Contacts of the helix formed by residues 164 - 180 (chain A) in PDB entry 5ZF6
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 GLU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A THR* 4.6 0.2 - - - -
126A LYS* 3.6 31.7 + - - -
162A VAL 3.7 3.1 + - - +
163A ASN* 1.3 72.8 - - - +
165A PRO* 1.3 73.6 - - - +
166A ASP* 3.4 19.3 + - - +
167A VAL* 3.7 16.6 - - + +
168A LEU* 3.8 8.1 - - - +
192A ARG* 4.3 9.0 - - - +
204A PRO 5.2 5.4 + - - +
206A ARG* 3.4 35.4 + - - +
209A MET* 3.5 30.0 - - + +
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Residues in contact with PRO 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.6 18.4 - - + -
80A VAL* 3.5 22.2 - - + +
102A TYR* 3.4 18.4 - - - +
156A LEU* 3.7 20.4 - - + -
159A VAL* 4.5 8.1 - - + -
163A ASN 3.6 4.9 - - - +
164A GLU* 1.3 93.6 - - + +
166A ASP* 1.3 58.7 + - - +
167A VAL 3.3 1.3 - - - -
168A LEU* 3.0 7.9 + - + +
169A ALA* 2.8 30.3 + - - +
206A ARG* 4.6 7.0 - - - +
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Residues in contact with ASP 166 (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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102A TYR* 3.5 11.6 + - - +
126A LYS* 4.2 12.5 + - - -
130A THR* 3.7 31.8 + - + +
164A GLU* 3.8 18.1 - - - +
165A PRO* 1.3 76.3 - - - +
167A VAL* 1.3 81.4 + - - +
169A ALA* 3.3 11.3 + - - +
170A ILE* 3.3 18.4 + - - +
192A ARG* 2.8 41.7 + - - -
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Residues in contact with VAL 167 (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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164A GLU* 3.7 13.9 - - + +
166A ASP* 1.3 92.5 + - - +
168A LEU* 1.3 64.5 + - + +
170A ILE* 3.3 12.2 + - + +
171A ASN* 2.6 38.4 + - - +
190A ALA* 4.7 2.8 - - - +
191A VAL* 4.1 7.0 - - - +
192A ARG* 3.8 44.6 - - + +
203A ASN* 4.2 25.6 - - + +
217A VAL* 4.3 17.0 - - + -
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Residues in contact with LEU 168 (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 LEU* 4.6 12.8 - - + -
73A VAL* 3.5 38.6 - - + +
75A SER* 3.7 32.8 - - - +
78A THR* 3.6 43.5 - - + +
80A VAL* 4.0 11.5 - - + +
163A ASN* 5.2 1.1 - - + -
164A GLU 3.8 14.4 - - - +
165A PRO* 3.0 7.1 + - + +
167A VAL* 1.3 85.0 - - + +
169A ALA* 1.3 57.0 + - - +
171A ASN* 3.4 4.9 + - - +
172A GLY* 2.9 22.5 + - - -
203A ASN* 4.9 4.0 - - - +
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Residues in contact with ALA 169 (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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80A VAL* 4.0 18.3 - - + +
82A VAL* 3.7 5.1 - - - +
102A TYR* 3.5 33.7 - - + -
134A ILE* 3.7 15.2 - - + +
154A CYS* 4.1 4.7 - - - -
165A PRO 2.8 6.5 + - - +
166A ASP 3.6 5.8 - - - +
167A VAL 3.2 0.6 - - - -
168A LEU* 1.3 75.2 - - - +
170A ILE* 1.3 66.1 + - - +
172A GLY* 3.0 2.0 + - - +
173A ALA* 2.8 23.7 + - - +
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Residues in contact with ILE 170 (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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130A THR* 5.7 1.1 - - + -
133A ILE* 3.6 28.7 - - + -
134A ILE* 3.7 26.0 - - + +
137A SER* 3.7 29.6 - - - +
138A ILE* 5.1 2.3 - - + +
166A ASP 3.3 16.6 - - - +
167A VAL* 3.3 12.3 + - + +
169A ALA* 1.3 77.2 - - - +
171A ASN* 1.3 61.8 + - - +
173A ALA* 3.2 4.5 + - - +
174A SER* 3.1 19.2 + - - -
188A VAL* 5.0 3.9 - - + +
190A ALA* 3.6 23.8 - - + -
217A VAL* 4.1 17.5 - - + -
219A ALA* 4.9 0.4 - - + -
228A MET* 4.6 0.4 - - + -
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Residues in contact with ASN 171 (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 LEU* 4.8 12.8 - - + +
58A ILE* 5.4 0.4 - - + -
73A VAL* 3.9 15.2 - - + +
167A VAL* 2.6 30.5 + - - +
168A LEU* 3.7 8.6 - - - +
169A ALA 3.3 0.4 - - - -
170A ILE* 1.3 75.6 - - - +
172A GLY* 1.3 58.0 + - - +
174A SER* 3.0 9.0 + - - -
175A VAL* 2.8 35.3 + - + +
188A VAL* 5.0 1.1 - - - -
189A GLY* 3.9 1.4 - - - -
190A ALA 3.1 43.3 + - - +
203A ASN* 5.7 0.6 - - - +
255A ILE* 3.6 24.8 - - + +
259A ILE* 5.6 0.2 - - + -
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Residues in contact with GLY 172 (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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71A ALA* 3.9 5.6 - - - +
