Contacts of the helix formed by residues 160 - 180 (chain C) in PDB entry 4NEF
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 160 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 3.6 13.2 - - - +
157A PRO* 3.7 26.4 - - + +
158A GLY* 3.7 16.2 - - - +
148C SER* 3.3 40.8 - - - +
158C GLY 4.1 3.6 - - - +
159C THR* 1.4 82.4 - - + +
161C ALA* 1.3 63.7 + - - +
162C LEU 3.3 2.7 - - - +
163C SER* 3.7 9.9 - - - +
164C ILE* 3.3 23.6 + - - +
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PRO 5.9 0.2 - - - +
159B THR* 5.7 1.7 + - - +
163B SER* 5.0 3.1 - - - +
53C GLY* 3.3 32.8 - - - +
56C VAL* 3.9 17.4 - - + +
57C GLN* 3.7 33.2 - - + +
159C THR 3.1 11.2 + - - +
160C PRO* 1.3 69.2 - - - +
162C LEU* 1.4 59.5 + - + +
164C ILE* 3.5 3.3 + - - +
165C GLY 3.0 22.2 + - - -
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.9 21.8 - - + -
159B THR* 3.8 22.1 + - + +
162B LEU* 3.7 36.8 - - + -
163B SER* 4.2 12.6 - - - +
166B PHE* 3.6 35.4 - - + -
50C LEU* 5.5 3.8 - - + -
53C GLY* 5.0 10.3 - - - +
160C PRO* 3.3 1.2 - - - +
161C ALA* 1.4 76.7 - - + +
163C SER* 1.4 53.9 + - - +
165C GLY* 3.2 2.5 + - - +
166C PHE* 2.8 49.6 + - + -
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.7 2.8 + - - -
57A GLN* 3.9 25.4 + - - +
158A GLY* 3.7 29.1 + - - -
161A ALA* 5.1 1.0 - - - +
162A LEU* 4.2 15.6 - - - +
144C CYS* 3.9 6.3 - - - -
148C SER* 4.2 2.5 - - - -
160C PRO* 3.4 17.6 + - - +
162C LEU* 1.4 76.6 - - - +
164C ILE* 1.3 61.7 + - - +
166C PHE* 3.3 4.3 + - - +
167C SER* 3.1 21.8 + - - -
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.9 20.9 - - + -
56C VAL* 4.3 16.2 - - + -
141C LEU* 4.4 3.8 - - + -
144C CYS* 4.5 3.8 - - - -
145C ILE* 3.9 39.5 - - + -
148C SER* 4.0 21.5 - - - +
149C THR* 4.9 4.9 - - + -
159C THR* 3.9 22.7 - - + -
160C PRO 3.3 17.3 + - - +
161C ALA* 3.9 5.6 - - - +
163C SER* 1.3 74.1 - - - +
165C GLY* 1.3 62.1 + - - +
167C SER* 3.1 18.0 + - - -
168C VAL* 3.3 13.6 + - - +
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY* 3.2 34.9 - - - -
50C LEU* 6.4 0.2 - - - -
52C ILE* 4.5 4.3 - - - -
53C GLY* 3.8 9.8 - - - -
161C ALA 3.0 15.7 + - - -
162C LEU* 3.2 4.5 + - - -
164C ILE* 1.3 76.2 - - - +
166C PHE* 1.4 56.1 + - - +
168C VAL* 3.2 4.2 + - - +
169C ALA 3.1 21.3 + - - -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 5.0 1.1 - - + -
50A LEU* 3.7 39.7 - - + +
54A THR* 4.2 5.4 - - - +
162A LEU* 3.5 30.7 - - + -
166A PHE* 4.2 19.5 - + - -
166B PHE* 4.3 26.0 - + - -
46C MET* 3.7 26.7 - - + -
49C GLY 6.2 0.4 - - - -
50C LEU* 4.3 12.8 - - + -
162C LEU* 2.8 41.3 + - + +
163C SER 4.0 3.6 - - - +
165C GLY* 1.4 70.1 - - - +
167C SER* 1.4 59.3 + - - +
169C ALA* 3.5 9.4 + - + +
170C LEU* 3.0 28.2 + - - +
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Residues in contact with SER 167 (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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54A THR* 3.7 21.3 - - - +
140C GLN* 2.7 36.9 + - - -
141C LEU* 3.3 26.3 - - - -
144C CYS* 4.1 7.2 - - - -
163C SER 3.1 12.3 + - - -
164C ILE* 3.1 11.6 + - - -
166C PHE* 1.4 73.1 - - - +
168C VAL* 1.4 59.9 + - - +
170C LEU* 3.4 2.8 + - - +
171C GLY 3.0 23.4 + - - -
