Contacts of the helix formed by residues 183 - 189 (chain D) in PDB entry 1S9C
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 ASN 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.3 12.2 - - + +
36C ALA 4.8 0.6 + - - -
37C SER* 3.1 30.5 + - - +
38C ILE* 2.8 35.3 + - - +
47C ILE* 4.0 4.7 - - - +
181D SER* 2.8 12.8 + - - +
182D LEU* 1.3 86.5 - - - +
184D GLN* 1.3 64.6 + - - +
185D ALA 3.2 2.9 - - - -
186D ALA* 2.9 21.7 + - + +
187D LEU* 3.0 14.3 + - + +
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Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU 3.9 7.5 + - - -
33D GLY* 3.0 31.3 + - - -
35D GLY* 4.1 1.2 - - - +
179D THR 4.7 0.9 - - - +
180D THR* 3.3 30.1 - - + -
181D SER* 2.9 35.5 + - - +
182D LEU 3.5 0.4 - - - -
183D ASN* 1.3 77.3 - - - +
185D ALA* 1.3 58.7 + - - +
187D LEU* 3.2 6.6 + - - +
188D TYR* 2.8 31.0 + - - +
214D LEU* 3.6 15.7 - - + -
218D CYS* 3.9 10.3 - - - -
222D PHE* 3.6 23.3 - - + -
252D PRO* 4.6 0.6 - - + +
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU 6.0 0.2 - - - +
183D ASN 3.2 0.6 - - - -
184D GLN* 1.3 79.0 - - - +
186D ALA* 1.3 63.9 + - - +
188D TYR* 4.4 0.7 - - - +
189D ARG* 3.0 30.8 + - - +
198D HIS* 3.3 27.8 - - + +
213D ILE 4.5 1.8 - - - +
214D LEU* 3.5 13.8 - - + +
215D HIS* 3.8 14.8 - - + +
252D PRO* 3.9 21.6 - - + +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 4.9 1.0 - - - +
32C LEU* 3.8 8.9 - - + +
38C ILE* 4.4 10.2 - - + +
47C ILE* 3.8 28.2 - - + +
183D ASN* 2.9 28.4 + - + +
185D ALA* 1.3 81.4 - - - +
187D LEU* 1.3 57.6 + - - +
189D ARG* 3.3 24.8 + - - +
190D LEU* 3.8 11.3 - - - +
199D ILE* 4.4 7.1 - - + +
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.0 13.9 - - + -
187C LEU* 4.1 28.7 - - + -
29D MET* 4.8 13.9 - - + +
32D LEU* 3.8 15.3 - - + +
33D GLY* 3.5 30.5 - - - +
183D ASN* 3.0 11.1 + - + +
184D GLN* 3.8 9.6 - - - +
186D ALA* 1.3 77.7 - - - +
188D TYR* 1.3 66.6 + - - +
189D ARG 3.2 1.3 - - - -
190D LEU* 3.0 39.5 + - + +
191D SER* 4.3 1.0 + - - -
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Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET 5.9 0.4 - - - -
30D TYR* 3.4 39.5 + + - -
33D GLY* 3.6 30.7 - - - +
34D VAL* 4.2 3.1 - - + -
62D VAL* 5.5 1.6 - - - +
63D ILE* 4.5 10.6 - - + +
66D GLN* 5.0 3.9 + - - -
184D GLN 2.8 18.1 + - - +
185D ALA* 4.1 2.5 - - - +
187D LEU* 1.3 78.0 - - - +
189D ARG* 1.3 59.9 + - - +
191D SER* 3.0 25.4 + - - -
192D GLY 4.5 0.2 + - - -
193D ASP* 5.3 5.6 + - + -
215D HIS* 3.5 45.3 - + + +
217D LEU* 3.4 26.4 + - + +
218D CYS* 3.8 25.4 - - + -
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Residues in contact with ARG 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 4.6 1.2 - - - +
47C ILE 4.1 13.5 + - - -
48C TYR* 4.0 2.4 - - - -
49C GLU* 2.6 44.7 + - - -
185D ALA 3.0 22.8 + - - +
186D ALA* 3.3 23.1 + - - +
188D TYR* 1.3 72.1 - - - +
190D LEU* 1.3 56.6 + - + +
191D SER 2.7 16.0 + - - -
192D GLY* 2.9 15.4 + - - -
193D ASP 3.3 25.1 + - - +
194D TRP* 3.1 50.5 + - - +
195D ASN 4.7 1.8 + - - -
198D HIS* 5.3 0.8 - - - +
199D ILE* 3.7 36.7 - - - +
215D HIS* 3.7 13.4 - - - +
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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