73A VAL* 3.5 16.3 - - - +
82A VAL* 3.6 20.4 - - - +
168A LEU 2.9 12.8 + - - -
169A ALA 3.0 4.6 + - - -
171A ASN* 1.3 75.5 - - - +
173A ALA* 1.3 53.8 + - - +
175A VAL* 3.2 3.2 + - - +
176A ALA* 2.7 37.2 + - - +
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Residues in contact with ALA 173 (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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82A VAL* 3.6 12.6 - - + +
84A ALA* 5.5 0.2 - - - +
134A ILE* 3.7 27.6 - - + -
138A ILE* 4.2 13.7 - - + -
152A VAL* 3.8 18.2 - - + -
154A CYS* 5.3 0.2 - - - -
169A ALA 2.8 11.5 + - - +
170A ILE 3.5 8.3 - - - +
172A GLY* 1.3 71.8 - - - +
174A SER* 1.3 61.8 + - - +
176A ALA* 4.1 1.3 - - - +
177A LEU* 3.2 30.8 + - - +
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Residues in contact with SER 174 (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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138A ILE* 4.7 1.5 - - - +
170A ILE 3.1 11.1 + - - -
171A ASN* 3.0 9.7 + - - -
173A ALA* 1.3 75.0 - - - +
175A VAL* 1.3 59.8 + - - +
177A LEU 3.4 1.0 + - - -
178A SER* 2.9 33.0 + - - -
184A TRP* 3.7 17.2 - - - -
187A PRO* 3.7 2.4 - - - +
188A VAL* 2.7 53.2 + - - -
259A ILE* 3.6 6.1 - - - +
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Residues in contact with VAL 175 (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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58A ILE* 4.1 20.4 - - + -
59A SER 3.9 2.5 - - - +
71A ALA* 3.6 21.5 - - + -
73A VAL* 4.4 2.2 - - + -
171A ASN* 2.8 26.4 + - + +
172A GLY 4.5 0.2 - - - -
174A SER* 1.3 72.3 - - - +
176A ALA* 1.3 57.5 + - - +
178A SER* 3.1 1.0 + - - -
179A LEU* 2.8 53.1 + - + +
259A ILE* 3.7 37.7 - - + -
262A LEU* 3.9 18.8 - - + -
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Residues in contact with ALA 176 (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 GLY* 3.8 16.7 - - - +
70A SER 4.1 8.3 - - - -
71A ALA* 3.6 6.6 - - - +
82A VAL* 3.5 28.3 - - + +
84A ALA* 4.1 11.9 - - + -
172A GLY 2.7 23.1 + - - +
173A ALA* 4.1 2.7 - - - +
175A VAL* 1.3 73.4 - - - +
177A LEU* 1.3 58.1 + - - +
179A LEU 3.3 1.2 + - - -
180A SER* 2.9 30.5 + - - -
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Residues in contact with LEU 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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84A ALA* 3.8 21.5 - - + -
138A ILE* 3.9 19.7 - - + -
142A PHE* 3.9 24.5 - - + -
150A THR* 4.8 4.9 - - + -
152A VAL* 4.6 3.8 - - + -
173A ALA 3.2 19.7 + - - +
174A SER 4.0 0.2 - - - +
176A ALA* 1.3 78.9 - - - +
178A SER* 1.3 63.5 + - - +
180A SER* 2.9 18.5 + - - -
182A ILE* 3.8 26.9 - - + +
184A TRP* 3.7 45.7 - - + +
270A LYS* 3.2 11.4 + - - -
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Residues in contact with SER 178 (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 SER 2.9 17.1 + - - -
175A VAL 3.6 3.6 - - - -
177A LEU* 1.3 77.1 - - - +
179A LEU* 1.3 58.1 + - - +
184A TRP* 3.9 8.1 + - - -
186A GLY 4.6 1.0 + - - -
187A PRO* 3.3 31.4 - - - +
259A ILE* 3.9 17.5 - - - -
263A VAL* 4.2 14.0 - - - +
268A VAL* 3.5 13.2 - - - +
270A LYS* 3.1 20.7 + - - +
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Residues in contact with LEU 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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59A SER 4.0 7.6 - - - +
60A SER* 3.9 18.8 - - - +
68A ASP 4.5 1.6 - - - +
69A GLY* 4.7 4.9 - - - -
70A SER 3.6 23.3 - - - +
175A VAL* 2.8 35.2 + - + +
176A ALA 3.9 2.5 - - - +
178A SER* 1.3 76.4 - - - +
180A SER* 1.3 62.2 + - - +
259A ILE* 6.1 0.2 - - + -
262A LEU* 4.0 19.3 - - + +
263A VAL* 4.2 16.6 - - + -
266A THR* 3.8 34.2 - - + +
267A GLY 5.4 0.3 - - - +
268A VAL* 3.7 14.2 - - + +
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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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68A ASP 3.3 27.6 - - - -
69A GLY* 3.7 2.2 - - - -
84A ALA 4.7 0.9 - - - -
176A ALA 2.9 16.0 + - - -
177A LEU* 2.9 15.6 + - - -
179A LEU* 1.3 80.9 - - - +
181A ASP* 1.3 57.5 + - - +
182A ILE* 3.0 34.3 + - - +
268A VAL* 3.7 7.7 - - - +
270A LYS* 3.0 22.3 + - - -
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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