Contacts of the helix formed by residues 152 - 159 (chain A) in PDB entry 3T79
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A VAL* 1.3 83.8 - - - +
153A PHE* 1.3 59.9 + - - +
154A GLU* 3.3 16.3 + - - +
155A ASP* 3.5 26.2 + - - -
156A ARG* 2.9 24.1 + - - +
269A PHE 4.5 0.7 - - - -
270A GLN* 3.8 21.5 + - - -
271A VAL* 4.2 25.0 - - - +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 1.3 71.2 + - - +
154A GLU* 1.3 80.3 + - + +
156A ARG* 2.5 60.5 + - - +
157A THR* 2.9 34.4 + - + +
242A TYR* 4.4 6.1 - + - -
243A PRO 3.8 10.3 - - - -
245A GLU* 3.0 50.0 - - + -
248A LEU* 2.9 35.9 - - + -
269A PHE* 3.4 38.9 + + + +
270A GLN* 5.8 0.4 - - - +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 3.3 7.6 + - - +
153A PHE* 1.3 91.1 - - + +
155A ASP* 1.3 80.7 + - - +
157A THR* 3.2 10.4 + - - +
158A THR* 3.0 28.0 + - - -
245A GLU* 6.0 0.2 - - - +
270A GLN* 5.6 4.9 - - - +
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.7 13.3 - - + +
152A SER* 3.5 25.0 + - - +
153A PHE 3.1 0.2 - - - -
154A GLU* 1.3 92.1 - - - +
156A ARG* 1.3 61.8 + - - +
158A THR* 2.9 32.9 + - - +
159A VAL* 3.5 4.0 + - - +
182A LYS* 5.7 3.2 - - - +
183A PRO* 3.6 22.9 - - + +
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASP* 2.8 43.7 + - - -
145A TRP* 3.2 46.1 - - + -
146A LYS* 4.2 16.7 - - - +
151A VAL* 3.5 21.2 + - + +
152A SER 2.9 12.0 + - - +
153A PHE* 2.5 62.4 + - + +
155A ASP* 1.3 71.2 - - - +
157A THR* 1.3 54.6 + - - +
159A VAL* 3.1 20.0 - - - +
183A PRO* 5.7 0.2 - - - -
242A TYR* 3.6 16.1 - - + +
248A LEU* 5.5 0.4 - - - +
252A TYR* 4.7 1.8 + - - -
268A TRP 2.2 34.4 + - - -
269A PHE* 3.6 2.6 - - - +
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 2.9 51.1 + - + +
154A GLU* 3.5 9.8 + - - +
156A ARG* 1.3 74.2 - - - +
158A THR* 1.3 63.7 + - - +
159A VAL 3.3 2.0 + - - -
230A HIS* 3.9 19.8 + - - -
241A GLN* 5.7 0.3 - - - +
242A TYR* 3.5 34.7 - - + +
243A PRO 5.2 0.2 - - - +
245A GLU* 4.9 0.8 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 3.0 14.6 + - - -
155A ASP* 2.9 31.8 + - - +
157A THR* 1.3 78.6 - - - +
159A VAL* 1.3 62.3 + - - +
160A SER* 3.4 4.2 + - - -
163A ASP* 5.2 1.4 - - - +
182A LYS* 3.7 27.1 - - + +
183A PRO* 3.6 27.1 - - + -
230A HIS* 4.3 5.8 + - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TRP* 3.5 22.7 - - + -
155A ASP 3.8 4.7 - - - +
156A ARG 3.1 24.7 - - - +
157A THR 3.3 2.0 - - - +
158A THR* 1.3 79.2 - - + +
160A SER* 1.3 66.5 + - - +
161A LEU* 5.2 0.9 - - - -
163A ASP* 5.0 0.4 - - - -
164A LEU* 5.5 2.7 - - + +
179A HIS* 3.7 40.4 - - + +
183A PRO* 4.7 4.3 - - + -
185A PHE* 4.9 7.9 - - + -
230A HIS* 3.4 9.7 + - - -
232A PRO* 4.5 0.5 - - - +
233A ILE* 3.0 36.4 + - + +
242A TYR* 5.8 0.3 - - - -
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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