Contacts of the helix formed by residues 145 - 160 (chain J) in PDB entry 4PHZ
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 SER 145 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252F ILE* 2.8 32.4 + - - +
140J LEU* 3.4 4.4 - - - +
143J SER* 3.1 9.7 + - - -
144J GLY* 1.3 79.7 - - - +
146J TYR* 1.3 57.1 + - - +
147J VAL* 3.1 5.7 + - - +
148J ILE* 3.1 38.2 + - - +
149J THR* 2.9 27.5 + - - -
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Residues in contact with TYR 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F THR 4.7 7.7 + - - -
252F ILE* 3.0 27.0 + - - -
140J LEU* 4.0 6.6 - - - +
144J GLY 4.3 0.4 + - - -
145J SER* 1.3 70.1 - - - +
147J VAL* 1.3 77.5 + - + +
149J THR* 3.8 4.0 - - - -
150J ALA* 2.8 33.8 + - - +
233J TYR* 3.5 4.9 - + - +
234J PHE* 4.1 9.1 - + - -
237J TRP* 3.4 65.3 - + + -
238J PHE* 3.2 40.1 - + - -
241J ARG* 6.2 1.1 - - - -
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ILE* 3.6 21.5 + - + +
184G LEU* 5.9 6.1 - - + -
188G ILE* 4.2 32.8 - - + -
303G PGT 4.6 11.7 - - + -
145J SER* 3.1 8.4 + - - +
146J TYR* 1.3 91.2 - - + +
148J ILE* 1.3 69.8 + - + +
150J ALA* 3.3 8.3 + - - +
151J VAL* 3.1 22.5 + - + +
234J PHE* 3.8 24.2 - - + -
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Residues in contact with ILE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ILE* 4.4 12.3 - - + -
303G PGT 4.5 40.6 - - + -
139J ILE* 4.1 3.6 - - + -
143J SER* 3.7 30.7 - - - +
145J SER* 3.1 26.4 + - - +
147J VAL* 1.3 76.9 - - + +
149J THR* 1.3 58.3 + - - +
151J VAL* 2.9 5.7 + - - +
152J VAL* 2.8 53.5 + - + -
153J GLY 3.5 0.7 + - - -
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Residues in contact with THR 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J GLN* 3.8 5.8 - - - +
136J LEU* 3.6 29.8 - - + +
139J ILE* 3.7 10.4 - - + +
140J LEU* 3.3 24.7 + - + +
145J SER 2.9 19.7 + - - -
146J TYR* 3.9 2.7 - - - -
148J ILE* 1.3 73.6 - - - +
150J ALA* 1.3 61.7 + - - +
153J GLY* 2.7 24.3 + - - -
154J SER* 2.8 9.5 + - - -
233J TYR* 3.2 34.3 - - + +
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Residues in contact with ALA 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G MET* 6.2 0.4 - - - -
146J TYR 2.8 23.8 + - - +
147J VAL 3.4 6.1 - - - +
149J THR* 1.3 73.3 - - - +
151J VAL* 1.3 58.0 + - + +
154J SER* 2.5 24.8 + - - -
230J MET* 3.3 15.1 - - - +
233J TYR* 3.4 27.2 - - + -
234J PHE* 3.5 29.8 - - + -
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Residues in contact with VAL 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ILE* 5.1 11.2 - - + -
191G PHE* 4.6 21.8 - - + +
192G MET* 5.3 7.6 - - - -
303G PGT 4.5 37.2 - - + -
147J VAL* 3.1 12.2 + - + +
148J ILE* 2.9 10.0 + - - +
150J ALA* 1.3 80.1 - - + +
152J VAL* 1.3 77.1 + - + +
153J GLY 3.3 0.2 - - - -
155J LEU* 3.2 26.5 + - + +
230J MET* 3.8 23.4 - - + +
234J PHE* 5.9 1.8 - - + -
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G PGT 4.8 22.7 - - + -
135J TRP* 2.8 25.1 + - + -
139J ILE* 3.7 34.8 - - + -
148J ILE* 2.8 22.6 + - + +
151J VAL* 1.3 84.0 - - + +
153J GLY* 1.3 68.1 + - - +
155J LEU* 3.9 8.5 - - + +
156J GLY 3.1 10.6 + - - -
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Residues in contact with GLY 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J TRP* 2.9 31.1 + - - -
