Contacts of the helix formed by residues 176 - 186 (chain A) in PDB entry 4IX8
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 PRO 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 3.3 19.5 - - - +
56A PRO* 4.3 9.5 - - + +
57A LEU* 4.4 15.9 - - + -
174A SER* 3.2 7.8 - - - +
175A PHE* 1.3 97.4 - - + +
177A HIS* 1.3 61.9 + - - +
178A TYR 3.3 0.9 - - - -
179A LYS* 3.3 12.6 + - + +
180A SER* 3.1 20.1 + - - -
414A ILE* 4.1 24.9 - - + +
415A PHE* 3.8 24.9 - - + -
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Residues in contact with HIS 177 (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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55A GLN* 3.5 23.1 + - - +
151A SER* 3.6 48.2 + - - -
154A ILE* 3.9 12.6 - - + -
155A VAL* 4.6 3.4 - - - +
175A PHE* 3.0 30.3 + + + -
176A PRO* 1.3 79.1 - - - +
178A TYR* 1.3 63.2 + - - +
180A SER* 4.2 5.7 - - - -
181A VAL* 2.9 55.2 + - + +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.3 47.1 - - + +
158A LEU* 4.5 10.2 - - + +
168A ILE* 5.4 0.4 - - + -
170A VAL* 4.0 25.8 - - + -
174A SER* 5.7 0.7 - - - +
175A PHE* 3.8 20.4 - + - +
176A PRO 3.3 0.8 - - - -
177A HIS* 1.3 74.8 - - - +
179A LYS* 1.3 63.3 + - - +
181A VAL* 3.4 1.2 + - - +
182A CYS* 3.0 32.0 + - - -
189A CYS* 4.7 0.4 - - - -
219A VAL* 3.9 35.2 - - + +
221A ILE* 3.9 22.4 - - + -
251A ILE* 5.0 3.9 - - + +
253A ASP* 2.7 38.5 + - + +
281A LEU* 3.6 10.5 - - + +
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Residues in contact with LYS 179 (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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56A PRO* 6.1 5.4 - - + -
174A SER* 5.8 2.0 + - - +
175A PHE 5.0 0.8 + - - +
176A PRO* 3.3 12.5 + - + +
177A HIS 3.2 0.2 - - - -
178A TYR* 1.3 80.2 - - - +
180A SER* 1.3 63.7 + - - +
182A CYS* 3.5 0.9 + - - +
183A ASP* 3.0 56.9 + - - +
189A CYS* 3.9 32.1 + - + +
191A TYR* 3.6 33.1 - - + +
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Residues in contact with SER 180 (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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53A THR* 5.2 2.9 - - - +
54A LEU 2.8 31.6 + - - +
55A GLN* 3.1 34.1 + - - -
56A PRO* 3.9 4.2 - - - +
176A PRO 3.1 9.9 + - - -
177A HIS* 3.2 11.4 + - - -
179A LYS* 1.3 79.6 - - - +
181A VAL* 1.3 56.2 + - - +
183A ASP* 4.1 4.6 - - - +
184A SER* 3.1 26.7 + - - -
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Residues in contact with VAL 181 (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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154A ILE* 4.1 6.3 - - + -
155A VAL* 4.2 26.7 - - + -
158A LEU* 3.9 26.0 - - + -
159A THR* 4.7 1.1 - - + -
177A HIS* 2.9 49.4 + - + +
178A TYR 3.9 2.5 - - - +
180A SER* 1.3 73.2 - - - +
182A CYS* 1.3 68.5 + - - +
184A SER* 3.1 6.9 + - - -
185A TYR* 3.1 39.5 + - + +
187A ILE* 5.7 0.4 - - + -
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Residues in contact with CYS 182 (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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158A LEU* 4.2 6.7 - - - -
168A ILE* 3.5 37.5 - - - -
178A TYR 3.0 25.1 + - - +
179A LYS 3.7 3.6 - - - +
181A VAL* 1.3 78.6 - - - +
183A ASP* 1.3 59.4 + - - +
185A TYR 3.1 2.1 + - - -
186A GLY 2.9 8.1 + - - -
187A ILE* 2.8 57.0 + - - +
189A CYS* 4.0 20.2 - - + -
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Residues in contact with ASP 183 (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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52A ARG* 3.2 34.5 - - + +
54A LEU 6.0 0.9 - - - +
179A LYS* 3.0 56.3 + - - +
180A SER* 4.1 4.3 - - - +
182A CYS* 1.3 82.2 - - - +
184A SER* 1.3 63.6 + - - +
185A TYR 3.2 0.5 + - - -
186A GLY* 3.4 6.2 + - - +
187A ILE 4.2 6.7 - - - +
188A GLU* 5.5 0.5 - - - -
189A CYS 5.0 3.6 + - - -
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Residues in contact with SER 184 (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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49A HIS* 2.8 39.6 + - - -
52A ARG* 3.0 20.9 + - - +
53A THR* 2.6 35.4 + - - +
180A SER 3.1 19.2 + - - -
181A VAL* 3.1 9.6 + - - -
183A ASP* 1.3 76.6 - - - +
185A TYR* 1.3 64.8 + - - +
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Residues in contact with TYR 185 (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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49A HIS* 3.9 23.6 + + - -
52A ARG* 3.6 11.4 + - - +
155A VAL* 3.9 20.4 - - + +
159A THR* 3.6 33.0 - - + -
164A GLU* 3.9 14.2 + - - +
181A VAL* 3.1 35.2 + - + +
184A SER* 1.3 89.1 - - - +
186A GLY* 1.3 63.1 + - - +
187A ILE* 3.1 22.0 + - + +
49B HIS* 4.8 14.7 + + - -
185B TYR* 4.6 16.4 + + - -
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Residues in contact with GLY 186 (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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52A ARG* 3.6 14.9 - - - +
164A GLU* 3.5 15.4 - - - +
165A GLY* 3.2 22.7 + - - -
182A CYS 2.9 4.5 + - - -
183A ASP* 3.4 8.9 + - - -
184A SER 3.4 0.6 - - - -
185A TYR* 1.3 79.1 - - - +
187A ILE* 1.3 61.6 + - - +
188A GLU 4.0 0.9 + - - -
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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