Contacts of the helix formed by residues 129 - 143 (chain F) 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 LEU 129 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TYR* 4.6 8.5 - - - +
46F PHE* 4.9 10.8 - - + -
69F VAL* 4.2 12.1 - - + +
70F PRO* 5.6 0.2 - - + -
73F GLY* 5.5 1.3 - - - -
98F ALA* 4.2 16.6 - - + -
101F LEU* 3.6 32.1 - - + -
102F LEU* 3.7 15.2 - - + +
105F GLU* 5.6 0.7 - - - +
127F SER* 4.4 9.4 - - - +
128F ALA* 1.3 79.8 - - - +
130F ILE* 1.3 62.3 + - - +
131F VAL 3.3 0.2 - - - -
132F PRO* 2.6 30.9 - - + +
133F ALA* 2.9 13.8 + - - +
157F TRP* 4.2 24.4 - - + -
161F PHE* 3.8 23.3 - - + -
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E TRP* 3.6 34.8 - - + +
192E MET* 3.8 33.0 - - + +
195E GLY* 4.5 10.1 - - - -
95F VAL* 5.2 4.3 - - + -
98F ALA* 4.7 3.1 - - + -
99F LEU* 3.9 28.3 - - + +
102F LEU* 3.5 27.1 - - + +
128F ALA* 4.0 0.6 - - - +
129F LEU* 1.3 74.7 - - - +
131F VAL* 1.3 67.1 + - - +
133F ALA* 3.2 7.3 + - + +
134F ILE* 3.0 37.6 + - + +
164F ASN* 4.4 0.6 + - - -
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Residues in contact with VAL 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E TRP* 5.6 0.2 - - + -
191E TRP* 3.5 38.5 - - + +
239E THR* 3.8 12.9 - - + +
240E ILE* 5.8 1.6 - - + +
243E THR* 3.5 27.6 - - - +
130F ILE* 1.3 75.0 - - - +
132F PRO* 1.4 75.1 - - + +
134F ILE* 2.8 20.3 + - - +
135F TRP* 3.1 10.5 + - + +
160F LEU* 4.3 23.1 - - + -
164F ASN* 3.8 22.6 + - + +
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Residues in contact with PRO 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ALA 4.6 0.9 - - - +
129F LEU* 2.6 27.1 - - + +
131F VAL* 1.4 89.4 - - + +
133F ALA* 1.3 53.9 + - - +
135F TRP* 3.6 7.3 + - + +
136F LEU* 3.0 22.9 + - - +
157F TRP* 3.3 58.3 - - + +
160F LEU* 4.3 11.4 - - + +
161F PHE* 4.3 8.1 - - + -
164F ASN* 3.7 21.3 - - - +
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ALA* 3.3 21.4 - - + +
95F VAL* 3.7 15.0 - - + +
98F ALA* 3.6 30.7 - - + -
129F LEU 2.9 8.1 + - - +
130F ILE* 3.4 10.5 - - - +
132F PRO* 1.3 74.1 - - - +
134F ILE* 1.3 59.8 + - - +
136F LEU 3.4 0.7 + - - -
137F ASP* 2.9 24.9 + - - +
157F TRP* 3.7 11.6 - - + -
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Residues in contact with ILE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E TRP* 4.2 8.7 - - + -
194E VAL* 4.4 10.8 - - + -
195E GLY* 5.6 2.2 - - - -
198E TRP* 5.6 10.1 - - + +
235E VAL* 4.6 12.3 - - + -
236E LEU* 4.5 6.5 - - + -
239E THR* 4.0 37.2 - - + +
95F VAL* 3.8 19.3 - - + -
130F ILE* 3.0 36.9 + - + +
131F VAL 2.8 6.6 + - - +
133F ALA* 1.3 73.4 - - - +
135F TRP* 1.3 68.5 + - - +
137F ASP* 2.9 4.6 + - - +
138F VAL* 2.9 38.2 + - + +
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Residues in contact with TRP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LEU* 3.7 40.2 - - + +
239E THR* 5.8 0.2 - - - +
240E ILE* 4.0 22.4 - - + -
131F VAL* 3.1 8.6 + - + +
132F PRO* 3.8 6.3 - - + +
134F ILE* 1.3 75.6 - - - +
136F LEU* 1.3 63.1 + - - +
138F VAL* 4.3 0.2 - - - +
139F ILE* 3.0 42.7 + - + +
152F VAL* 2.9 34.5 + - + -
153F GLY* 3.0 24.3 + - - -
156F GLY* 3.4 17.0 - - - -
157F TRP 3.8 2.2 - - - -
