Contacts of the strand formed by residues 145 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.6 30.5 - - + -
30A ILE* 4.4 7.0 - - + -
76A GLY* 4.3 5.8 - - - -
77A VAL 3.7 22.7 - - - -
78A ILE* 3.6 19.7 - - + -
104A VAL* 3.6 21.8 - - + -
105A VAL 3.2 20.2 - - - -
106A GLY* 2.9 42.4 - - - -
107A ILE* 3.2 8.7 + - - +
143A ALA 3.7 0.2 - - - -
144A ASP* 1.3 82.5 - - - +
146A ALA* 1.3 62.1 + - - +
183A ILE* 3.7 5.5 - - - +
184A VAL* 2.9 22.0 - - + +
186A ILE* 3.6 35.0 - - + -
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Residues in contact with ALA 146 (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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78A ILE* 5.8 0.2 - - - -
107A ILE* 3.2 17.7 - - + +
109A VAL* 3.9 17.5 - - + -
135A CYS* 5.7 0.2 - - - -
145A PHE* 1.3 79.6 - - - +
147A LYS* 1.3 61.4 + - - +
174A TYR* 3.2 10.1 - - + +
178A CYS* 4.1 11.0 - - - -
183A ILE* 3.7 15.5 - - + +
184A VAL 2.8 7.4 + - - +
186A ILE* 2.8 32.1 + - - +
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Residues in contact with LYS 147 (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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32A ALA* 5.1 0.8 - - - +
34A ASP* 3.2 33.4 + - - +
78A ILE* 4.0 28.3 - - + -
107A ILE 3.0 5.1 + - - -
108A LYS* 3.4 12.2 - - + +
109A VAL* 3.0 27.0 + - - +
110A ASP* 3.9 1.7 + - - +
146A ALA* 1.3 77.5 - - - +
148A TRP* 1.3 64.3 + - - +
149A ARG* 4.2 16.2 - - - +
174A TYR* 3.3 4.5 - - - -
186A ILE* 4.0 8.7 - - + +
188A GLU* 2.8 29.7 + - + +
230A LYS* 3.0 32.1 - - + +
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Residues in contact with TRP 148 (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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109A VAL* 4.0 3.1 - - + -
110A ASP* 3.6 22.4 - - + -
125A THR* 3.3 35.7 - - + -
126A GLN 3.5 0.7 - - - -
127A GLY* 3.4 27.6 - - - -
128A LEU* 3.4 39.7 - - + -
131A LEU* 4.4 4.7 - - + -
147A LYS* 1.3 75.5 - - - +
149A ARG* 1.3 63.5 + - - +
150A CYS* 3.6 12.8 - - - -
170A VAL* 3.3 26.8 - - + +
171A LEU* 3.6 18.9 - - + +
174A TYR* 3.3 50.8 + + + -
186A ILE 3.7 1.6 + - - -
188A GLU* 3.3 24.9 + - - +
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Residues in contact with ARG 149 (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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108A LYS* 5.7 2.9 - - - +
110A ASP* 3.2 17.7 + - - +
113A VAL* 5.6 2.3 + - - +
125A THR* 2.8 22.0 + - - +
147A LYS* 4.2 11.8 - - - +
148A TRP* 1.3 77.1 - - - +
150A CYS* 1.3 69.5 + - - +
151A VAL* 3.4 32.1 - - + +
188A GLU* 3.3 34.1 - - + +
190A GLU* 2.4 43.6 + - - +
192A LEU* 4.3 7.3 - - - +
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Residues in contact with CYS 150 (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 THR* 3.3 9.9 - - - -
148A TRP* 3.6 24.4 + - - -
149A ARG* 1.3 78.6 - - - +
151A VAL* 1.3 64.9 + - - +
152A LEU* 5.6 1.8 - - + -
167A ASN* 3.3 36.8 - - + +
170A VAL* 4.6 2.5 - - - -
171A LEU* 3.6 25.8 - - + -
188A GLU 3.0 12.7 + - - +
189A PRO* 4.5 6.5 - - + -
190A GLU* 3.2 22.0 + - - +
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Residues in contact with VAL 151 (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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113A VAL* 4.7 13.3 - - + +
123A THR* 3.5 30.2 + - - +
124A THR 5.9 0.2 - - - -
125A THR* 4.5 1.4 + - - -
149A ARG* 3.4 40.2 - - + +
150A CYS* 1.3 83.0 - - - +
152A LEU* 1.3 72.4 + - - +
153A LYS* 5.9 0.2 - - + -
167A ASN* 4.2 2.9 + - - +
190A GLU 3.4 3.1 - - - +
192A LEU* 3.5 40.6 - - + -
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Residues in contact with LEU 152 (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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122A GLU* 5.5 0.7 - - - +
123A THR 5.2 0.2 - - - +
150A CYS* 5.6 1.8 - - + -
151A VAL* 1.3 80.6 - - - +
153A LYS* 1.3 61.1 + - - +
159A PRO* 5.0 9.9 - - + -
163A ALA* 3.8 18.8 - - + +
164A ILE* 4.6 13.0 - - + -
167A ASN* 3.5 35.4 - - + +
189A PRO* 5.6 5.4 - - + -
190A GLU 2.8 12.3 + - - +
191A ILE* 4.2 12.8 - - + -
192A LEU* 2.9 31.7 + - - +
209A VAL* 3.3 46.2 - - + -
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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