Contacts of the strand formed by residues 184 - 187 (chain E) in PDB entry 3V56
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 LYS 184 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E LEU* 4.9 3.4 - - - -
180E GLU* 3.6 6.6 - - - +
181E LYS* 2.9 32.9 + - + +
182E GLU* 3.8 17.3 - - + +
183E ASN* 1.3 83.0 - - - +
185E ILE* 1.3 63.6 + - - +
215E LYS* 6.4 0.7 - - + -
258E GLU* 3.4 35.4 - - + +
259E LEU 3.4 15.9 - - - +
260E GLN* 4.2 21.8 - - + +
279E PHE* 5.4 0.7 - - - -
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Residues in contact with ILE 185 (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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147E LEU* 3.8 16.4 - - + -
149E LEU* 3.7 20.2 - - + -
178E LEU* 3.6 35.0 - - + -
179E GLU 3.5 8.5 - - - +
180E GLU* 4.9 0.2 - - - +
184E LYS* 1.3 71.3 - - - +
186E LEU* 1.3 61.5 + - - +
187E VAL* 3.9 1.1 + - + +
258E GLU* 3.2 4.7 - - - -
259E LEU* 2.8 52.6 + - + +
279E PHE* 3.8 30.9 - - + -
280E GLY* 4.0 29.4 - - - -
281E ALA* 4.3 6.7 - - + +
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Residues in contact with LEU 186 (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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178E LEU* 3.6 5.9 - - - +
179E GLU* 2.7 51.8 + - + +
181E LYS* 4.0 24.9 - - + -
184E LYS 3.7 1.0 + - - -
185E ILE* 1.3 71.5 - - - +
187E VAL* 1.3 71.5 + - - +
188E LYS* 3.6 26.8 + - + -
256E GLY* 4.0 13.2 - - - +
257E ASP 3.7 11.9 - - - +
258E GLU* 3.8 22.2 - - + +
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Residues in contact with VAL 187 (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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177E ALA 3.8 2.7 - - - -
178E LEU* 4.3 12.6 - - + -
185E ILE 4.7 1.3 - - - +
186E LEU* 1.3 75.2 - - - +
188E LYS* 1.3 60.6 + - - +
189E GLU 3.2 24.7 - - - +
193E PHE* 3.9 17.0 - - + -
253E LEU* 3.8 30.1 - - + -
254E GLU 3.6 22.0 - - - +
255E GLU* 4.4 0.2 - - - +
256E GLY* 2.9 28.2 + - - -
257E ASP* 2.9 25.3 + - + +
259E LEU* 4.7 9.4 - - + -
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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