Contacts of the helix formed by residues 179 - 195 (chain C) in PDB entry 4QOZ
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 SER 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A A 3.0 23.2 + - - -
7A G 3.4 23.0 + - - -
8A C 3.4 21.1 - - - -
138C ARG* 5.3 0.4 - - - -
178C TYR* 1.3 76.6 - - - +
180C ARG* 1.3 66.0 + - - +
181C ARG 3.7 0.6 + - - -
182C SER* 3.1 16.0 + - - -
183C TRP* 3.0 22.2 + - - +
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Residues in contact with ARG 180 (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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8A C 3.0 45.8 + - + +
9A U 3.0 53.8 + - + +
10A C 3.0 52.7 + - - +
137C ARG* 3.3 33.6 - - - +
138C ARG* 6.0 0.7 - - - +
141C GLN* 5.6 1.8 - - - +
178C TYR 3.9 0.4 + - - -
179C SER* 1.3 71.3 - - - +
181C ARG* 1.3 62.9 + - - +
183C TRP* 3.9 5.4 - - - +
184C ASP* 2.9 58.7 + - - +
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Residues in contact with ARG 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A A 3.6 12.9 - - - +
6A G 3.0 69.2 + - - +
7A G 2.8 60.5 + - - +
8A C 3.9 22.5 + - + +
19A G 5.1 0.8 + - - -
20A C 4.4 3.4 - - - +
179C SER* 3.2 1.2 + - - -
180C ARG* 1.3 74.8 - - - +
182C SER* 1.3 65.9 + - - +
184C ASP* 4.1 3.5 - - - +
185C GLN* 2.9 27.4 + - - +
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A A 2.8 39.0 + - - -
5A A 3.5 21.7 - - - -
178C TYR* 3.4 10.2 - - - -
179C SER* 3.1 23.3 + - - -
181C ARG* 1.3 76.6 - - - +
183C TRP* 1.3 58.1 + - - +
186C GLN* 2.9 40.6 + - - +
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Residues in contact with TRP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 6.1 1.6 - - - -
138C ARG* 3.6 44.7 - - + +
141C GLN* 3.1 27.5 + - - -
142C ILE* 4.1 7.9 - - + -
172C PRO* 3.4 30.3 - - + -
173C ASN 3.4 22.4 - - - -
174C LYS* 3.5 23.6 - - + -
178C TYR* 4.2 24.8 - + + +
179C SER 3.0 16.5 + - - +
180C ARG* 3.9 5.8 - - - +
182C SER* 1.3 77.2 - - - +
184C ASP* 1.3 72.9 + - - +
186C GLN* 3.1 10.7 + - - +
187C ILE* 3.0 46.5 + - + +
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A C 5.6 0.9 + - - -
9A U 4.3 9.7 - - - +
10A C 5.4 3.6 + - - -
141C GLN* 3.0 24.9 + - - +
180C ARG* 2.9 55.5 + - - +
181C ARG* 4.1 3.3 - - - +
183C TRP* 1.3 84.3 - - - +
185C GLN* 1.3 58.0 + - - +
187C ILE* 3.4 7.5 + - - +
188C LYS* 3.0 27.6 + - - +
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Residues in contact with GLN 185 (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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4A A 3.4 30.1 - - - +
5A A 3.7 17.0 + - - +
181C ARG 2.9 19.0 + - - +
184C ASP* 1.3 75.6 - - - +
186C GLN* 1.3 65.5 + - - +
188C LYS* 3.1 23.5 + - - +
189C LEU* 2.9 50.8 + - + +
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Residues in contact with GLN 186 (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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3A A 3.8 21.9 - - + +
4A A 3.8 18.2 - - - +
172C PRO* 4.1 23.8 - - + +
173C ASN 5.4 0.5 + - - -
178C TYR* 3.5 35.0 + - - -
182C SER* 2.9 37.5 + - - +
183C TRP* 3.5 11.8 - - - +
185C GLN* 1.3 75.8 - - - +
187C ILE* 1.3 57.6 + - - +
189C LEU* 3.6 8.1 + - - +
190C TRP* 3.0 29.8 + - - +
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Residues in contact with ILE 187 (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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14A U 6.1 0.7 - - - +
141C GLN* 4.3 29.2 - - + +
142C ILE* 4.4 8.1 - - + -
172C PRO* 3.8 20.6 - - + -
183C TRP* 3.0 48.8 + - + +
184C ASP* 3.5 9.0 - - - +
186C GLN* 1.3 74.8 - - - +
188C LYS* 1.3 65.9 + - - +
190C TRP* 3.3 15.0 + - + +
191C LYS* 2.9 45.8 + - + +
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Residues in contact with LYS 188 (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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16A A 3.0 59.3 + - - +
