Contacts of the helix formed by residues 180 - 198 (chain A) in PDB entry 3G4C
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 GLN 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.3 21.3 - - - -
75A GLN* 3.3 21.0 + - - +
105A ARG* 4.2 0.6 - - - +
179A ALA* 1.3 75.3 - - - +
181A TRP* 1.3 68.5 + - - +
182A GLU* 3.0 27.9 + - + +
183A ILE* 3.3 6.5 + - + +
184A GLN* 3.1 18.2 + - - +
90D ARG* 3.4 28.1 - - - +
144D GLU* 3.1 43.5 + - - +
145D VAL* 5.0 0.4 - - - +
147D ARG* 3.1 23.7 + - - -
148D ILE* 5.0 0.2 - - - +
318D UMP 4.5 1.4 + - - -
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Residues in contact with TRP 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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6A LEU* 3.7 25.6 - - + -
99A TYR* 3.9 10.8 - + - -
102A SER* 6.1 0.9 - - - -
105A ARG* 3.7 44.2 - - + +
179A ALA 3.5 2.2 + - - -
180A GLN* 1.3 74.1 - - - +
182A GLU* 1.3 68.8 - - - +
184A GLN* 3.1 23.3 - - - +
185A GLN* 3.0 63.4 + - + +
144D GLU* 4.6 2.9 + - - +
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Residues in contact with GLU 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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6A LEU* 4.0 11.6 - - + +
71A PHE* 4.0 8.5 - - + -
72A VAL* 3.9 18.4 - - + -
99A TYR* 2.6 49.1 + - + +
101A PRO* 5.0 0.2 - - - +
105A ARG* 2.8 38.7 + - - +
180A GLN* 3.0 21.0 + - + +
181A TRP* 1.3 82.5 - - + +
183A ILE* 1.3 59.9 + - - +
185A GLN* 3.3 11.7 + - - +
186A TYR* 3.1 23.7 - - - -
145D VAL* 4.6 4.2 - - - +
148D ILE* 6.0 0.4 - - - +
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Residues in contact with ILE 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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72A VAL* 3.8 25.1 - - + +
75A GLN* 3.6 26.5 - - + +
76A TRP* 3.9 43.1 - - + +
170A PHE* 4.6 3.4 - - + -
174A ARG* 3.8 41.3 - - + +
179A ALA* 4.1 11.2 - - + -
180A GLN* 3.3 11.9 + - - +
182A GLU* 1.3 72.9 - - - +
184A GLN* 1.3 63.6 + - - +
185A GLN 3.1 1.6 - - - -
186A TYR* 3.0 4.1 + - + -
187A ALA* 2.7 28.6 + - - +
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Residues in contact with GLN 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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174A ARG 3.4 15.0 - - - +
176A ASP 3.3 24.6 + - - +
177A SER* 3.4 12.7 + - - +
179A ALA 2.6 24.4 + - - +
180A GLN 3.1 15.0 + - - +
181A TRP* 3.1 30.9 - - - +
183A ILE* 1.3 78.4 - - - +
185A GLN* 1.3 63.5 + - - +
187A ALA* 3.2 2.9 + - - +
188A LEU* 2.9 32.9 + - - +
214A ILE* 3.5 27.0 - - + +
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Residues in contact with GLN 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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5A ILE* 3.6 27.8 - - + +
6A LEU* 4.4 2.9 - - + +
181A TRP* 3.0 74.1 + - + +
182A GLU 3.4 8.3 - - - +
183A ILE 3.1 0.2 - - - -
184A GLN* 1.3 80.5 + - - +
186A TYR* 1.3 66.3 + - - +
188A LEU* 3.4 31.3 + - - +
189A ALA 3.4 8.1 + - - -
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Residues in contact with TYR 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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5A ILE* 3.6 29.8 + - + -
6A LEU* 3.7 20.0 - - + +
9A GLY* 3.5 12.5 - - - -
10A PHE 3.9 11.4 - - - -
11A VAL* 3.5 18.1 - - + +
66A VAL* 3.9 1.6 - - + -
67A LYS 2.5 29.6 + - - -
68A ALA* 3.2 23.4 - - + -
69A PRO* 3.7 5.9 - - + +
72A VAL* 3.9 9.6 - - + -
76A TRP* 3.4 26.7 - + + -
155A TYR* 3.9 1.0 - - - -
182A GLU 3.1 20.4 - - - -
183A ILE* 3.0 8.6 + - + +
185A GLN* 1.3 77.0 - - - +
187A ALA* 1.3 65.1 + - - +
189A ALA* 3.0 5.7 + - - +
190A ILE* 2.9 26.3 + - - +
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Residues in contact with ALA 187 (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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170A PHE* 4.0 19.1 - - + -
171A LEU* 3.2 10.1 - - + +
174A ARG* 3.5 14.1 - - + -
175A ALA* 3.4 34.2 - - + +
183A ILE 2.7 19.6 + - - +
184A GLN 3.6 3.6 - - - +
186A TYR* 1.3 73.1 - - - +
188A LEU* 1.3 59.0 + - - +
190A ILE* 4.2 0.9 - - - -
191A ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 188 (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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175A ALA* 4.9 1.1 - - + -
184A GLN 2.9 18.1 + - - +
185A GLN* 3.6 30.3 - - - +
186A TYR 3.1 0.6 - - - -
187A ALA* 1.3 78.1 - - - +
189A ALA* 1.3 57.1 + - - +
191A ALA* 3.4 3.8 + - - +
192A ARG* 3.0 27.9 + - - +
