Contacts of the helix formed by residues 180 - 196 (chain A) in PDB entry 4CYM
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 ASN 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PHE* 4.3 11.6 - - + +
172A GLU* 2.9 29.6 + - - +
173A THR* 4.2 5.1 - - + +
178A ASN 3.9 2.6 + - - -
179A ILE* 1.3 81.4 - - - +
181A ILE* 1.3 59.0 + - - +
183A GLU* 3.3 33.8 + - - +
184A ALA* 3.0 30.3 + - - +
163B LYS* 3.9 26.0 - - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.3 28.9 - - + -
44A ARG* 3.9 18.8 - - + -
45A TYR* 3.6 36.8 - - + -
141A LEU* 6.2 0.7 - - + -
173A THR* 4.3 12.8 - - + -
174A SER 3.7 22.2 - - - +
175A ALA* 3.8 15.3 - - - -
178A ASN* 4.3 8.6 + - - +
179A ILE 3.1 9.8 - - - +
180A ASN* 1.3 76.4 - - - +
182A GLU* 1.3 70.8 + - + +
183A GLU 3.0 0.5 + - - -
184A ALA* 3.1 5.1 + - - +
185A ALA* 2.9 24.2 + - + +
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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
----------------------------------------------------------
45A TYR* 3.6 32.7 + - + +
48A GLN* 6.0 0.3 + - - -
65A LYS* 4.5 7.6 + - - -
178A ASN* 4.8 15.6 + - - +
181A ILE* 1.3 79.4 - - + +
183A GLU* 1.3 64.0 + - - +
185A ALA* 3.5 2.9 - - - +
186A ARG* 3.1 56.1 + - - +
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Residues in contact with GLU 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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171A PHE* 4.0 15.2 - - + -
180A ASN* 3.3 39.2 + - - +
181A ILE 3.0 0.6 + - - -
182A GLU* 1.3 84.5 + - - +
184A ALA* 1.3 62.3 + - - +
186A ARG* 3.2 15.5 + - - +
187A PHE* 2.9 28.2 + - - +
156B SER* 5.1 0.3 + - - -
159B ASP* 3.5 33.8 - - + +
163B LYS* 6.0 1.8 - - - -
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Residues in contact with ALA 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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103A PHE* 3.9 10.2 - - + -
139A VAL* 4.8 0.6 - - + +
141A LEU* 3.8 20.9 - - + -
171A PHE* 3.6 34.6 - - + -
173A THR* 5.0 0.2 - - + -
180A ASN 3.0 19.0 + - - +
181A ILE* 3.7 4.3 - - - +
183A GLU* 1.3 74.6 - - - +
185A ALA* 1.3 65.9 + - - +
187A PHE* 3.3 2.9 + - - +
188A LEU* 3.0 24.4 + - - +
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Residues in contact with ALA 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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45A TYR* 3.2 43.7 - - + +
77A LEU* 5.4 4.3 - - + -
103A PHE* 3.9 16.6 - - + -
181A ILE* 2.9 16.8 + - + +
182A GLU 3.5 4.0 - - - +
184A ALA* 1.3 76.3 - - - +
186A ARG* 1.3 63.4 + - + +
188A LEU* 3.2 3.8 + - - +
189A VAL* 2.9 29.1 + - - +
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Residues in contact with ARG 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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45A TYR* 6.0 0.4 - - - +
67A LEU* 5.4 6.3 - - + -
69A TRP* 3.8 25.9 - - + -
182A GLU* 3.1 41.6 + - - +
183A GLU* 3.2 24.1 + - - +
185A ALA* 1.3 78.4 - - + +
187A PHE* 1.3 64.5 + - - +
188A LEU 3.2 0.3 + - - -
189A VAL* 3.2 3.1 + - - +
190A GLU* 3.0 24.1 + - - +
155B PRO* 3.2 33.6 + - - +
156B SER* 3.9 9.4 - - - +
159B ASP* 2.1 48.5 + - - +
170B TRP* 5.1 6.6 - - - +
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Residues in contact with PHE 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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139A VAL* 3.8 15.3 - - + -
168A ALA* 3.2 44.4 - - + -
169A GLY* 3.9 9.4 - - - -
171A PHE* 3.5 32.8 - + + -
183A GLU 2.9 11.3 + - - +
184A ALA 3.6 3.6 - - - +
186A ARG* 1.3 73.7 - - - +
188A LEU* 1.3 67.1 + - - +
190A GLU* 3.5 4.6 - - - +
191A LYS* 3.3 40.5 + - + +
156B SER* 3.3 14.7 + - - +
160B GLN* 3.5 31.2 - - - +
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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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28A VAL* 3.8 25.4 - - + -
102A ALA 4.0 14.4 - - - +
103A PHE* 3.6 28.0 - - + -
137A PRO* 3.9 29.2 - - + +
