Contacts of the strand formed by residues 23 - 32 (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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 4.1 12.9 + - + +
21A PHE* 3.2 34.6 + - + +
22A LYS* 1.3 88.4 - - - +
24A LYS* 1.3 66.1 + - - +
25A ARG 4.4 1.8 - - - +
123A ILE* 4.0 17.3 - - + -
124A GLU 4.0 4.7 - - - +
125A VAL* 4.3 1.3 - - + -
226A PHE* 3.8 25.4 - - + -
251A SER* 4.2 10.5 - - - -
253A ASP* 5.2 5.0 - - - +
256A VAL* 3.6 31.4 - - + -
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Residues in contact with LYS 24 (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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22A LYS* 4.4 18.8 - - + +
23A VAL* 1.3 81.4 - - - +
25A ARG* 1.3 79.1 + - + +
124A GLU* 2.7 57.5 + - + +
125A VAL 4.0 14.5 + - - -
126A GLU* 4.1 12.2 - - + +
171A TYR* 6.3 0.2 - - - +
253A ASP* 4.2 16.5 - - - +
255A MET* 4.9 2.6 - - - +
256A VAL* 4.8 1.4 - - - +
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Residues in contact with ARG 25 (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* 1.3 93.8 + - - +
26A PHE* 1.3 72.6 + - - +
73A ASP* 5.5 14.5 + - - +
75A ARG* 6.0 1.8 - - - +
123A ILE* 3.5 2.2 - - - -
124A GLU* 2.8 52.0 + - + +
255A MET* 5.2 9.4 - - + +
256A VAL* 3.8 18.2 - - - +
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Residues in contact with PHE 26 (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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25A ARG* 1.3 88.1 + - - +
27A HIS* 1.3 60.7 + - - +
28A HIS 5.0 1.6 - - - +
29A ILE* 5.2 0.7 - - + -
73A ASP 5.4 2.9 - - - +
75A ARG* 4.8 2.8 + - - -
121A VAL* 3.9 22.2 - - + -
122A ALA 3.8 7.0 - - - +
123A ILE* 3.9 13.2 - - + -
202A ARG* 5.4 0.4 - - - -
203A LEU* 3.4 54.1 - - + +
204A ASP 3.8 17.3 - - - -
206A ALA* 4.3 5.4 - - + -
255A MET 3.9 8.3 - - - -
256A VAL* 3.8 13.2 - - + +
257A LEU 3.5 41.5 - - - -
258A LEU* 4.0 8.5 - - + -
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Residues in contact with HIS 27 (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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25A ARG 3.4 0.6 + - - -
26A PHE* 1.3 75.9 - - - +
28A HIS* 1.3 94.1 + + - +
73A ASP 4.7 1.4 - - - +
75A ARG* 2.9 51.0 + - - +
122A ALA* 2.8 20.5 + - + +
123A ILE 4.0 1.1 - - - -
124A GLU* 3.8 29.8 - - + +
169A VAL* 4.2 12.9 - - + +
171A TYR* 2.7 43.2 + + - -
181A PHE* 3.6 21.5 - + - -
182A LEU* 4.9 1.8 - - + -
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Residues in contact with HIS 28 (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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26A PHE* 5.0 1.1 - - - +
27A HIS* 1.3 107.6 + + - +
29A ILE* 1.3 79.4 + - - +
30A GLU* 4.3 4.7 - - + -
68A LEU* 5.3 1.1 - - + -
75A ARG* 3.5 25.4 - - + +
77A LEU* 4.5 5.0 - - + +
120A ALA 5.2 0.2 - - - -
122A ALA* 2.9 45.0 + - + +
167A ARG* 3.0 37.4 + - - -
169A VAL* 4.1 7.4 - - + -
181A PHE* 3.5 27.1 - + + -
182A LEU* 5.0 6.0 - - + +
203A LEU* 5.6 1.1 - - - +
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Residues in contact with ILE 29 (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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26A PHE* 5.2 0.4 - - + -
28A HIS* 1.3 85.4 - - - +
30A GLU* 1.3 61.3 + - - +
31A PHE* 3.9 16.8 + - + -
74A LEU* 5.4 0.9 - - + -
75A ARG 3.2 4.7 + - - +
76A PHE* 3.6 22.2 - - + -
77A LEU* 2.8 27.0 + - - +
118A VAL* 3.7 31.2 - - + -
120A ALA 3.5 1.6 - - - -
121A VAL* 3.9 28.7 - - + -
203A LEU* 3.6 33.2 - - + -
206A ALA* 4.9 0.2 - - + -
288A LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 30 (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* 4.3 1.7 - - + -
29A ILE* 1.3 74.0 - - - +
31A PHE* 1.3 66.2 + - - +
32A TRP* 3.5 17.4 + - + -
77A LEU* 3.4 26.2 - - + +
79A THR* 2.7 31.5 + - - +
99A ILE* 4.0 8.1 - - - +
102A PHE* 5.4 0.7 - - - -
118A VAL* 3.4 3.6 - - - -
119A ARG* 2.7 33.7 + - + +
120A ALA* 2.9 19.7 + - + +
167A ARG* 2.7 49.8 + - - +
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Residues in contact with PHE 31 (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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29A ILE* 3.9 18.6 - - + -
30A GLU* 1.3 76.9 - - - +
32A TRP* 1.3 64.1 + - - +
33A CYS* 3.7 7.4 - - - -
43A PHE* 3.8 26.5 - + - -
76A PHE* 4.0 22.4 - + - -
77A LEU 2.8 15.1 + - - +
78A PHE* 3.8 26.9 - + + -
79A THR 3.0 25.5 + - - -
116A LEU* 4.5 12.6 - - + -
117A GLY* 3.3 23.3 - - - +
118A VAL* 4.0 11.7 - - + -
288A LEU* 3.8 21.1 - - + -
364A LEU* 4.2 8.5 - - + -
370A ILE* 4.2 12.8 - - + -
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Residues in contact with TRP 32 (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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30A GLU* 3.5 28.3 + - - -
31A PHE* 1.3 74.1 - - - +
33A CYS* 1.3 60.8 + - - +
79A THR* 3.6 9.2 - - - -
101A SER* 5.3 3.4 - - - -
102A PHE* 3.9 33.3 - + - -
103A ASP 4.5 6.5 - - - -
106A SER* 3.5 17.7 - - - -
107A CYS* 3.4 43.1 - - + +
110A PHE* 3.5 35.5 - + + -
111A PHE* 3.4 16.7 - - + -
115A GLY 4.5 0.7 - - - +
116A LEU* 3.9 1.7 - - - +
117A GLY 3.1 19.9 + - - +
119A ARG* 3.5 55.6 - - + +
167A ARG* 5.9 3.4 - - - -
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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