Contacts of the strand formed by residues 145 - 152 (chain J) in PDB entry 1XFB
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 145 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J ILE* 3.6 30.1 - - + -
30J ILE* 4.4 7.4 - - + -
76J GLY* 4.3 5.6 - - - -
77J VAL 3.7 22.2 - - - -
78J ILE* 3.6 19.5 - - + -
104J VAL* 3.6 20.6 - - + -
105J VAL 3.2 20.4 - - - -
106J GLY* 2.9 42.9 - - - -
107J ILE* 3.2 9.0 + - - +
143J ALA 3.7 0.4 - - - -
144J ASP* 1.3 80.9 - - - +
146J ALA* 1.3 62.2 + - - +
183J ILE* 3.7 6.4 - - - +
184J VAL* 2.9 20.9 - - + +
186J ILE* 3.6 35.0 - - + -
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Residues in contact with ALA 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J ILE* 3.2 17.9 - - + +
109J VAL* 3.9 17.7 - - + -
135J CYS* 5.7 0.2 - - - -
145J PHE* 1.3 77.6 - - - +
147J LYS* 1.3 60.8 + - - +
174J TYR* 3.2 10.1 - - + +
178J CYS* 4.1 11.2 - - - -
183J ILE* 3.7 15.0 - - + +
184J VAL 2.8 7.3 + - - -
186J ILE* 2.8 32.1 + - - +
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Residues in contact with LYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ALA* 5.1 0.6 - - - +
34J ASP* 3.2 32.9 + - - +
78J ILE* 4.0 28.0 - - + -
107J ILE 3.0 5.1 + - - -
108J LYS* 3.4 11.9 - - + +
109J VAL* 3.0 27.4 + - - +
110J ASP* 3.9 2.0 + - - +
146J ALA* 1.3 77.8 - - - +
148J TRP* 1.3 63.2 + - - +
149J ARG* 4.2 16.6 - - - +
174J TYR* 3.3 4.5 - - - -
186J ILE* 4.0 9.2 - - + +
188J GLU* 2.8 28.8 + - - +
230J LYS* 3.0 31.9 - - + +
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Residues in contact with TRP 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 4.0 3.1 - - + -
110J ASP* 3.6 23.1 - - + -
125J THR* 3.3 36.3 - - + -
126J GLN 3.5 0.4 - - - -
127J GLY* 3.4 28.3 - - - -
128J LEU* 3.4 39.0 - - + -
131J LEU* 4.4 4.9 - - + -
147J LYS* 1.3 75.2 - - - +
149J ARG* 1.3 64.1 + - - +
150J CYS* 3.6 12.9 - - - -
170J VAL* 3.3 25.7 - - + +
171J LEU* 3.6 18.5 - - + +
174J TYR* 3.3 49.9 + + + -
186J ILE 3.7 1.6 + - - -
188J GLU* 3.3 25.1 + - - +
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Residues in contact with ARG 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J LYS* 5.7 2.5 - - - +
110J ASP* 3.2 18.4 + - - +
112J GLY 5.7 0.2 - - - -
113J VAL* 5.6 1.9 + - - +
125J THR* 2.8 21.7 + - - +
147J LYS* 4.2 11.0 - - - +
148J TRP* 1.3 75.8 - - - +
150J CYS* 1.3 69.1 + - - +
151J VAL* 3.4 31.6 + - + +
188J GLU* 3.3 33.0 - - + +
190J GLU* 2.4 44.3 + - - +
192J LEU* 4.3 6.9 - - - +
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Residues in contact with CYS 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J THR* 3.3 10.5 - - - -
148J TRP* 3.6 23.7 + - - -
149J ARG* 1.3 78.0 - - - +
151J VAL* 1.3 67.4 + - - +
152J LEU* 5.6 2.2 - - + -
167J ASN* 3.3 36.1 - - + +
170J VAL* 4.6 3.1 - - - -
171J LEU* 3.6 26.2 - - + -
188J GLU 3.0 12.5 + - - +
189J PRO* 4.5 6.1 - - + -
190J GLU* 3.2 21.5 + - - +
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Residues in contact with VAL 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J VAL* 4.7 13.6 - - + +
123J THR* 3.5 30.8 + - - +
124J THR 5.9 0.2 - - - -
125J THR* 4.5 1.4 + - - -
149J ARG* 3.4 39.9 - - + +
150J CYS* 1.3 81.8 - - - +
152J LEU* 1.3 73.1 + - - +
153J LYS* 5.9 0.2 - - + -
167J ASN* 4.2 3.3 + - - +
190J GLU 3.4 4.0 - - - +
192J LEU* 3.5 40.2 - - + -
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Residues in contact with LEU 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J GLU* 5.5 1.3 - - - +
123J THR 5.2 0.2 - - - +
150J CYS* 5.6 2.0 - - + -
151J VAL* 1.3 78.9 - - - +
153J LYS* 1.3 59.7 + - - +
159J PRO* 5.0 9.6 - - + -
163J ALA* 3.8 18.8 - - + +
164J ILE* 4.6 12.3 - - + -
167J ASN* 3.5 34.1 - - + +
189J PRO* 5.6 5.2 - - + -
190J GLU 2.8 12.8 + - - +
191J ILE* 4.2 13.2 - - + -
192J LEU* 2.9 31.1 + - - +
209J VAL* 3.3 46.7 - - + -
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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