Contacts of the helix formed by residues 147 - 159 (chain C) in PDB entry 2P82
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 GLY 147 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C MET* 4.2 4.3 - - - -
145C TRP* 3.7 16.0 - - - -
146C PHE* 1.3 79.3 - - - +
148C PRO* 1.3 77.3 - - - +
149C ASN 3.4 2.2 - - - -
150C THR* 3.3 7.7 + - - -
151C VAL* 3.1 19.9 + - - +
361C EDO 4.0 4.0 - - - -
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Residues in contact with PRO 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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78C MET* 3.9 17.4 - - + -
147C GLY* 1.3 81.9 - - - +
149C ASN* 1.3 66.6 + - - +
151C VAL* 3.3 13.1 - - + +
152C ALA* 2.9 23.6 + - - +
228C PRO* 5.4 0.4 - - + -
257C LEU* 4.4 6.9 - - + +
258C GLY* 4.7 0.7 - - - -
259C GLY 5.9 0.2 - - - +
317C SER* 3.7 27.8 - - - +
318C VAL* 3.9 9.6 - - - +
319C ALA* 3.7 30.5 - - + +
361C EDO 3.7 16.2 - - - +
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Residues in contact with ASN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLY 3.4 1.0 + - - -
148C PRO* 1.3 78.7 - - - +
150C THR* 1.3 68.2 + - - +
152C ALA* 3.1 6.5 + - - +
153C GLN* 2.9 44.8 + - - +
171C VAL* 3.9 10.4 - - - +
172C SER 5.3 0.9 - - - +
228C PRO* 4.1 19.2 - - + +
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Residues in contact with THR 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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138C GLU* 3.8 30.3 - - + -
140C LYS* 3.7 22.8 + - + +
146C PHE* 3.5 37.3 - - + +
147C GLY 3.3 7.0 + - - -
149C ASN* 1.3 81.5 + - - +
151C VAL* 1.3 58.7 + - - +
153C GLN* 3.1 8.7 + - - +
154C VAL* 2.9 25.9 + - + +
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Residues in contact with VAL 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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78C MET* 3.8 29.8 - - + +
79C LEU* 4.0 10.3 - - + -
82C GLY* 4.4 7.0 - - - -
131C MET* 3.9 27.1 - - + -
146C PHE* 3.9 9.3 - - + -
147C GLY 3.1 8.6 + - - +
148C PRO* 3.3 20.4 - - + +
150C THR* 1.3 74.7 - - - +
152C ALA* 1.3 61.1 + - - +
154C VAL* 3.1 3.9 + - + +
155C LEU* 2.8 31.6 + - + +
257C LEU* 3.6 24.7 - - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO 2.9 15.2 + - - +
149C ASN* 3.1 11.6 + - - +
151C VAL* 1.3 77.0 - - - +
153C GLN* 1.3 58.5 + - - +
155C LEU* 3.4 4.4 + - - +
156C LYS* 3.0 27.9 + - - +
171C VAL* 3.7 25.7 - - + +
226C ILE* 3.7 37.6 - - + +
228C PRO* 4.6 0.9 - - + -
257C LEU* 5.8 0.7 - - + -
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Residues in contact with GLN 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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138C GLU* 3.6 28.0 - - - +
149C ASN* 2.9 39.8 + - - +
150C THR* 3.6 8.1 - - - +
152C ALA* 1.3 72.2 - - - +
154C VAL* 1.3 66.2 + - - +
156C LYS* 3.3 20.5 + - - +
157C LYS* 3.1 36.2 + - - +
171C VAL* 3.6 24.0 + - - +
173C MET* 6.1 2.6 - - - +
157D LYS* 5.3 2.8 + - - -