136J LEU* 3.3 17.9 - - - +
139J ILE* 3.9 14.4 - - - -
148J ILE 3.5 1.4 + - - -
149J THR* 2.7 19.7 + - - -
152J VAL* 1.3 76.8 - - - +
154J SER* 1.3 58.4 + - - +
157J TRP 3.0 10.0 + - - -
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Residues in contact with SER 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J VAL* 4.7 3.1 - - - -
136J LEU* 3.7 7.6 - - - +
149J THR 2.8 7.4 + - - -
150J ALA 2.5 27.3 + - - -
151J VAL 3.7 0.4 + - - -
153J GLY* 1.3 75.5 - - - +
155J LEU* 1.3 61.3 + - - +
157J TRP* 3.4 12.8 - - - +
158J GLY 3.2 15.9 + - - -
226J GLY* 3.7 10.7 - - - +
229J SER* 3.8 22.0 - - - -
230J MET* 3.2 18.4 + - - +
233J TYR* 4.3 10.1 - - - -
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303G PGT 4.3 28.9 - - + -
151J VAL* 3.2 19.4 + - + +
152J VAL* 4.0 9.0 - - + +
154J SER* 1.3 74.8 + - - +
156J GLY* 1.3 65.2 + - - +
157J TRP 3.1 0.7 - - - -
158J GLY* 3.1 3.1 + - - -
159J LEU* 3.0 39.8 + - + +
223J PHE* 4.5 18.8 - - + +
226J GLY* 4.1 21.7 + - - -
227J PHE* 4.0 27.8 - - + +
230J MET* 4.1 11.4 - - + -
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Residues in contact with GLY 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J TRP* 3.3 31.6 - - - -
152J VAL 3.1 11.3 + - - -
155J LEU* 1.3 75.2 - - - +
157J TRP* 1.3 62.4 + - - +
159J LEU* 4.5 8.1 - - - -
160J LEU* 2.9 35.7 + - - +
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Residues in contact with TRP 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J TYR* 4.5 1.8 - - - -
70J PRO* 2.8 32.7 + - + +
73J GLY* 3.5 9.0 - - - -
74J VAL* 3.2 33.6 - - + +
77J CYS* 3.7 31.6 - - - -
129J LEU* 4.2 24.7 - - + -
132J PRO* 3.4 53.1 - - + +
133J ALA* 3.7 18.2 - - + -
135J TRP* 3.8 0.8 - - - -
136J LEU* 4.0 16.2 - - + -
153J GLY 3.0 13.9 + - - +
154J SER* 3.4 16.4 - - - +
155J LEU 3.1 0.6 - - - -
156J GLY* 1.3 78.3 - - - +
158J GLY* 1.3 66.3 + - - +
161J PHE* 3.7 11.7 + + - +
229J SER* 4.0 14.4 - - - -
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Residues in contact with GLY 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J PRO 5.3 0.5 - - - +
70J PRO* 4.3 4.3 - - - -
154J SER 3.2 4.4 + - - -
155J LEU 3.1 6.0 + - - -
157J TRP* 1.3 84.3 - - - +
159J LEU* 1.3 64.9 + - - +
161J PHE* 3.2 17.0 + - - +
162J TYR 4.7 0.3 + - - -
222J ALA* 3.8 8.9 - - - +
225J SER* 3.4 26.7 + - - -
226J GLY* 4.0 9.2 - - - -
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Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J LEU* 3.0 33.5 + - + +
156J GLY* 3.9 7.2 - - - +
158J GLY* 1.3 76.1 - - - +
160J LEU* 1.3 59.2 + - + +
161J PHE 3.2 1.6 + - - -
162J TYR 4.1 0.7 + - - -
163J PRO* 3.1 23.4 - - - +
222J ALA* 3.9 23.5 + - + +
223J PHE* 3.8 55.6 - - + +
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Residues in contact with LEU 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I ILE* 5.3 13.7 - - + -
243I THR* 4.2 26.0 - - + -
131J VAL* 4.3 19.5 - - + -
132J PRO* 4.4 7.6 - - + -
135J TRP* 4.0 33.9 - - + -
156J GLY* 2.9 28.6 + - - +
157J TRP 4.3 3.4 - - - +
159J LEU* 1.3 78.8 - - + +
161J PHE* 1.3 67.9 + - - +
162J TYR 3.5 0.2 - - - -
163J PRO* 3.6 9.2 - - + -
164J ASN* 3.1 22.9 + - - +
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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