214A ILE* 3.6 32.8 - - + +
215A LEU* 3.7 24.8 - - + +
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Residues in contact with ALA 189 (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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3A ILE* 3.9 26.1 - - + +
5A ILE* 3.3 31.2 - - + -
11A VAL* 4.1 13.2 - - + -
185A GLN 3.4 2.0 + - - -
186A TYR 3.0 7.7 + - - +
188A LEU* 1.3 77.0 - - - +
190A ILE* 1.3 64.6 + - - +
192A ARG* 3.4 1.6 + - - +
193A ILE* 3.1 31.0 + - - +
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Residues in contact with ILE 190 (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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11A VAL* 3.6 25.6 - - + -
64A PHE* 3.7 23.3 - - + -
66A VAL* 5.3 0.2 - - + -
76A TRP* 4.1 21.5 - - + -
160A TRP* 3.9 18.2 - - + -
167A LEU* 4.0 33.9 - - + -
170A PHE* 4.2 8.7 - - + -
171A LEU* 4.1 7.2 - - + -
186A TYR 2.9 18.4 + - - +
187A ALA* 3.8 7.4 - - - +
188A LEU 3.4 0.2 - - - -
189A ALA* 1.3 75.4 - - - +
191A ALA* 1.3 58.0 + - - +
193A ILE* 3.4 4.3 + - - +
194A PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 191 (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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171A LEU* 3.8 21.1 - - + +
187A ALA 3.0 18.6 + - - +
188A LEU 3.6 3.6 - - - +
190A ILE* 1.3 77.8 - - - +
192A ARG* 1.3 56.2 + - - +
194A PHE* 3.4 2.0 + - - +
195A LYS* 2.8 31.1 + - - +
202A PHE* 3.6 9.8 - - + -
215A LEU* 3.5 34.3 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 6.7 - - + -
3A ILE* 3.8 22.9 - - + -
188A LEU 3.0 16.4 + - - +
189A ALA* 3.4 4.9 + - - +
191A ALA* 1.3 75.2 - - - +
193A ILE* 1.3 57.4 + - - +
195A LYS* 3.5 11.3 + - + +
196A GLU* 3.1 29.2 + - + +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 31.4 - - + -
3A ILE* 4.2 10.1 - - + -
11A VAL* 3.7 35.2 - - + +
13A LEU* 3.8 37.2 - - + +
62A PHE* 4.7 2.2 - - + -
64A PHE* 3.8 24.9 - - + -
189A ALA 3.1 18.1 + - - +
190A ILE 3.9 3.8 - - - +
192A ARG* 1.3 74.3 - - - +
194A PHE* 1.3 66.2 + - - +
196A GLU* 3.2 3.8 + - - +
197A LYS* 3.1 23.5 + - + +
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.5 26.5 - + - -
64A PHE* 5.5 0.6 - - - -
164A ALA* 4.0 23.6 - - + -
167A LEU* 3.3 25.1 - - + -
168A MET* 3.7 28.9 - - + -
171A LEU* 4.0 5.8 - - + -
190A ILE 3.0 17.1 + - - +
191A ALA* 3.5 4.0 - - - +
193A ILE* 1.3 74.1 - - - +
195A LYS* 1.3 58.6 + - - +
197A LYS* 3.2 1.9 + - - +
198A CYS* 2.9 48.2 + - + +
201A THR* 3.7 24.5 - - + -
202A PHE* 3.6 29.4 - + - -
205A PHE* 4.7 1.8 - + - -
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Residues in contact with LYS 195 (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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191A ALA 2.8 17.8 + - - +
192A ARG* 3.6 12.8 - - + +
193A ILE 3.3 0.2 - - - -
194A PHE* 1.3 76.9 - - - +
196A GLU* 1.3 62.6 + - - +
199A PRO* 3.3 31.1 - - + +
202A PHE* 3.5 45.2 - - + -
203A GLU* 4.9 12.6 - - - +
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Residues in contact with GLU 196 (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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1A MET* 3.8 33.2 - - + +
192A ARG* 3.1 14.2 + - + +
193A ILE 3.2 8.7 + - - +
195A LYS* 1.3 77.8 - - - +
197A LYS* 1.3 71.4 + - + +
199A PRO* 4.1 6.4 - - - +
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Residues in contact with LYS 197 (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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-1A HIS* 4.2 19.3 - - - +
0A HIS 4.9 1.8 - - - +
1A MET* 4.3 16.4 - - - +
13A LEU* 3.7 31.0 - - + -
16A VAL* 4.1 17.5 - - + -
18A GLY 5.0 0.9 - - - +
19A ASN* 4.3 15.6 - - - +
20A ASP* 4.7 0.2 - - - +
62A PHE* 3.9 19.3 - - + -
193A ILE 3.1 17.0 + - - +
196A GLU* 1.3 88.1 + - + +
198A CYS* 1.3 65.2 + - - +
199A PRO* 3.5 6.5 - - - +
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Residues in contact with CYS 198 (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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16A VAL* 5.5 0.2 - - - -
18A GLY 5.1 0.9 - - - -
19A ASN* 4.3 8.3 - - - -
20A ASP* 3.2 19.6 - - - +
60A ILE* 3.6 39.3 - - - -
62A PHE* 3.9 14.4 - - - -
194A PHE* 2.9 23.5 + - + +
195A LYS 3.8 2.5 - - - -
197A LYS* 1.3 84.6 - - - +
199A PRO* 1.4 60.9 - - - +
200A TRP 3.3 0.2 + - - -
201A THR* 4.1 4.5 - - - -
202A PHE* 2.9 28.1 + - - +
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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