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Residues in contact with VAL 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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79C LEU* 5.1 0.4 - - + -
131C MET* 3.8 45.8 - - + +
134C MET* 4.0 16.1 - - + +
135C GLY* 3.8 31.2 - - - +
138C GLU* 4.4 6.1 - - + -
146C PHE* 4.2 12.1 - - + -
150C THR* 2.9 17.1 + - + +
151C VAL* 3.1 10.3 + - + +
153C GLN* 1.3 76.1 - - - +
155C LEU* 1.3 57.3 + - - +
157C LYS* 3.3 3.1 + - - +
158C LEU* 2.9 34.6 + - + +
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Residues in contact with LEU 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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82C GLY* 4.0 27.8 - - - +
83C GLN* 5.4 0.2 - - - -
85C MET* 5.4 4.9 - - - -
86C LEU* 4.0 31.8 - - + +
126C TYR* 5.2 1.8 - - + -
131C MET* 3.8 27.1 - - + -
151C VAL* 2.8 26.1 + - + +
152C ALA* 3.8 3.6 - - - +
154C VAL* 1.3 71.6 - - + +
156C LYS* 1.3 64.6 + - - +
158C LEU* 3.3 6.9 + - + +
159C ALA* 3.0 25.3 + - - +
169C VAL* 4.3 2.8 - - - +
224C LEU* 4.6 13.9 - - + +
226C ILE* 4.1 23.3 - - + -
257C LEU* 5.0 7.4 - - + -
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Residues in contact with LYS 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 ALA 3.0 17.6 + - - +
153C GLN* 3.6 23.6 - - - +
154C VAL 3.3 0.2 - - - -
155C LEU* 1.3 78.1 - - - +
157C LYS* 1.3 62.3 + - + +
159C ALA* 3.5 5.9 + - - +
160C LEU* 3.9 2.0 + - - +
169C VAL* 2.9 45.4 + - + +
170C TYR* 5.0 0.4 - - - +
171C VAL* 4.4 12.6 - - + +
185C MET* 4.1 4.2 - - - +
363C EDO 2.7 48.7 + - - -
137D GLY 2.7 29.5 + - - -
138D GLU* 4.4 2.2 - - - -
157D LYS* 4.0 25.6 - - - +
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Residues in contact with LYS 157 (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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134C MET* 3.7 35.0 - - + +
137C GLY* 6.0 1.6 - - - -
138C GLU* 2.8 31.2 + - - +
153C GLN* 3.1 26.6 + - - +
156C LYS* 1.3 73.5 - - + +
158C LEU* 1.3 67.0 + - - +
160C LEU* 3.1 27.7 + - + +
161C PHE* 3.4 10.0 - - - -
153D GLN* 5.4 2.8 + - - -
156D LYS* 4.2 24.4 - - - +
157D LYS* 4.2 40.1 - - - +
160D LEU* 4.2 14.8 - - + -
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Residues in contact with LEU 158 (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 CYS* 3.7 22.9 - - - +
126C TYR* 3.9 25.9 - - + -
130C GLN* 3.8 19.3 - - + +
131C MET* 3.5 43.1 - - + +
134C MET* 3.6 27.1 - - + -
154C VAL* 2.9 21.9 + - + +
155C LEU* 4.0 5.8 - - + +
157C LYS* 1.3 76.7 - - - +
159C ALA* 1.3 57.1 + - - +
161C PHE* 2.8 35.3 + - + +
162C ASP 3.8 2.1 + - - -
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 6.1 1.6 - - + -
126C TYR* 3.8 18.7 - - + +
155C LEU 3.0 17.4 + - - +
156C LYS 3.6 7.9 - - - +
157C LYS 3.2 0.4 - - - -
158C LEU* 1.3 76.0 - - - +
160C LEU* 1.3 60.7 + - - +
161C PHE 3.1 0.9 + - - -
162C ASP* 3.3 18.8 + - - +
166C SER* 4.9 1.4 - - - -
167C LEU* 4.1 26.3 + - + +
169C VAL* 3.6 21.8 - - + -
363C EDO 4.1 2.2 - - - +
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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