Contacts of the helix formed by residues 122 - 134 (chain B) in PDB entry 3TJF
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 PHE 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A VAL* 4.2 10.8 - - + -
256A ILE* 3.3 30.5 - - + +
258A PRO* 3.5 39.0 - - + -
259A ASP* 3.5 26.9 - - - -
260A PRO* 3.9 2.2 - - + -
263A LYS* 3.8 25.1 - - + -
267A PHE* 3.5 6.7 - - - -
120B PHE 4.7 2.0 - - - -
121B THR* 1.3 92.8 + - - +
123B VAL* 1.3 67.3 + - - +
124B CYS 3.3 0.4 - - - -
125B PRO* 3.1 14.9 - - - +
126B THR* 3.6 1.7 - - - +
476B SO4 3.4 29.6 - - - -
154C PHE* 3.6 31.2 - + - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A VAL* 3.6 31.2 - - + -
245A CYS 3.2 31.6 - - - +
246A PRO* 4.4 0.9 - - + -
256A ILE* 4.1 2.9 - - + -
122B PHE* 1.3 80.0 - - - +
124B CYS* 1.3 62.7 + - - +
126B THR* 2.6 27.6 + - - +
127B GLU* 3.2 10.6 + - + +
200B ARG* 3.3 34.7 - - - +
219B LEU 4.5 0.4 - - - +
220B PRO 4.1 6.5 - - - +
222B GLY* 3.6 19.5 - - - -
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Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.5 23.1 - - + -
117B PRO* 3.5 20.4 - - - -
118B LEU 3.7 11.4 - - - +
121B THR* 3.0 23.6 - - - +
122B PHE 4.8 0.4 - - - -
123B VAL* 1.3 75.9 - - - +
125B PRO* 1.3 68.9 - - + +
127B GLU* 3.1 8.1 + - - +
128B ILE* 3.0 26.2 + - - +
159B TRP* 4.2 3.4 - - + -
200B ARG* 3.4 28.3 - - - +
476B SO4 4.4 0.2 - - - -
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 3.6 18.8 - - + -
121B THR 3.5 15.0 - - - +
122B PHE 3.1 26.0 - - - +
124B CYS* 1.3 95.2 - - + +
126B THR* 1.3 55.5 + - - +
128B ILE* 3.4 0.5 + - - +
129B ILE* 2.8 39.6 + - + +
159B TRP* 3.7 21.9 - - + -
167B GLY 4.0 11.2 - - - +
168B GLY 4.5 4.3 - - - +
169B LEU* 3.8 17.7 - - + -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 3.5 11.8 - - + +
247A ALA* 3.0 22.6 + - - +
256A ILE* 3.7 14.4 - - + -
266A TYR* 3.6 29.2 - - + +
267A PHE* 4.0 5.8 - - + -
122B PHE 3.6 17.0 - - - +
123B VAL 2.6 16.3 + - - -
125B PRO* 1.3 73.1 - - - +
127B GLU* 1.3 57.6 + - - +
129B ILE* 4.0 5.8 - - - +
130B ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA* 3.7 22.4 - - + -
114B PHE* 4.6 10.3 - - + -
116B TYR* 4.4 1.3 - - + +
123B VAL* 3.6 17.9 - - + +
124B CYS* 3.1 8.8 + - - +
126B THR* 1.3 79.8 + - - +
128B ILE* 1.3 65.9 + - - +
130B ALA* 3.3 1.0 + - - +
131B PHE* 3.1 39.0 + - + -
200B ARG* 2.9 25.9 + - - -
222B GLY* 3.3 3.1 - - - -
223B ARG* 2.7 64.2 + - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 4.1 24.5 - - + -
116B TYR* 3.5 28.7 - - + +
124B CYS 3.0 13.4 + - - +
125B PRO 3.9 3.1 - - - +
127B GLU* 1.3 75.7 - - - +
129B ILE* 1.3 57.7 + - - +
131B PHE* 3.6 1.4 + - - +
132B GLY 2.9 23.9 + - - -
147B ALA* 4.4 3.6 - - + -
159B TRP* 3.4 37.7 - - + -
169B LEU* 3.9 15.0 - - + -
172B ILE* 3.4 25.6 - - + +
174B ILE* 4.4 5.0 - - + +
176B LEU* 4.1 13.5 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 5.7 5.2 - - + -
125B PRO* 2.8 31.4 + - + +
126B THR* 4.0 6.1 - - - +
128B ILE* 1.3 73.1 - - - +
130B ALA* 1.3 54.6 + - - +
133B ASP* 2.8 54.3 + - - +
164B ARG* 3.5 48.2 - - + +
168B GLY 4.0 12.8 - - - +
169B LEU* 4.0 15.7 - - + +
172B ILE* 4.4 7.6 - - + -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA* 3.8 16.8 - - + +
126B THR 2.9 20.4 + - - +
127B GLU 3.3 3.6 + - - +
129B ILE* 1.3 77.9 - - - +
131B PHE* 1.3 61.1 + - - +
133B ASP* 4.2 1.7 - - - -
134B ARG* 3.4 31.5 + - - +
225B VAL* 3.7 18.7 - - + +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 4.1 7.4 - - + -
114B PHE* 3.9 23.1 - + + -
127B GLU* 3.1 34.0 + - + +
128B ILE 4.0 1.3 - - - +
130B ALA* 1.3 72.6 - - - +
132B GLY* 1.3 61.0 + - - +
134B ARG* 3.2 4.5 + - - -
135B LEU* 2.9 29.6 + - - +
138B PHE* 3.7 36.5 - + - -
145B VAL* 4.1 13.5 - - + -
174B ILE* 3.6 17.5 - - + +
202B LEU* 3.7 16.6 - - + -
223B ARG* 5.0 12.8 - - + -
224B SER 4.4 1.6 - - - -
225B VAL* 3.9 22.2 - - + -
228B THR* 3.6 29.4 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE 2.9 16.7 + - - -
129B ILE 3.7 0.4 - - - -
131B PHE* 1.3 76.9 - - - +
133B ASP* 1.3 63.3 - - - +
135B LEU* 3.2 18.4 + - - +
172B ILE* 4.2 12.6 - - - -
173B ARG* 4.5 17.3 + - - +
174B ILE* 3.3 19.0 - - - +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 2.8 27.8 + - - +
130B ALA* 4.4 3.6 - - - +
132B GLY* 1.3 74.4 - - - +
134B ARG* 1.3 63.5 + - + +
135B LEU 3.5 0.2 - - - -
136B GLU 5.5 0.2 + - - -
164B ARG* 3.0 43.0 + - - -
172B ILE* 5.9 0.2 - - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.4 20.5 + - - +
131B PHE 3.2 5.4 + - - +
132B GLY 3.1 0.6 - - - -
133B ASP* 1.3 83.6 - - + +
135B LEU* 1.3 64.3 + - - +
136B GLU* 3.2 3.6 - - - -
137B GLU* 2.8 63.2 + - - +
138B PHE* 3.7 6.3 - - - -
225B VAL* 3.7 33.2 - - + +
226B ASP* 2.8 35.0 + - - +
229B LEU* 3.4 9.9 - - - +
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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