Contacts of the helix formed by residues 134 - 140 (chain A) in PDB entry 3TIW
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 TYR 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A THR 5.5 6.5 - - - -
129A ASN 5.2 0.4 - - - -
130A LEU* 2.9 33.7 + - + +
131A PHE 3.5 0.2 + - - -
133A VAL* 1.3 97.8 - - + +
135A LEU* 1.3 66.2 + - - +
137A PRO* 3.1 12.3 - - - +
138A TYR* 3.1 18.2 + - - +
154A VAL* 3.3 45.8 - - + +
155A ARG 4.1 3.4 - - - -
156A GLY 2.9 33.0 + - - -
157A GLY* 4.3 2.6 + - - -
159A ARG* 3.7 16.1 - - - +
160A ALA* 4.1 0.2 - - - -
161A VAL* 3.2 32.2 - - + +
163A PHE* 3.8 16.6 - + + -
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Residues in contact with LEU 135 (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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116A VAL* 3.6 27.1 - - + -
130A LEU 2.9 19.7 + - - +
131A PHE* 4.0 17.7 - - + -
134A TYR* 1.3 71.9 - - - +
136A LYS* 1.3 66.4 + - - +
138A TYR* 3.3 2.3 + - - +
139A PHE* 3.0 35.6 + - + +
152A PHE* 4.3 17.7 - - + -
154A VAL* 4.8 1.1 - - + -
163A PHE* 3.4 38.4 - - + -
182A ILE* 4.3 15.9 - - + -
184A CYS* 3.9 25.1 - - + -
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Residues in contact with LYS 136 (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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131A PHE* 2.8 50.2 + - + +
132A GLU* 3.9 26.7 + - - +
135A LEU* 1.3 73.0 - - - +
137A PRO* 1.3 65.2 - - + +
139A PHE* 3.8 1.5 - - - -
140A LEU* 2.8 56.1 + - + +
182A ILE* 6.0 0.2 - - - -
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Residues in contact with PRO 137 (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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131A PHE 3.6 4.9 - - - +
132A GLU 3.5 16.4 - - - +
133A VAL 3.5 14.8 - - - +
134A TYR 3.1 17.7 - - - +
136A LYS* 1.3 96.5 - - + +
138A TYR* 1.3 62.2 + - - +
140A LEU* 3.7 16.0 + - + +
154A VAL* 6.1 0.7 - - + -
155A ARG 6.1 0.9 - - - +
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Residues in contact with TYR 138 (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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36A ASN* 3.0 41.9 + - - +
37A SER* 4.4 1.2 + - - -
134A TYR 3.1 17.9 + - - +
135A LEU* 3.5 4.5 - - - +
137A PRO* 1.3 84.2 - - - +
139A PHE* 1.3 79.7 + + - +
142A ALA* 3.5 6.2 - - - +
144A ARG* 3.0 63.4 + - - +
146A ILE* 5.9 1.8 - - + -
152A PHE* 3.4 38.1 - + - +
153A LEU 4.2 2.5 - - - -
154A VAL* 3.7 25.1 - - + +
636C ARG* 5.5 0.2 - - - -
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Residues in contact with PHE 139 (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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114A ILE* 4.3 13.7 - - + -
116A VAL* 5.1 1.8 - - + -
135A LEU* 3.0 30.1 + - + +
136A LYS* 4.4 1.8 - - - +
138A TYR* 1.3 101.0 - + - +
140A LEU* 1.3 66.6 + - - +
141A GLU 3.0 1.9 + - - -
142A ALA* 2.9 17.9 + - - +
143A TYR 4.1 2.9 + - - -
144A ARG* 4.0 15.5 - - + -
146A ILE* 4.1 17.7 - - + -
152A PHE* 4.0 23.6 - + - -
176A VAL* 3.6 44.5 - - + +
177A ALA 5.9 1.4 - - - -
182A ILE* 3.8 28.7 - - + -
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Residues in contact with LEU 140 (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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136A LYS* 2.8 40.3 + - + +
137A PRO* 3.7 13.6 + - + +
138A TYR 3.5 2.2 - - - -
139A PHE* 1.3 75.1 - - - +
141A GLU* 1.3 83.3 + - + +
142A ALA* 2.9 5.6 + - - +
178A PRO* 6.4 2.0 - - + -
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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