.8 7.4 - - - +
40C GLU* 3.1 23.1 - - - +
41C ALA 3.6 2.9 - - - +
42C PHE* 1.3 77.9 - - - +
44C VAL* 1.3 55.3 + - - +
45C PHE 3.0 5.8 - - - -
46C LYS* 3.0 41.7 + - + +
47C LYS* 4.6 0.5 + - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.0 4.4 + - + +
43C PRO* 1.3 79.4 - - - +
45C PHE* 1.3 71.4 + - + +
46C LYS 3.3 1.6 + - - -
47C LYS* 3.7 14.5 + - - +
28D LYS* 5.4 9.9 - - + -
31D ALA* 6.0 5.8 - - + -
165D SER 3.5 25.1 - - - +
166D THR* 4.8 7.0 - - - +
167D GLN* 3.0 37.7 + - + +
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Residues in contact with PHE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 4.0 9.4 - - + +
42C PHE* 2.9 22.2 + + + +
44C VAL* 1.3 84.9 - - + +
46C LYS* 1.3 58.1 + - - +
47C LYS 3.2 6.6 + - - -
57C ILE* 3.7 19.8 - - - +
154C PHE* 3.5 33.7 - + - -
157C GLN* 4.6 5.2 - - + -
158C ILE* 3.5 37.0 - - + +
161C LEU* 3.5 32.5 - - + -
164D ASN 3.5 21.3 - - - -
165D SER 3.8 7.9 - - - -
167D GLN* 3.6 18.6 - - + +
220D PHE* 3.9 20.0 - - + -
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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