Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 1TFZ
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 VAL 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE* 5.2 2.7 - - + -
118A VAL* 3.8 21.1 - - + +
119A ARG 3.3 12.8 - - - +
121A VAL* 4.1 20.4 - - + -
159A LYS* 4.2 1.0 - - - +
160A LEU* 2.9 27.0 + - + +
161A TYR* 2.9 35.7 + - + +
162A GLY 4.9 0.3 - - - +
163A ASP* 1.3 81.1 - - - +
165A VAL* 1.3 69.7 + - - +
283A ALA 4.9 0.2 - - - +
284A GLY* 3.7 26.2 - - - -
285A LEU* 3.9 5.6 - - + +
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Residues in contact with VAL 165 (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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119A ARG* 2.9 42.9 + - - +
120A ALA* 3.4 14.3 - - + -
121A VAL* 3.1 25.8 + - - +
143A SER* 3.3 26.0 - - - +
157A GLU* 3.6 29.6 - - + +
158A VAL 3.2 15.0 - - - +
159A LYS* 4.5 5.6 - - + -
160A LEU* 4.1 3.3 - - - +
163A ASP 4.4 1.3 - - - +
164A VAL* 1.3 82.1 - - - +
166A LEU* 1.3 60.5 + - - +
167A ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 166 (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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121A VAL* 3.4 26.2 - - + +
123A ILE* 4.4 20.4 - - + -
156A ALA 3.9 0.3 - - - +
157A GLU* 3.4 2.1 - - - -
158A VAL* 2.8 39.7 + - + +
160A LEU* 4.1 20.1 - - + +
165A VAL* 1.3 71.0 - - - +
167A ARG* 1.3 59.5 + - - +
168A TYR* 3.6 35.5 + - + +
223A PHE* 3.8 18.6 - - + -
224A THR* 4.1 9.9 - - + -
226A PHE* 5.4 0.4 - - + -
258A LEU* 4.4 21.5 - - + -
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Residues in contact with ARG 167 (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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28A HIS* 3.0 37.3 + - - -
30A GLU* 2.7 31.5 + - - -
32A TRP* 5.7 3.0 - - - +
77A LEU* 4.6 3.2 - - - +
99A ILE* 4.0 9.7 - - - +
101A SER* 3.7 8.3 + - - -
119A ARG* 5.4 3.8 - - - +
120A ALA* 3.8 24.9 - - + +
121A VAL 3.0 7.0 + - - +
122A ALA* 3.2 11.1 - - + +
123A ILE* 2.9 29.5 + - - +
155A ILE* 3.4 35.4 - - + +
156A ALA 3.3 6.5 - - - +
157A GLU* 2.7 34.6 + - + -
165A VAL* 3.8 1.6 - - - +
166A LEU* 1.3 72.3 - - - +
168A TYR* 1.3 63.8 + - - +
169A VAL* 4.1 3.1 - - + -
182A LEU* 5.9 0.8 - - - +
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Residues in contact with TYR 168 (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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21A PHE* 3.3 23.1 - + - -
123A ILE* 3.7 23.3 - - + -
125A VAL* 4.0 12.8 - - + -
128A ALA* 3.6 17.7 - - + +
131A ALA* 3.7 20.6 - - + -
132A PHE* 3.9 15.9 - - + -
135A SER* 2.8 27.9 + - - -
154A THR 3.6 0.5 - - - +
155A ILE* 3.2 7.1 - - - +
156A ALA* 2.7 41.6 + - + +
158A VAL* 4.1 18.2 - - + -
166A LEU* 3.6 22.6 - - + +
167A ARG* 1.3 73.2 - - - +
169A VAL* 1.3 62.2 + - - +
223A PHE* 3.3 20.3 - - - -
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A HIS* 4.2 14.1 - - + +
28A HIS* 4.1 20.2 - - + -
122A ALA* 4.5 5.2 - - + -
123A ILE 3.1 9.6 + - - +
124A GLU* 3.2 7.4 - - - +
125A VAL* 2.9 22.7 + - - +
128A ALA* 4.3 0.9 - - - -
153A VAL* 3.9 17.0 - - + -
154A THR 3.3 4.0 - - - +
155A ILE* 4.6 6.1 - - + -
167A ARG* 4.1 18.2 - - + -
168A TYR* 1.3 79.4 - - - +
170A SER* 1.3 63.7 + - - +
171A TYR* 3.6 29.8 - - + +
182A LEU* 4.4 7.2 - - + -
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Residues in contact with SER 170 (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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125A VAL 3.1 22.2 - - - -
126A GLU 3.7 11.7 - - - -
127A ASP* 3.7 2.8 + - - -
128A ALA* 2.8 35.0 + - - +
153A VAL* 3.3 6.9 - - - +
154A THR* 2.9 41.3 + - - -
169A VAL* 1.3 72.5 - - - +
171A TYR* 1.3 65.5 + - - +
172A LYS* 5.7 0.6 - - - +
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Residues in contact with TYR 171 (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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24A LYS* 6.3 0.4 - - - +
27A HIS* 2.7 42.1 + + - -
75A ARG* 5.5 1.2 + - - -
124A GLU* 3.6 23.7 + - - +
125A VAL 4.7 0.8 + - - -
126A GLU 4.7 7.6 - - - +
152A ALA 3.5 3.8 - - - -
153A VAL* 3.6 28.7 - - + -
169A VAL* 3.6 17.3 - - + +
170A SER* 1.3 79.7 - - - +
172A LYS* 1.3 70.7 + - - +
180A GLU 3.8 23.7 + - - -
181A PHE* 4.5 7.5 - - - -
182A LEU* 4.6 1.9 - - - +
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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