Contacts of the helix formed by residues 138 - 156 (chain C) in PDB entry 5ZR1
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 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C SER 3.4 0.4 - - - -
137C PRO* 1.3 82.6 - - - +
139C VAL* 1.3 65.4 + - + +
140C ARG* 4.2 18.4 - - - +
141C MET* 3.3 29.3 + - - +
142C MET* 3.3 24.3 + - - +
215C THR* 3.6 14.1 - - - -
485D PHE* 5.8 2.4 - - - -
488D SER* 3.3 44.7 + - - +
489D ASN* 4.4 7.4 - - - +
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASN* 1.3 75.6 - - - +
140C ARG* 1.3 65.2 + - - +
142C MET* 3.2 7.1 + - - +
143C LEU* 3.2 21.0 + - - +
215C THR* 3.8 22.0 - - + +
218C ASN* 3.7 42.2 - - + +
219C PHE* 4.2 9.0 - - + -
222C LEU* 3.7 28.0 - - + -
68E VAL* 4.8 1.1 - - + -
139E GLN* 4.5 19.3 - - + -
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASN* 4.1 19.5 - - - +
139C VAL* 1.3 78.3 - - - +
141C MET* 1.3 75.1 + - + +
143C LEU* 4.0 2.8 - - - +
144C ARG* 3.0 67.0 + - + +
485D PHE* 4.6 19.6 - - - -
488D SER* 5.9 1.3 - - - -
68E VAL* 3.6 29.8 - - + +
69E SER* 3.7 30.5 + - - -
72E PRO* 5.8 1.2 - - - +
139E GLN* 5.9 0.2 - - - +
140E ASP* 5.2 10.3 - - - -
15G T 3.1 25.5 + - - -
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Residues in contact with MET 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B TYR* 4.6 6.5 - - - -
135C GLU 4.3 1.6 - - - -
137C PRO* 3.6 22.4 - - + -
138C ASN* 3.3 22.2 + - - +
139C VAL 3.2 0.8 - - - -
140C ARG* 1.3 101.9 - - + +
142C MET* 1.3 64.5 + - - +
143C LEU 3.3 0.2 - - - -
144C ARG* 3.7 13.9 - - + +
145C ARG* 3.2 37.1 + - - +
489D ASN* 5.9 0.9 - - - +
15G T 3.3 54.5 - - + +
16G T 3.7 17.9 - - - +
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Residues in contact with MET 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 3.8 12.5 - - + +
135C GLU 4.6 3.1 - - - -
136C SER* 3.4 31.0 - - - +
138C ASN 3.3 13.3 + - - +
139C VAL* 3.2 8.6 + - - +
141C MET* 1.3 78.7 - - - +
143C LEU* 1.3 53.4 + - - +
145C ARG* 4.1 1.4 - - - +
146C SER* 2.5 36.8 + - - -
205C PHE* 3.7 22.2 - - + -
211C ILE* 4.3 9.9 - - + -
215C THR* 3.6 28.3 - - - +
216C LEU* 5.0 2.7 - - - -
219C PHE* 3.6 45.3 - - + -
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Residues in contact with LEU 143 (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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139C VAL 3.2 15.3 + - - +
140C ARG* 3.5 6.0 + - - +
141C MET 3.3 0.2 - - - -
142C MET* 1.3 76.3 - - - +
144C ARG* 1.3 60.4 + - + +
145C ARG 3.2 0.4 - - - -
146C SER* 4.3 0.4 - - - -
147C MET* 2.8 60.4 + - + +
183C TYR 4.9 1.3 - - - +
184C ASP* 3.8 9.6 - - + -
185C LEU* 3.7 27.1 - - + +
219C PHE* 3.9 13.2 - - + -
222C LEU* 3.8 24.0 - - + -
223C LEU* 5.3 0.9 - - + -
66E GLU 3.8 5.4 - - - +
68E VAL* 3.7 26.9 - - + -
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Residues in contact with ARG 144 (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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359A LYS 3.9 13.3 + - - -
360A PHE* 4.5 11.1 - - - +
395B TYR* 2.9 42.5 + - + +
140C ARG* 3.0 49.2 + - + +
141C MET* 3.7 11.2 - - + +
143C LEU* 1.3 76.2 - - + +
145C ARG* 1.3 58.8 + - - +
148C TYR* 3.3 24.5 + - - +
