Contacts of the strand formed by residues 277 - 281 (chain F) in PDB entry 2CNW
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 ILE 277 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F LEU* 4.9 5.9 + - + +
252F VAL* 3.6 22.4 - - + +
254F VAL* 4.3 12.8 - - + -
266F LEU* 3.6 29.6 - - + -
269F ILE* 5.3 1.1 - - + -
270F VAL* 3.5 31.0 - - + -
275F VAL 4.2 2.0 - - - +
276F PRO* 1.3 73.5 - - - +
278F LYS* 1.3 60.6 + - - +
279F PHE 4.2 9.0 - - - +
292F PHE* 3.2 65.8 - - + +
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Residues in contact with LYS 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL* 4.2 26.2 - - + +
99F GLU 5.3 4.8 + - - -
223F GLU* 4.3 8.3 + - - -
225F TRP* 3.8 29.1 - - + +
250F THR 3.4 21.3 + - - -
251F GLY* 3.9 11.9 - - - -
252F VAL 2.8 13.8 + - - +
253F ILE* 4.4 4.9 - - + -
276F PRO* 3.8 25.9 - - + +
277F ILE* 1.3 75.1 - - - +
279F PHE* 1.3 79.6 + - + +
291F PRO* 3.9 3.3 - - - +
292F PHE 3.3 15.8 + - - -
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Residues in contact with PHE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F VAL* 3.6 25.8 - - + -
122F LEU* 3.7 10.1 - - + -
125F TYR* 3.8 34.3 - + - -
126F TYR* 3.5 17.7 - - - -
225F TRP* 3.6 28.5 - + - -
252F VAL 3.8 3.0 + - - +
253F ILE* 3.6 26.2 - - + -
254F VAL* 3.3 23.0 + - - +
277F ILE* 3.8 2.1 - - - +
278F LYS* 1.3 88.1 - - + +
280F VAL* 1.3 67.8 + - - +
289F LEU* 3.8 29.4 - - + -
290F GLN 3.4 17.5 - - - +
291F PRO* 4.2 1.1 - - + -
292F PHE* 4.1 2.9 - - - +
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ILE* 4.9 0.2 - - - -
254F VAL* 3.3 23.3 - - + +
257F LEU* 3.5 42.2 - - + -
279F PHE* 1.3 75.8 - - - +
281F GLY* 1.3 65.3 + - - +
282F VAL* 3.8 12.8 + - + +
289F LEU* 3.4 9.1 - - - +
290F GLN* 2.7 45.8 + - + +
291F PRO 5.0 0.9 - - - +
292F PHE* 3.8 28.0 - - + -
293F ASP 5.6 0.4 - - - +
297F PHE* 5.6 0.2 - - + -
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Residues in contact with GLY 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F THR* 6.1 0.2 - - - -
121F LYS* 3.9 6.1 - - - -
253F ILE* 4.8 1.8 - - - +
254F VAL 2.7 15.4 + - - -
255F THR* 3.9 7.6 - - - -
256F LYS 3.3 0.9 + - - -
257F LEU 3.1 25.5 + - - -
280F VAL* 1.3 73.8 - - - +
282F VAL* 1.3 63.2 + - - +
288F ASP 3.5 6.7 - - - -
289F LEU* 4.5 6.0 - - - +
1001F GDP 3.0 17.4 - - - +
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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
------------------------------------------------------------
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