Contacts of the strand formed by residues 258 - 267 (chain B) in PDB entry 3IO6
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 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU 3.8 7.3 - - - +
112B ALA* 3.9 13.3 - - - +
113B LEU* 4.5 1.9 + - - +
155B TYR* 3.7 35.2 + + + -
158B TRP* 3.1 47.8 - + + -
159B PRO* 5.1 1.2 - - - +
168B ALA* 4.4 0.4 - - + -
257B PRO* 1.3 77.2 - - - +
259B VAL* 1.3 59.9 + - - +
328B GLU* 3.5 35.2 - - + -
330B MET* 3.6 31.0 - - + -
331B PRO* 3.9 14.4 - - + -
336B MET* 4.0 4.3 - - + -
339B PHE* 4.0 17.3 - + - -
340B TRP* 3.3 28.9 - + - -
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.3 14.9 + - - -
92B PHE* 4.3 7.6 - - + -
110B VAL* 3.7 30.1 - - + -
111B GLU 3.5 4.0 - - - +
112B ALA* 5.1 0.2 - - + -
257B PRO 4.2 1.8 - - - +
258B PHE* 1.3 76.0 - - - +
260B GLY* 1.3 62.1 + - - +
261B VAL* 4.0 14.8 - - + -
324B ALA* 3.4 33.9 - - + +
327B GLY 4.1 4.3 - - - +
328B GLU 3.1 24.2 + - - +
329B ILE* 4.0 14.4 - - + +
330B MET* 3.3 18.8 + - - +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 5.5 6.5 - - - -
64B HIS* 3.8 5.4 - - - -
65B ASP* 5.6 2.5 - - - -
109B ALA 3.9 0.7 - - - +
110B VAL* 3.7 1.0 - - - -
111B GLU* 2.8 50.8 + - - +
155B TYR* 5.5 1.8 + - - -
258B PHE 4.1 0.4 + - - -
259B VAL* 1.3 72.5 - - - +
261B VAL* 1.3 63.3 + - - -
262B LEU 3.9 1.1 + - - -
330B MET* 5.5 5.6 - - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.2 2.2 - - - +
64B HIS* 2.7 47.5 + - + -
92B PHE* 5.3 1.1 - - + -
93B THR* 4.8 10.5 - - + +
96B ALA* 3.7 24.5 - - + -
97B VAL* 4.9 0.9 - - + -
107B PRO* 4.0 24.7 - - + -
108B ILE 4.5 0.4 - - - +
109B ALA 3.3 10.1 - - - +
110B VAL* 4.4 12.1 - - + -
259B VAL* 4.0 19.1 - - + -
260B GLY* 1.3 74.8 - - - +
262B LEU* 1.3 75.1 + - - +
263B SER* 3.2 6.6 + - - +
329B ILE* 5.8 0.2 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 5.1 4.9 - - + -
15B LYS* 4.3 32.5 - - + +
61B PHE* 3.9 19.7 - - + +
62B TRP* 3.6 31.9 - - - +
63B ALA* 4.2 5.3 - - - +
108B ILE* 2.7 42.4 + - + -
109B ALA* 2.8 33.1 + - + +
260B GLY 3.9 2.4 + - - -
261B VAL* 1.3 74.0 - - - +
263B SER* 1.3 61.0 + - - +
299B LEU* 4.6 9.9 - - + -
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 3.6 2.8 - - - -
62B TRP 3.1 30.1 + - - +
64B HIS* 3.5 15.8 - - - +
67B PHE* 3.3 16.0 - - - -
97B VAL* 3.6 22.6 - - - +
105B ALA* 4.1 3.1 - - - -
106B TYR 3.1 15.9 - - - -
107B PRO* 3.8 2.5 - - - -
108B ILE* 4.0 4.7 - - - -
261B VAL* 3.2 14.2 + - - -
262B LEU* 1.3 76.7 - - - +
264B ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 3.8 9.4 - - + -
60B ILE 3.2 5.6 - - - +
61B PHE* 3.6 34.1 - - + -
105B ALA* 3.3 2.1 - - - -
106B TYR* 2.6 47.4 + - + +
108B ILE* 4.1 1.5 - - + +
263B SER* 1.3 72.8 - - - +
265B GLY* 1.3 58.4 + - - +
280B LEU* 3.7 18.6 - - + -
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 3.4 8.1 - - - +
60B ILE* 3.1 36.1 + - - -
67B PHE* 3.8 11.0 - - - -
76B LEU* 4.7 4.7 - - - -
79B ILE* 5.6 0.2 - - - -
104B ILE 3.7 17.9 - - - -
105B ALA* 3.9 4.0 - - - -
264B ALA* 1.3 75.4 - - - +
266B ILE* 1.3 64.4 + - - -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP 3.4 10.3 - - - +
59B ILE* 4.7 0.4 - - + -
76B LEU* 3.4 7.2 - - - +
77B ALA* 2.8 39.6 + - + +
78B GLU 5.8 0.9 - - - +
79B ILE* 4.0 25.0 - - + +
104B ILE 4.3 4.4 + - - -
106B TYR* 4.2 10.3 - - + -
265B GLY* 1.3 76.0 - - - +
267B ASN* 1.3 67.4 + - - +
270B SER* 4.5 4.0 - - - +
273B LYS* 3.9 26.9 - - + +
276B ALA* 3.8 33.4 - - + -
277B LYS* 4.1 13.9 - - + +
280B LEU* 4.3 9.4 - - + -
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Residues in contact with ASN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 4.0 6.3 - - - -
47B PHE* 3.6 25.6 - - + -
51B ALA* 3.6 11.2 - - - +
55B ASP 3.4 20.4 + - - -
57B PRO* 3.4 27.6 + - - +
58B ASP 3.0 11.7 + - - +
60B ILE* 5.6 1.2 - - - +
75B LEU 3.6 10.2 - - - +
76B LEU* 5.0 0.2 - - - +
77B ALA* 3.8 4.6 - - - +
265B GLY 4.2 0.6 + - - -
266B ILE* 1.3 79.7 - - - +
268B ALA* 1.3 66.2 + - - +
269B ALA* 2.7 34.3 + - - +
270B SER* 3.4 20.5 + - - -
273B LYS* 4.2 2.6 - - - +
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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