Contacts of the strand formed by residues 145 - 152 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ILE* 3.6 30.7 - - + -
30G ILE* 4.4 7.2 - - + -
76G GLY* 4.3 5.4 - - - -
77G VAL 3.7 23.1 - - - -
78G ILE* 3.6 20.2 - - + -
104G VAL* 3.6 21.5 - - + -
105G VAL 3.2 20.2 - - - -
106G GLY* 2.9 42.0 - - - -
107G ILE* 3.2 8.5 + - - +
143G ALA 3.7 0.4 - - - -
144G ASP* 1.3 82.2 - - - +
146G ALA* 1.3 63.5 + - - +
183G ILE* 3.7 4.9 - - - +
184G VAL* 2.9 22.2 - - + +
186G ILE* 3.6 34.8 - - + -
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G ILE* 5.8 0.2 - - - -
107G ILE* 3.2 17.9 - - + +
109G VAL* 3.9 17.5 - - + -
135G CYS* 5.7 0.4 - - - -
145G PHE* 1.3 79.1 - - - +
147G LYS* 1.3 61.2 + - - +
174G TYR* 3.2 11.2 - - + +
178G CYS* 4.1 10.8 - - - -
183G ILE* 3.9 14.8 - - + -
184G VAL 2.8 7.3 + - - -
186G ILE* 2.8 31.5 + - - +
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Residues in contact with LYS 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ALA* 5.1 0.4 - - - +
34G ASP* 3.2 32.6 + - - +
78G ILE* 4.0 27.6 - - + -
107G ILE 3.0 5.3 + - - -
108G LYS* 3.4 12.1 - - - +
109G VAL* 3.0 27.5 + - - +
110G ASP* 3.9 2.0 + - - +
146G ALA* 1.3 76.3 - - - +
148G TRP* 1.3 64.4 + - - +
149G ARG* 4.2 16.2 - - - +
174G TYR* 3.3 4.3 - - - -
186G ILE* 4.0 9.4 - - + +
188G GLU* 2.8 29.9 + - + +
230G LYS* 3.0 32.9 - - + +
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Residues in contact with TRP 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G VAL* 4.0 2.7 - - + -
110G ASP* 3.6 23.1 - - + -
125G THR* 3.3 36.8 - - + -
126G GLN 3.5 0.9 - - - -
127G GLY* 3.4 28.3 - - - -
128G LEU* 3.4 38.6 - - + -
131G LEU* 4.4 5.4 - - + -
147G LYS* 1.3 75.2 - - - +
149G ARG* 1.3 64.2 + - - +
150G CYS* 3.6 13.1 - - - -
170G VAL* 3.3 26.2 - - + +
171G LEU* 3.6 18.5 - - + +
174G TYR* 3.3 49.7 + + + -
186G ILE 3.7 2.2 + - - -
188G GLU* 3.3 25.1 + - - +
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Residues in contact with ARG 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G LYS* 5.7 2.7 - - - +
110G ASP* 3.2 17.8 + - - +
113G VAL* 5.6 2.3 + - - +
125G THR* 2.8 20.9 + - - +
147G LYS* 4.2 12.3 - - - +
148G TRP* 1.3 76.4 - - - +
150G CYS* 1.3 69.4 + - - +
151G VAL* 3.4 31.0 - - + +
188G GLU* 3.3 34.1 - - + +
190G GLU* 2.4 43.7 + - - +
192G LEU* 4.3 7.5 - - - +
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Residues in contact with CYS 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G THR* 3.3 9.4 - - - -
148G TRP* 3.6 23.3 + - - -
149G ARG* 1.3 78.3 - - - +
151G VAL* 1.3 66.3 + - - +
152G LEU* 5.6 2.2 - - + -
167G ASN* 3.3 35.2 - - + +
170G VAL* 4.6 3.4 - - - -
171G LEU* 3.6 26.5 - - + -
188G GLU 3.0 12.7 + - - +
189G PRO* 4.5 6.5 - - + -
190G GLU* 3.2 21.7 + - - +
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Residues in contact with VAL 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G VAL* 4.7 13.6 - - + +
123G THR* 3.5 30.9 + - - +
124G THR 5.9 0.2 - - - -
125G THR* 4.5 1.6 + - - -
149G ARG* 3.4 40.2 - - + +
150G CYS* 1.3 82.4 - - - +
152G LEU* 1.3 72.6 + - - +
153G LYS* 5.9 0.2 - - + -
167G ASN* 4.2 2.9 + - - +
190G GLU 3.4 3.4 - - - +
192G LEU* 3.5 40.6 - - + -
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Residues in contact with LEU 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLU* 5.5 0.4 - - - +
123G THR 5.2 0.2 - - - +
150G CYS* 5.6 1.6 - - + -
151G VAL* 1.3 81.7 - - - +
153G LYS* 1.3 61.9 + - - +
159G PRO* 5.0 9.2 - - + -
163G ALA* 3.8 18.8 - - + +
164G ILE* 4.6 12.8 - - + -
167G ASN* 3.5 35.2 - - + +
189G PRO* 5.6 5.4 - - + -
190G GLU 2.8 12.6 + - - +
191G ILE* 4.2 12.6 - - + -
192G LEU* 2.9 31.3 + - - +
209G VAL* 3.3 46.4 - - + -
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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