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Residues in contact with VAL 168 (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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23C PHE* 5.0 3.4 - - + -
48C PHE* 3.7 25.1 - - + +
49C GLY* 4.1 1.8 - - - -
52C ILE* 3.8 30.3 - - + -
141C LEU* 3.8 24.5 - - + -
164C ILE 3.6 13.0 - - - +
165C GLY 3.2 8.0 + - - +
167C SER* 1.4 72.9 - - - +
169C ALA* 1.4 62.7 + - - +
171C GLY 3.3 1.7 + - - -
172C HIS* 2.8 40.0 + - + +
183C MET* 3.4 20.1 - - + +
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Residues in contact with ALA 169 (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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50A LEU* 3.9 15.5 - - + -
45C ALA* 3.4 33.4 - - + +
46C MET* 4.6 7.0 - - - +
49C GLY* 3.9 4.4 - - - -
165C GLY 3.1 12.0 + - - +
166C PHE* 3.6 16.4 - - + +
167C SER 3.4 0.2 - - - -
168C VAL* 1.4 75.7 - - - +
170C LEU* 1.3 55.2 + - - +
172C HIS 3.2 2.3 + - - -
173C LEU* 3.0 34.4 + - + +
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.9 32.2 - - + -
30A SER* 5.2 1.0 + - - +
47A ALA* 3.3 32.1 - - + +
50A LEU* 3.8 12.1 - - + +
51A GLY* 3.6 17.9 - - - +
54A THR* 3.8 19.7 - - + +
55A LEU* 6.0 1.8 - - + -
140C GLN* 3.6 25.6 - - + +
166C PHE 3.0 17.9 + - - +
167C SER 3.4 3.8 - - - +
169C ALA* 1.3 71.4 - - - +
171C GLY* 1.3 65.4 - - - +
173C LEU* 3.3 21.5 + - - +
174C LEU 3.7 4.0 + - - -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.0 2.2 - - - -
137C LEU* 3.3 17.5 - - - +
140C GLN* 3.9 7.8 - - - +
167C SER 3.0 11.8 + - - -
168C VAL 3.3 4.5 + - - -
170C LEU* 1.3 75.8 - - - +
172C HIS* 1.3 51.8 + - - +
174C LEU* 3.4 0.7 + - - -
175C GLY* 2.8 31.0 + - - -
181C CYS* 3.7 7.4 - - - -
183C MET* 3.9 17.5 - - - -
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Residues in contact with HIS 172 (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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23C PHE* 5.5 1.2 - - - -
45C ALA* 3.6 20.9 - - - -
48C PHE* 3.4 49.2 - + + +
168C VAL* 2.8 36.1 + - + +
169C ALA* 3.2 8.0 + - - +
171C GLY* 1.3 72.1 - - - +
173C LEU* 1.3 62.7 + - - +
174C LEU 3.1 2.5 - - - -
176C ILE* 3.1 44.0 + - + +
180C GLY 4.5 1.5 + - - -
181C CYS* 3.5 34.0 - - - +
182C SER 4.9 3.5 + - - -
183C MET* 3.4 19.6 - - + +
187C ARG* 5.0 0.7 - - - -
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Residues in contact with LEU 173 (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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30A SER* 3.4 20.6 + - - +
43A GLN* 4.0 21.0 + - + +
46A MET 4.7 0.2 - - - -
47A ALA* 4.3 17.9 - - + +
50A LEU* 4.2 15.9 - - + -
41C VAL* 3.9 14.2 - - + +
42C LEU* 3.9 33.0 - - + -
45C ALA* 3.5 21.8 - - + -
46C MET* 6.5 0.2 - - - -
169C ALA* 3.0 32.4 + - + +
170C LEU* 3.3 13.6 + - - +
172C HIS* 1.3 73.8 - - - +
174C LEU* 1.4 55.7 + - - +
177C HIS* 3.5 22.3 + - - -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.6 38.8 - - + +
26A PHE* 3.6 34.8 - - + +
29A GLY* 3.6 34.8 - - - -
30A SER* 3.7 9.0 - - - +
104A LEU* 4.6 2.5 - - + -
133C VAL* 4.4 4.3 - - + -
137C LEU* 3.9 8.7 - - + -
170C LEU 3.7 1.0 + - - -
171C GLY 3.4 2.7 + - - +
172C HIS 3.1 0.2 - - - -
173C LEU* 1.4 77.4 - - - +
175C GLY* 1.3 63.5 + - - +