139A VAL* 3.9 19.3 - - + -
184A ALA 3.0 13.2 + - - +
185A ALA 3.6 6.7 - - - +
187A PHE* 1.3 78.5 - - - +
189A VAL* 1.3 68.9 + - + +
191A LYS* 2.9 18.2 + - + +
192A ILE* 3.0 28.2 + - + +
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Residues in contact with VAL 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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26A PHE* 4.8 3.8 - - + -
67A LEU* 4.5 12.1 - - + -
69A TRP* 3.8 20.6 - - + -
75A VAL* 4.5 12.8 - - + -
77A LEU* 4.1 34.3 - - + -
185A ALA* 2.9 21.6 + - + +
186A ARG 3.7 4.0 - - - +
188A LEU* 1.3 77.3 - - + +
190A GLU* 1.3 57.6 + - - +
192A ILE* 3.2 14.4 + - + +
193A LEU* 2.8 48.2 + - + +
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Residues in contact with GLU 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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69A TRP* 4.0 19.2 - - + -
186A ARG 3.0 9.6 + - - +
187A PHE* 3.5 12.0 - - - +
189A VAL* 1.3 75.9 - - - +
191A LYS* 1.3 77.7 + - - +
193A LEU* 3.0 7.1 + - + +
194A VAL* 2.9 35.9 + - + +
154B SER* 2.2 35.1 + - - +
156B SER* 3.4 18.6 + - - +
157B GLN* 3.6 16.3 + - - +
160B GLN* 5.0 3.8 - - - +
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Residues in contact with LYS 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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137A PRO* 4.2 17.3 - - + -
168A ALA* 3.7 27.6 - - + +
187A PHE* 3.4 39.6 + - + +
188A LEU* 2.9 12.8 + - + +
190A GLU* 1.3 93.1 + - - +
192A ILE* 1.3 62.7 + - - +
194A VAL* 3.4 15.4 + - - +
195A ASN* 3.2 28.5 + - - +
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Residues in contact with ILE 192 (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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26A PHE* 3.5 44.0 - - + -
28A VAL* 4.2 16.2 - - + -
100A VAL* 3.4 30.7 - - + +
101A GLY* 4.1 7.4 - - - -
137A PRO* 4.0 7.9 - - + -
188A LEU* 3.0 37.9 + - + +
189A VAL* 3.4 13.7 - - + +
191A LYS* 1.3 75.4 - - - +
193A LEU* 1.3 66.4 + - - +
195A ASN* 3.1 16.1 + - - +
196A HIS* 3.1 20.6 + - + +
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Residues in contact with LEU 193 (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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24A HIS* 3.8 33.7 - - + +
26A PHE* 4.0 14.4 - - + -
69A TRP* 3.4 43.5 - - + +
73A THR* 5.9 1.8 - - - +
75A VAL* 4.7 4.7 - - + -
189A VAL* 2.8 34.4 + - + +
190A GLU* 3.5 4.9 - - - +
192A ILE* 1.3 73.1 - - - +
194A VAL* 1.3 63.8 + - + +
196A HIS* 3.1 7.2 + - + +
197A GLN* 3.0 48.8 + - + +
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Residues in contact with VAL 194 (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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190A GLU* 2.9 25.6 + - + +
191A LYS* 3.5 19.7 - - - +
193A LEU* 1.3 78.2 - - + +
195A ASN* 1.3 64.8 + - - +
197A GLN* 3.8 5.2 + - - -
198A SER* 3.7 20.1 + - - -
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Residues in contact with ASN 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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100A VAL 4.8 0.4 + - - -
130A LEU* 3.9 22.5 - - + +
132A ASN* 6.1 0.7 - - - +
137A PRO* 3.6 33.7 - - - +
191A LYS* 3.2 18.2 + - - +
192A ILE* 3.1 8.2 + - - +
194A VAL* 1.3 82.0 - - - +
196A HIS* 1.3 68.2 + - + +
197A GLN 3.3 0.9 - - - -
198A SER 3.3 26.2 + - - +
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Residues in contact with HIS 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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22A ARG* 5.7 0.3 + - - -
24A HIS* 5.4 12.5 + + + +
26A PHE* 3.8 23.9 - + + -
100A VAL* 3.6 39.0 - - + +
130A LEU* 4.6 14.8 - - + -
131A PRO* 6.1 2.7 - - + -
192A ILE* 3.1 20.9 + - + +
193A LEU* 3.1 7.5 + - + +
195A ASN* 1.3 80.1 - - + +
197A GLN* 1.3 65.2 + - + +
198A SER 3.7 0.7 - - - -
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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