Contacts of the strand formed by residues 274 - 279 (chain B) in PDB entry 1D0G
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A MET* 3.7 24.2 - - + -
245A GLY 3.0 29.4 - - - -
248A PHE* 5.3 0.7 - + - -
125B HIS* 3.4 30.7 - + + +
126B ILE 3.4 13.7 - - - +
127B THR* 3.8 3.6 - - + -
154B TRP* 3.6 7.4 - - - -
185B TYR* 3.7 17.7 - + - -
186B SER* 2.8 20.6 + - - -
187B GLN* 2.9 50.9 + - + +
243B TYR* 4.7 0.4 - + - -
270B HIS 3.8 12.6 - - - -
271B GLU* 3.7 20.0 - - - -
273B SER* 1.3 80.3 - - - +
275B PHE* 1.3 61.3 - - - +
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Residues in contact with PHE 275 (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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125B HIS* 3.6 1.1 - - - -
126B ILE* 2.8 50.3 + - + +
154B TRP* 3.5 35.7 - - + -
172B GLY 4.6 2.7 - - - -
174B LEU* 3.7 24.0 - - + +
184B ILE* 4.1 20.2 - - + -
185B TYR* 3.3 21.3 - - - -
186B SER* 4.3 0.4 - - - -
210B ILE* 4.7 4.5 - - + -
256B ILE* 3.6 38.8 - - + -
257B PHE* 3.8 14.1 - - - -
258B VAL* 3.5 18.6 - - + -
274B PHE* 1.3 80.5 - - - +
276B GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 276 (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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124B ALA 3.1 14.8 - - - -
174B LEU* 4.5 7.0 - - - -
184B ILE* 3.6 4.0 - - - +
185B TYR* 2.9 52.4 + - - +
275B PHE* 1.3 78.1 - - - +
277B ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 277 (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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247A ILE* 3.6 1.4 - - - +
123B ALA* 3.2 1.1 - - - -
124B ALA* 2.9 33.6 + - - +
167B LEU* 4.9 11.2 - - + -
174B LEU* 5.0 1.1 - - + -
182B TYR* 4.4 12.6 - - + -
183B TYR 3.2 14.4 - - - +
184B ILE* 4.1 15.5 - - + -
185B TYR* 3.7 4.0 - - - -
256B ILE* 4.3 14.8 - - + -
276B GLY* 1.3 75.5 - - - +
278B PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.8 20.2 - + - -
247A ILE* 3.4 21.5 - - + -
278A PHE* 4.0 9.2 - + - -
280A VAL* 3.9 30.5 - - + -
281A GLY 5.5 1.1 - - - +
122B VAL 3.5 6.3 - - - +
123B ALA* 3.7 17.5 - - + +
182B TYR* 3.4 7.4 - - - -
183B TYR* 3.0 59.3 + + + -
185B TYR* 4.5 2.0 - + - -
277B ALA* 1.3 78.8 - - - +
279B LEU* 1.3 70.8 + - - +
280B VAL* 3.1 25.8 - - + -
278D PHE* 3.9 18.2 - + - -
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Residues in contact with LEU 279 (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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281A GLY 4.3 16.6 + - - +
122B VAL* 3.0 40.9 + - + +
178B GLU* 3.7 21.8 - - - +
179B LYS 4.5 1.8 - - - +
180B GLY* 4.1 14.6 - - - -
181B PHE 3.4 17.7 - - - +
182B TYR* 3.5 30.6 - - + +
278B PHE* 1.3 78.4 - - - +
280B VAL* 1.3 59.7 + - - +
281B GLY* 3.4 13.9 - - - +
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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