17A G 4.8 10.2 + - - -
77B ASN* 5.2 4.3 - - - +
184C ASP 3.0 13.6 + - - +
185C GLN* 3.1 28.2 + - - +
187C ILE* 1.3 79.4 - - - +
189C LEU* 1.3 65.0 + - + +
191C LYS* 3.9 4.5 - - - +
192C VAL* 3.0 31.9 + - + +
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Residues in contact with LEU 189 (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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3A A 5.5 2.0 - - - +
4A A 4.0 32.8 - - - +
185C GLN* 2.9 41.3 + - + +
186C GLN* 3.9 5.6 - - - +
188C LYS* 1.3 77.8 - - + +
190C TRP* 1.3 62.1 + - - +
192C VAL* 3.4 8.2 + - + +
193C ALA* 2.9 24.8 + - - +
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Residues in contact with TRP 190 (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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141C GLN 4.3 1.8 - - - -
142C ILE* 3.4 47.3 - - + -
145C GLY* 3.7 19.1 - - - -
146C LYS* 3.9 12.8 - - + -
151C TYR* 4.3 5.5 - + - -
154C TYR* 5.9 0.4 - - - -
169C PRO* 4.2 17.4 + - + -
170C LYS 3.5 20.6 - - - +
171C TPO 3.7 32.5 + - + -
172C PRO* 3.7 11.4 - - + -
186C GLN 3.0 19.7 + - - +
187C ILE* 3.5 16.6 - - + +
189C LEU* 1.3 75.4 - - - +
191C LYS* 1.3 79.2 + - + +
193C ALA* 3.0 8.8 + - - +
194C LEU* 3.0 47.0 + - + +
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Residues in contact with LYS 191 (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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14A U 2.5 64.4 + - - +
15A C 3.6 17.3 - - - +
16A A 5.5 1.1 + - - -
141C GLN 4.7 2.7 + - - +
144C TYR* 3.9 10.8 - - - +
145C GLY* 4.3 19.1 - - - +
187C ILE* 2.9 39.5 + - + +
188C LYS* 3.9 4.9 - - - +
190C TRP* 1.3 88.4 - - + +
192C VAL* 1.3 65.9 + - - +
194C LEU* 3.4 16.0 + - + +
195C HIS* 3.1 22.4 + - - -
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Residues in contact with VAL 192 (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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15A C 3.8 34.1 - - - +
16A A 3.9 15.7 - - - +
78B ARG* 4.4 22.4 - - - +
188C LYS* 3.0 24.9 + - + +
189C LEU* 3.7 8.3 - - + +
191C LYS* 1.3 76.8 - - - +
193C ALA* 1.3 63.6 + - - +
195C HIS* 3.2 18.9 + - - +
196C PHE 4.5 0.9 + - - -
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Residues in contact with ALA 193 (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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169C PRO* 3.8 24.9 - - + -
189C LEU 2.9 14.7 + - - +
190C TRP* 3.0 10.7 + - - +
192C VAL* 1.3 78.5 - - - +
194C LEU* 1.3 62.6 + - - +
195C HIS 3.2 1.4 + - - -
196C PHE* 3.3 19.8 + - - +
197C TRP* 3.7 5.7 - - - -
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Residues in contact with LEU 194 (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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145C GLY* 4.0 20.6 - - - +
148C THR* 5.9 1.6 - - + +
150C ALA* 3.3 20.9 - - + +
151C TYR* 4.0 15.7 - - + +
154C TYR* 3.8 33.0 - - + -
169C PRO* 4.0 14.4 - - + -
190C TRP* 3.0 52.6 + - + +
191C LYS* 3.7 13.7 - - - +
192C VAL 3.3 0.8 - - - -
193C ALA* 1.3 77.2 - - - +
195C HIS* 1.3 56.9 + - + +
196C PHE 3.1 5.9 + - - -
197C TRP* 3.1 20.8 + - - +
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Residues in contact with HIS 195 (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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15A C 2.7 85.4 + + + +
148C THR* 4.0 23.9 + - + +
150C ALA* 4.1 5.6 - - + +
191C LYS 3.1 24.4 + - - -
192C VAL 3.2 8.2 + - - +
193C ALA 3.2 2.2 + - - -
194C LEU* 1.3 73.9 - - + +
196C PHE* 1.3 65.2 + - - +
197C TRP 3.0 1.8 - - - +
198C ASP* 3.1 38.0 + - - +
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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