Contacts of the helix formed by residues 183 - 192 (chain H) in PDB entry 4GUN
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 VAL 183 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 5.2 1.8 - - - +
180H TYR* 3.1 25.2 + - + +
181H GLN 4.5 0.2 - - - -
182H ASN* 1.3 93.1 - - - +
184H ARG* 1.3 64.0 + - - +
185H PRO* 4.1 12.3 - - + -
186H ASP* 3.1 48.7 + - + +
187H TYR 3.7 2.9 + - - -
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Residues in contact with ARG 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LEU 3.2 18.0 + - - -
127H ALA* 2.6 32.5 + - - +
129H ILE* 2.9 35.4 + - - +
131H GLY 4.7 4.8 + - - +
171H ALA* 4.5 6.1 + - - +
176H TYR* 3.2 46.4 - - + +
182H ASN 2.8 11.8 + - - +
183H VAL* 1.3 70.5 - - - +
185H PRO* 1.4 67.5 - - + +
187H TYR* 3.1 13.7 + - - +
188H PHE* 3.2 36.9 + - + -
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Residues in contact with PRO 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ALA* 5.7 9.4 - - + -
182H ASN 4.8 0.9 - - - +
183H VAL* 3.5 14.1 - - + -
184H ARG* 1.4 92.3 - - + +
186H ASP* 1.4 59.1 + - - +
188H PHE* 3.4 14.7 + - + +
189H LYS* 3.1 27.5 + - - +
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Residues in contact with ASP 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.0 44.7 + - + +
27A GLU* 3.8 8.4 - - - +
180H TYR* 3.7 19.8 - - + -
183H VAL* 3.1 33.9 + - - +
185H PRO* 1.4 78.6 - - - +
187H TYR* 1.4 60.7 + - - +
189H LYS* 3.6 6.6 + - - +
190H ALA* 3.1 30.0 + - - +
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Residues in contact with TYR 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR 5.3 0.4 - - - -
24H ILE* 4.5 15.3 - - + -
83H PHE* 3.6 11.8 - - - -
169H ILE* 4.8 1.3 - - + -
170H ASP 2.8 29.3 + - - -
171H ALA* 4.8 0.2 - - - -
175H ALA* 3.6 23.2 - - + +
176H TYR* 3.3 43.1 - + + -
180H TYR* 3.7 29.5 - + + -
183H VAL 3.7 2.2 + - - -
184H ARG 3.1 8.6 + - - +
186H ASP* 1.4 76.1 - - - +
188H PHE* 1.3 87.1 + + - +
190H ALA* 3.3 1.4 + - + +
191H ILE* 3.0 56.2 + - + +
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Residues in contact with PHE 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H ASN* 3.7 23.6 - - + +
126H LEU* 3.4 63.7 - - + -
127H ALA* 3.7 9.2 - - + -
169H ILE* 4.6 1.8 - - + -
171H ALA* 3.9 15.3 - - + -
184H ARG* 3.2 48.2 + - + -
185H PRO* 3.4 10.5 + - + +
187H TYR* 1.3 103.7 - + - +
189H LYS* 1.3 58.3 + - - +
191H ILE* 3.2 10.0 - - - +
192H TRP* 3.0 27.7 + - - -
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Residues in contact with LYS 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 2.7 34.0 + - - +
123H ASN* 4.3 13.1 - - - +
185H PRO 3.1 16.0 + - - +
186H ASP* 3.9 6.5 - - - +
188H PHE* 1.3 76.9 - - - +
190H ALA* 1.3 62.0 + - - +
192H TRP* 3.7 13.7 + - - +
193H ASN* 3.9 6.9 + - - +
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Residues in contact with ALA 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 5.0 9.0 - - - +
23H TYR* 3.6 23.0 - - + +
180H TYR* 3.3 27.8 - - + +
186H ASP 3.1 17.0 + - - +
187H TYR* 3.3 2.7 + - + +
189H LYS* 1.3 76.4 - - - +
191H ILE* 1.4 62.9 + - - +
193H ASN* 2.8 32.1 + - - +
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Residues in contact with ILE 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 5.2 1.8 + - - -
24H ILE* 4.1 11.7 - - + -
83H PHE* 3.6 27.6 - - + -
87H LEU* 4.0 13.9 - - + -
126H LEU* 5.6 0.2 - - + -
169H ILE* 4.1 25.6 - - + -
187H TYR* 3.0 49.0 + - + +
188H PHE* 3.2 23.6 - - - +
190H ALA* 1.4 75.9 - - - +
192H TRP* 1.3 63.5 + - + +
194H VAL* 3.0 27.5 + - - +
195H ILE* 3.4 10.6 + - + +
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Residues in contact with TRP 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H GLY* 3.4 15.4 - - - +
97H HIS* 6.1 0.2 - - - -
119H ILE* 3.7 47.6 - - + -
122H THR* 3.6 36.8 - - + -
123H ASN* 2.8 26.6 + - - +
126H LEU* 4.6 1.5 - - + +
137H ILE* 4.0 13.9 - - + -
167H ILE* 4.4 3.6 - - + -
169H ILE* 4.2 16.4 - - + -
188H PHE 3.0 23.3 + - - -
189H LYS 3.7 10.3 - - - +
190H ALA 3.3 1.0 + - - -
191H ILE* 1.3 79.7 - - + +
193H ASN* 1.3 61.2 + - - +
194H VAL 3.2 1.3 + - - -
195H ILE* 3.5 37.1 + - + +
197H TRP* 3.6 31.9 + + - -
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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