182C SER* 5.4 1.0 + - - -
183C TYR* 3.7 44.7 + - + +
72E PRO* 5.0 13.5 - - - +
14G T 5.2 1.8 + - - -
15G T 3.0 15.2 + - - -
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Residues in contact with ARG 145 (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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394B LYS 3.5 10.1 + - - -
395B TYR* 2.4 51.7 + - + -
396B TRP* 4.1 10.5 + - - +
397B GLY* 4.5 1.4 - - - +
129C ILE* 5.3 0.2 - - - -
131C LEU* 4.5 6.7 - - + -
134C LYS 5.2 1.2 + - - -
135C GLU* 3.3 49.4 + - - +
141C MET* 3.2 24.0 + - - +
142C MET 4.2 2.2 - - - +
143C LEU 3.2 0.4 - - - -
144C ARG* 1.3 78.7 - - - +
146C SER* 1.3 59.0 + - - +
148C TYR* 3.8 4.1 - - - +
149C LYS* 2.9 48.0 + - - +
15G T 3.8 4.9 + - - -
16G T 2.3 39.0 + - - -
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Residues in contact with SER 146 (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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129C ILE* 3.5 26.5 - - - +
131C LEU* 3.7 7.8 - - - +
142C MET 2.5 22.9 + - - -
143C LEU* 3.1 7.0 + - - -
145C ARG* 1.3 76.8 - - - +
147C MET* 1.3 71.2 + - - +
149C LYS 3.5 0.3 + - - -
150C LEU* 3.2 23.6 + - - +
203C PHE* 3.4 32.3 - - - -
219C PHE* 3.8 3.1 - - - -
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Residues in contact with MET 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 2.8 36.2 + - + +
146C SER* 1.3 80.4 - - - +
148C TYR* 1.3 62.8 + - - +
150C LEU* 3.7 29.6 - - + -
151C TYR* 3.3 24.4 + - - +
183C TYR* 3.6 25.1 - - + -
184C ASP* 3.3 37.7 - - - +
185C LEU* 3.9 9.9 - - + -
187C LEU* 3.4 13.8 - - + +
188C VAL* 4.0 12.8 - - + -
201C MET* 3.9 16.6 - - + -
203C PHE* 5.2 1.6 - - + -
223C LEU* 5.5 0.4 - - + -
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Residues in contact with TYR 148 (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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357A ILE* 3.7 39.3 + - + +
358A ARG 4.2 0.2 - - - -
359A LYS* 3.8 31.4 + - + -
390B ARG* 4.3 11.0 + - - +
391B SER* 6.0 0.3 - - - -
393B THR 5.0 2.5 - - - -
394B LYS* 5.1 2.7 - - - -
395B TYR* 3.8 39.0 - + + -
144C ARG 3.3 20.8 + - - +
145C ARG 3.9 4.0 - - - +
146C SER 3.3 0.2 - - - -
147C MET* 1.3 80.6 - - - +
149C LYS* 1.3 64.9 + - + +
151C TYR 3.9 0.2 - - - -
152C SER* 2.9 42.7 + - - -
183C TYR* 3.7 31.3 - + + -
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Residues in contact with LYS 149 (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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394B LYS* 4.5 30.6 + - + +
395B TYR* 5.3 1.8 - - - +
127C VAL* 5.0 1.2 - - - +
128C LEU 5.2 4.5 - - - +
129C ILE* 4.1 30.0 - - + +
130C GLU* 3.7 23.6 - - - +
131C LEU* 5.1 1.2 - - + +
135C GLU* 3.9 20.1 + - - -
145C ARG* 2.9 37.6 + - - +
146C SER 3.5 4.0 + - - +
147C MET 3.4 0.2 - - - -
148C TYR* 1.3 84.7 - - + +
150C LEU* 1.3 57.5 + - - +
152C SER* 4.5 3.0 - - - -
153C ALA* 3.2 26.2 + - - +
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Residues in contact with LEU 150 (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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127C VAL* 4.1 26.9 - - + +
129C ILE* 4.3 2.2 - - + +
