Contacts of the helix formed by residues 36 - 43 (chain C) in PDB entry 1YI8
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ALA 4.7 4.7 - - - +
35C LEU* 1.3 75.9 - - - +
37C LEU* 1.3 57.7 + - - +
38C GLY* 2.8 35.8 + - - -
39C HIS* 2.8 60.4 + + - +
40C LEU 3.2 7.4 + - - -
216C MET* 2.9 48.3 + - + +
217C SER* 4.1 6.5 - - - -
218C LYS* 4.6 5.6 - - + -
223C ALA* 4.2 11.9 - - + -
224C ILE 3.1 20.2 - - - +
225C ALA* 4.1 2.0 - - + -
226C LEU* 3.2 11.9 - - - +
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Residues in contact with LEU 37 (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 HIS* 1.3 74.8 - - - +
38C GLY* 1.3 61.7 + - - +
40C LEU* 3.3 9.8 + - + +
41C ALA* 3.1 20.3 + - - +
207C LEU* 3.5 11.1 - - + +
216C MET* 3.7 10.8 - - + -
224C ILE* 3.0 29.8 + - + +
226C LEU* 3.5 7.0 - - + +
263C PHE* 3.9 33.4 - - + -
267C PHE* 3.7 30.1 - - + -
299C LEU* 4.3 12.6 - - + -
303C LEU* 3.7 33.7 - - + -
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Residues in contact with GLY 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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36C HIS* 2.8 22.6 + - - -
37C LEU* 1.3 77.8 - - - +
39C HIS* 1.3 58.1 + - - +
41C ALA* 4.1 0.5 - - - +
42C GLY* 2.8 27.0 + - - -
207C LEU* 3.7 25.5 + - - +
216C MET* 3.6 5.1 - - - +
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Residues in contact with HIS 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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29C ASP* 4.3 15.7 - - - +
34C ALA 4.5 2.5 - - - -
35C LEU* 3.5 35.3 - - + +
36C HIS* 2.8 57.5 + + - +
38C GLY* 1.3 74.6 - - - +
40C LEU* 1.3 60.1 + - - +
42C GLY* 4.3 0.9 - - - +
43C SER* 2.7 36.3 + - - +
44C LEU* 2.9 17.2 + - + -
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Residues in contact with LEU 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 HIS 3.2 3.0 + - - +
37C LEU* 3.4 19.1 - - + +
38C GLY 3.2 0.2 - - - -
39C HIS* 1.3 80.7 - - - +
41C ALA* 1.3 62.0 + - - +
44C LEU* 3.3 34.9 + - + +
45C GLN* 3.1 46.8 + - + +
90C ALA* 4.8 5.8 - - + +
226C LEU* 4.4 6.5 - - + -
267C PHE* 4.1 9.2 - - + -
302C VAL* 3.7 29.2 - - + -
303C LEU* 4.0 12.6 - - + -
306C ILE* 3.8 25.1 - - + -
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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 LEU 3.1 7.6 + - - +
38C GLY 4.1 1.8 - - - +
40C LEU* 1.3 81.1 - - - +
42C GLY* 1.3 63.5 + - - +
43C SER 5.3 0.2 - - - -
45C GLN* 4.3 9.6 - - - +
46C ASN* 5.9 0.5 + - - +
203C ARG* 4.5 11.8 - - - +
207C LEU* 4.6 13.5 - - + +
266C ALA* 4.5 13.9 - - + +
267C PHE* 3.4 30.3 - - + -
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Residues in contact with GLY 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 GLY 2.8 23.9 + - - -
39C HIS* 3.9 1.1 - - - -
41C ALA* 1.3 75.6 - - - +
43C SER* 1.4 60.9 + - - +
46C ASN* 5.1 2.1 - - - +
203C ARG* 3.3 27.4 - - - +
204C VAL 6.0 0.2 - - - -
205C PRO 5.9 2.7 - - - -
206C ARG* 6.2 3.4 - - - -
207C LEU* 5.9 2.0 - - - +
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Residues in contact with SER 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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29C ASP* 4.8 3.3 + - - -
39C HIS* 2.7 24.8 + - - +
41C ALA 3.5 1.4 - - - -
42C GLY* 1.4 76.5 - - - +
44C LEU* 1.3 67.8 + - - +
45C GLN 3.5 1.3 - - - -
46C ASN* 3.3 16.2 + - - +
47C ARG* 3.0 58.4 + - - -
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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