Contacts of the strand formed by residues 277 - 281 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E LEU* 4.0 16.8 + - + +
252E VAL* 3.5 14.6 - - + +
254E VAL* 4.6 4.0 - - + -
266E LEU* 3.7 37.9 - - + -
270E VAL* 3.5 28.5 - - + +
275E VAL 4.5 0.2 - - - +
276E PRO* 1.3 73.2 - - - +
278E LYS* 1.3 61.4 + - - +
279E PHE 4.2 9.9 - - - +
292E PHE* 3.5 67.2 - - + +
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Residues in contact with LYS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E VAL* 3.8 32.7 - - + +
99E GLU 5.4 2.6 + - - -
223E GLU* 4.3 12.6 + - - -
225E TRP* 3.8 24.7 - - + +
250E THR 3.4 24.2 + - - -
251E GLY* 3.9 16.8 - - - -
252E VAL 2.9 14.0 + - - +
253E ILE* 4.4 3.6 - - + -
276E PRO* 4.1 14.8 - - + +
277E ILE* 1.3 76.1 - - - +
279E PHE* 1.3 80.9 + - + +
291E PRO* 3.7 3.8 - - - +
292E PHE* 3.1 19.8 + - - +
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Residues in contact with PHE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E VAL* 3.7 24.2 - - + -
122E LEU* 3.6 24.5 - - + -
125E TYR* 4.0 27.4 - + - -
126E TYR* 3.8 13.5 - - - -
225E TRP* 3.9 18.8 - + - -
252E VAL 3.8 3.0 + - - +
253E ILE* 3.4 24.4 - - + +
254E VAL* 3.1 24.8 + - - +
277E ILE* 4.2 3.1 - - - +
278E LYS* 1.3 92.5 - - + +
280E VAL* 1.3 64.9 + - - +
289E LEU* 3.6 33.0 - - + -
290E GLN 3.4 15.7 - - - +
291E PRO* 3.8 6.3 - - + -
292E PHE 4.1 1.6 - - - +
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Residues in contact with VAL 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E ILE* 4.9 0.4 - - - -
254E VAL* 3.3 15.7 - - + -
257E LEU* 3.5 31.0 - - + -
279E PHE* 1.3 75.2 - - - +
281E GLY* 1.3 60.3 + - - +
282E VAL* 4.1 8.4 + - + +
289E LEU* 3.5 8.8 - - - +
290E GLN* 2.9 65.4 + - + +
291E PRO 4.7 3.8 - - - +
292E PHE* 3.8 25.6 - - + -
293E ASP 5.8 0.7 - - - +
297E PHE* 5.4 0.4 - - + -
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Residues in contact with GLY 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E THR* 6.0 0.4 - - - -
121E LYS* 3.7 6.1 - - - -
253E ILE* 4.7 1.6 - - - +
254E VAL 2.7 14.9 + - - -
255E THR* 4.2 7.4 - - - -
256E LYS 3.2 2.1 + - - -
257E LEU* 3.0 27.2 + - - +
280E VAL* 1.3 73.4 - - - +
282E VAL* 1.3 63.0 + - - +
288E ASP 3.6 7.4 - - - -
289E LEU* 4.6 5.8 - - - +
1001E GDP 3.0 14.6 - - - -
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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