146C SER 3.2 13.7 + - - +
147C MET* 3.7 38.1 - - + +
149C LYS* 1.3 76.6 - - - +
151C TYR* 1.3 65.3 + - - +
153C ALA* 3.8 0.9 - - - +
154C ALA* 3.0 30.7 + - - +
187C LEU* 3.7 22.4 - - + +
188C VAL* 4.6 5.8 - - + -
191C PHE* 3.6 29.8 - - + -
199C LEU* 4.3 8.7 - - + -
201C MET* 3.7 19.1 - - + -
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Residues in contact with TYR 151 (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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357A ILE* 3.7 26.7 - - + -
147C MET 3.3 20.5 + - - +
148C TYR 4.2 1.8 - - - +
150C LEU* 1.3 80.3 - - - +
152C SER* 1.3 61.7 + - - +
154C ALA* 4.2 2.7 - - - +
155C ASP* 3.2 43.0 + - - +
179C ASN* 2.8 37.8 + - - -
180C ASP* 5.2 2.0 - - - -
181C VAL* 3.6 28.3 - - + +
183C TYR* 4.1 15.5 - + + -
187C LEU* 3.8 23.8 - - + -
194C LEU* 4.4 7.5 - - + +
195C PHE* 4.1 24.0 - + - -
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Residues in contact with SER 152 (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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357A ILE* 4.4 21.0 - - - +
391B SER* 5.4 7.6 + - - -
148C TYR* 2.9 43.8 + - - -
149C LYS* 4.5 3.1 - - - -
151C TYR* 1.3 78.4 - - - +
153C ALA* 1.3 56.2 + - - +
155C ASP* 3.6 3.1 + - - +
156C ALA* 3.2 24.1 + - - +
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Residues in contact with ALA 153 (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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127C VAL* 4.1 21.4 - - + +
128C LEU 6.2 0.7 - - - +
149C LYS 3.2 20.0 + - - +
150C LEU 3.8 0.2 - - - -
151C TYR 3.4 0.2 - - - -
152C SER* 1.3 78.0 - - - +
154C ALA* 1.3 59.8 + - - +
156C ALA* 3.9 9.5 - - + +
157C GLU* 3.8 26.3 + - - +
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Residues in contact with ALA 154 (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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125C TYR* 4.2 21.2 + - + -
127C VAL* 5.3 1.8 - - + -
150C LEU 3.0 18.9 + - - +
151C TYR 3.7 1.3 + - - +
152C SER 3.3 0.2 - - - -
153C ALA* 1.3 76.8 - - - +
155C ASP* 1.3 62.1 + - - +
156C ALA 3.3 1.3 - - - -
157C GLU* 3.6 2.5 + - - -
158C GLU* 3.2 24.6 + - - +
191C PHE* 4.2 12.3 - - + -
195C PHE* 3.6 33.0 - - + -
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Residues in contact with ASP 155 (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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357A ILE* 3.3 25.8 - - + +
151C TYR* 3.2 46.0 + - - +
152C SER 4.1 0.4 - - - +
153C ALA 3.5 0.2 - - - -
154C ALA* 1.3 75.1 - - - +
156C ALA* 1.3 63.9 + - - +
157C GLU 3.3 0.7 - - - -
158C GLU* 3.5 14.9 + - + +
159C HIS* 3.6 10.9 + - - -
195C PHE* 3.5 23.1 - - - -
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Residues in contact with ALA 156 (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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152C SER 3.2 17.1 + - - +
153C ALA* 4.0 11.2 - - - +
154C ALA 3.3 0.4 - - - -
155C ASP* 1.3 79.6 - - - +
157C GLU* 1.3 60.5 + - + +
159C HIS* 3.1 28.4 + - - -
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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