160F LEU* 4.0 28.3 - - + -
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 4.1 16.6 - - + -
77F CYS* 4.0 16.8 - - + -
81F GLN* 3.1 17.9 + - - +
94F ALA* 3.9 17.7 - - + -
132F PRO 3.0 14.8 + - - +
133F ALA 3.4 8.7 - - - +
135F TRP* 1.3 79.4 - - - +
137F ASP* 1.3 60.8 + - - +
139F ILE 3.7 0.2 + - - -
140F LEU 3.4 14.4 + - - -
149F THR* 3.6 19.5 - - + +
153F GLY* 3.2 36.3 - - - +
154F SER* 3.6 12.6 - - - +
157F TRP* 4.1 12.8 - - + -
233F TYR* 4.2 11.7 - - + -
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Residues in contact with ASP 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 4.5 5.6 - - + +
81F GLN* 2.8 23.3 + - - +
91F PRO* 3.3 29.7 - - - +
92F PHE* 3.2 6.4 - - - -
93F GLY 3.1 9.7 + - - -
94F ALA* 2.8 15.7 + - - +
95F VAL* 2.7 40.4 + - + +
133F ALA 2.9 8.9 + - - +
134F ILE* 2.9 8.5 + - - +
136F LEU* 1.3 71.8 - - - +
138F VAL* 1.3 60.8 + - - +
140F LEU* 3.6 5.3 + - - +
141F LEU* 3.2 22.2 + - - +
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 3.7 32.1 - - + -
232E GLY* 3.7 27.4 - - - +
236E LEU* 3.7 32.5 - - + +
134F ILE* 2.9 24.3 + - + +
135F TRP 4.3 1.6 - - - +
137F ASP* 1.3 72.2 - - - +
139F ILE* 1.3 60.1 + - - +
140F LEU 3.1 1.6 - - - -
141F LEU* 2.9 5.1 + - + -
142F LEU* 2.7 51.8 + - + +
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LEU* 5.1 8.1 - - + -
135F TRP* 3.0 56.7 + - + +
136F LEU 3.7 2.4 + - - +
138F VAL* 1.3 78.8 - - - +
140F LEU* 1.3 57.4 + - - +
142F LEU* 4.9 9.0 - - + -
143F SER* 3.0 24.9 + - - +
148F ILE* 4.0 6.7 - - + -
149F THR* 3.6 25.8 - - - +
152F VAL* 3.6 32.5 - - + -
153F GLY* 4.0 5.6 - - - -
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLN* 3.6 34.3 - - + +
85F TRP* 3.6 53.7 - - + +
91F PRO* 6.2 2.2 - - + -
136F LEU 3.4 11.3 + - - +
137F ASP* 3.8 8.5 - - - +
138F VAL 3.1 0.8 - - - -
139F ILE* 1.3 73.1 - - - +
141F LEU* 1.3 56.7 + - - +
143F SER* 2.6 21.5 - - - +
144F GLY* 3.7 5.2 - - - +
145F SER 3.4 24.7 - - - +
146F TYR* 3.9 9.2 - - + +
149F THR* 3.3 19.0 + - - +
237F TRP* 4.1 6.5 - - + -
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 4.2 7.4 - - + -
202E TRP* 4.1 15.7 - - + -
224E ILE* 3.8 36.1 - - + -
228E ASP 3.9 19.3 - - - +
229E ARG* 3.8 23.1 + - + +
232E GLY* 4.0 19.5 - - - -
85F TRP* 4.1 10.4 - - + -
91F PRO* 3.8 22.0 - - + -
137F ASP 3.2 13.8 + - - +
138F VAL* 2.9 9.3 + - + +
140F LEU* 1.3 74.3 - - - +
142F LEU* 1.3 70.8 + - + +
143F SER 2.9 6.2 - - - +
144F GLY* 4.5 1.2 - - - -
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ARG* 3.3 55.8 + - + +
232E GLY 4.8 0.4 - - - -
233E ALA* 4.1 22.0 - - + +
236E LEU* 4.8 7.4 - - + -
138F VAL* 2.7 39.9 + - + +
139F ILE* 4.6 9.0 - - + +
141F LEU* 1.3 72.8 - - + +
143F SER* 1.3 66.6 + - - +
144F GLY* 3.5 1.0 + - - -
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Residues in contact with SER 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F ILE* 3.0 16.8 + - - -
140F LEU 2.6 30.5 - - - +
141F LEU 2.9 0.9 - - - +
142F LEU* 1.3 81.6 - - - +
144F GLY* 1.3 51.2 + - - +
145F SER* 3.2 23.4 + - - -
148F ILE* 3.6 32.1 - - - +
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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