Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 5DVX
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 LEU 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B LEU* 3.9 26.5 - - + -
191B PRO 3.7 5.8 - - - +
192B GLU* 1.3 80.3 - - - +
194B ARG* 1.3 63.5 + - - +
195B LEU 3.5 0.7 + - - -
204B LEU* 3.7 34.8 - - + -
205B THR 3.5 20.2 - - - +
206B LEU* 4.1 7.0 - - + -
207B PRO* 4.2 9.4 - - + -
307B GLN* 3.3 6.9 - - - -
308B VAL* 2.7 38.5 + - + +
309B PRO 4.4 0.4 - - - -
310B GLY* 3.5 29.4 - - - +
311B LEU* 4.5 4.0 - - + -
313B ILE* 4.5 2.9 - - + -
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Residues in contact with ARG 194 (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 GLU* 4.4 14.3 + - - -
193B LEU* 1.3 70.5 - - - +
195B LEU* 1.3 65.7 + - - +
196B ARG* 3.3 30.2 - - + +
203B GLN 3.6 1.0 - - - +
204B LEU* 3.4 5.8 - - - +
205B THR* 2.9 54.0 + - + +
305B GLU* 2.4 47.5 + - + +
306B THR 3.7 0.7 - - - -
307B GLN* 3.7 20.3 + - - +
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Residues in contact with LEU 195 (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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193B LEU 3.5 0.2 + - - -
194B ARG* 1.3 72.9 - - - +
196B ARG* 1.3 59.9 + - - +
202B VAL* 3.5 27.1 - - + -
203B GLN 3.5 7.9 - - - +
204B LEU* 3.9 25.8 - - + -
292B LEU* 4.2 27.8 - - + +
295B ARG* 4.2 24.0 - - + -
296B LEU* 4.6 2.9 - - + -
299B ILE* 3.9 19.6 - - + +
305B GLU* 3.2 3.4 - - - -
306B THR* 2.8 41.9 + - + +
308B VAL* 4.2 16.8 - - + -
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Residues in contact with ARG 196 (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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245A ARG 5.7 2.6 + - - -
194B ARG* 3.3 41.1 - - + +
195B LEU* 1.3 74.9 - - - +
197B ASN* 1.3 68.7 + - - +
198B ASN* 3.4 33.3 + - + +
202B VAL* 3.3 3.3 - - - -
203B GLN* 2.9 44.5 + - + +
299B ILE* 4.2 4.9 - - - -
302B GLU* 5.3 2.8 + - - -
303B GLY* 4.2 19.2 + - - -
304B SER 3.6 10.5 - - - +
305B GLU* 3.9 10.7 + - + -
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Residues in contact with ASN 197 (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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196B ARG* 1.3 73.1 - - - +
198B ASN* 1.3 56.8 + - - +
199B GLY* 2.9 18.5 + - - -
201B SER 3.8 3.8 - - - -
202B VAL* 4.6 1.3 - - - +
299B ILE* 3.1 28.6 + - + +
300B ALA 3.1 20.6 + - - -
301B GLU 3.3 9.6 + - - +
302B GLU* 4.0 2.0 - - - -
303B GLY* 2.8 32.9 + - - -
304B SER 2.9 12.8 + - - +
363B LEU* 3.9 13.7 - - + +
364B TRP 3.0 20.5 + - - -
371B LEU* 3.5 15.5 - - - +
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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