176C ILE 3.4 2.8 + - - -
177C HIS* 3.5 13.4 + - - -
178C TYR* 3.2 42.5 - - + +
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Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 4.5 2.2 - - - -
137C LEU* 3.8 22.4 - - - +
171C GLY 2.8 20.9 + - - -
174C LEU* 1.3 73.0 - - - +
176C ILE* 1.4 62.9 + - - +
178C TYR* 3.1 7.6 + - - +
179C THR* 3.0 23.9 + - - -
181C CYS* 3.2 12.5 + - - -
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Residues in contact with ILE 176 (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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41C VAL* 3.7 47.1 - - + +
44C ILE* 3.7 35.4 - - + -
122C SER* 4.4 6.2 + - - -
172C HIS* 3.1 40.3 + - + +
174C LEU 3.4 0.2 - - - -
175C GLY* 1.4 73.0 - - - +
177C HIS* 1.3 61.5 + - + +
178C TYR 4.3 0.2 - - - -
180C GLY* 3.1 42.6 + - - +
181C CYS* 3.7 0.8 - - - +
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Residues in contact with HIS 177 (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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29A GLY 4.7 2.9 - - - -
30A SER 4.8 4.4 + - - -
33A ASN* 3.4 57.6 + - + +
35A PRO* 4.9 3.2 - - - +
37A ALA* 4.3 13.2 + - + +
39A PRO* 5.2 0.2 - - - +
43A GLN* 4.4 9.0 + - - -
41C VAL* 3.6 32.8 - - + +
122C SER* 3.4 15.0 - - - +
123C ASN* 2.7 31.3 + - - +
125C THR* 4.5 0.7 + - - -
173C LEU 3.5 26.2 + - - -
174C LEU* 3.6 11.7 - - - +
175C GLY 3.3 0.6 - - - -
176C ILE* 1.3 76.5 - - - +
178C TYR* 1.3 58.6 + - + +
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Residues in contact with TYR 178 (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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33A ASN* 3.3 26.0 + - - -
104A LEU* 3.5 14.2 - - - +
107A ILE* 3.7 28.5 - - + -
108A THR* 2.9 26.8 + - - -
109A PRO* 4.6 2.9 - - + -
121C LEU* 3.6 9.0 - - - +
122C SER* 2.8 30.4 + - - +
125C THR* 3.8 31.8 - - + +
130C ALA* 5.2 0.4 - - - -
133C VAL* 3.8 30.7 - - + -
174C LEU* 3.2 45.0 - - + +
175C GLY 3.1 4.2 + - - +
177C HIS* 1.3 80.5 - - - +
179C THR* 1.3 63.1 + - + +
180C GLY 3.9 0.2 - - - -
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Residues in contact with THR 179 (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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119C ASN* 3.4 9.5 + - - +
120C ALA 3.1 34.7 + - - -
121C LEU* 4.2 4.7 - - + -
130C ALA* 3.6 29.6 - - + +
133C VAL* 5.5 1.5 - - + +
134C GLU* 2.7 30.1 + - + +
137C LEU* 4.9 0.7 - - - +
175C GLY* 3.0 6.7 + - - -
178C TYR* 1.3 79.2 - - + +
180C GLY* 1.3 60.4 + - - +
181C CYS* 3.1 6.8 + - - -
203C VAL* 4.4 4.5 - - + -
204C PHE* 3.6 25.8 - - + -
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 5.8 1.0 - - - +
48C PHE* 5.7 1.4 - - - -
118C VAL 5.6 1.6 - - - -
119C ASN* 3.4 8.3 + - - -
120C ALA 4.0 2.8 + - - -
122C SER* 5.1 1.2 - - - -
172C HIS* 4.5 2.9 + - - -
176C ILE* 3.1 35.3 + - - +
178C TYR 3.9 0.2 - - - -
179C THR* 1.3 75.9 - - - +
181C CYS* 1.4 68.9 + - - +
187C ARG* 4.2 8.0 + - - -
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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
------------------------------------------------------------
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