Contacts of the strand formed by residues 212 - 217 (chain L) in PDB entry 5DSV
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 GLU 212 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L GLY* 3.3 5.0 - - - -
49L VAL* 3.1 38.3 + - + +
51L LYS* 3.4 40.4 - - + +
64L LYS* 3.2 31.4 - - - +
65L ARG* 3.0 28.3 + - - +
66L LEU* 3.7 24.5 + - + +
210L GLU* 5.6 1.1 - - - +
211L LEU* 1.3 72.4 - - - +
213L LEU* 1.3 67.8 + - - +
226L ILE* 4.6 9.5 - - + +
232L ARG* 5.3 0.9 - - - +
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Residues in contact with LEU 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L VAL* 5.2 1.3 - - + -
47L PHE 3.4 13.9 - - - +
48L GLY* 3.7 9.9 - - - -
66L LEU* 3.6 5.7 - - - +
190L VAL* 4.0 26.5 - - + +
193L VAL* 4.0 16.8 - - + -
194L ALA* 5.0 3.8 - - + -
211L LEU* 4.0 27.3 + - + -
212L GLU* 1.3 85.2 - - - +
214L SER* 1.3 60.5 + - - +
226L ILE* 3.3 14.9 - - - +
227L VAL* 3.1 35.2 + - + -
232L ARG* 4.1 37.8 - - + +
235L ALA* 5.2 0.9 - - + -
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Residues in contact with SER 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L VAL* 3.3 17.3 - - - +
47L PHE* 2.9 49.9 + - - -
66L LEU* 3.9 13.5 - - - +
213L LEU* 1.3 76.1 + - - +
215L TRP* 1.3 57.9 + - - +
224L HIS* 2.5 38.2 + - - -
225L GLU 3.8 3.2 + - - -
226L ILE* 5.1 0.5 - - - -
227L VAL* 3.4 6.5 - - - +
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Residues in contact with TRP 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL 3.6 1.1 - - - -
46L VAL* 4.1 7.2 - - + -
47L PHE* 6.0 0.2 - - - -
186L CYS* 3.7 24.2 - - + -
187L ARG* 4.0 15.9 - - - -
190L VAL* 3.1 35.2 - - + -
214L SER* 1.3 77.5 - - - +
216L VAL* 1.3 64.0 + - - +
219L LEU* 3.2 37.4 - - + +
220L THR* 3.8 28.7 - - + +
224L HIS* 3.0 33.0 - - - -
225L GLU* 2.8 17.7 + - + +
226L ILE 3.6 20.9 - - - -
227L VAL* 3.7 17.7 - - + +
228L PRO* 3.4 21.6 - - + +
231L ILE* 4.6 7.8 - - + +
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Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L GLY* 3.1 0.7 - - - -
45L VAL* 2.5 60.5 + - + +
47L PHE* 5.6 1.1 - - + -
72L HIS 4.1 4.9 - - - +
138L GLY* 4.1 5.8 - - - +
139L SER* 3.8 27.1 - - - +
140L TYR* 3.7 13.7 - - + +
186L CYS* 4.3 3.0 - - - -
215L TRP* 1.3 79.1 - - - +
217L GLY* 1.3 59.9 + - - +
220L THR* 3.7 6.3 - - - -
222L GLY 3.3 28.0 - - - +
223L ARG 3.7 1.6 - - - +
224L HIS* 3.6 19.3 - - + +
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Residues in contact with GLY 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ASP* 3.0 15.3 - - - -
44L GLY* 3.6 4.3 - - - -
140L TYR* 3.4 13.7 - - - -
186L CYS* 5.0 0.9 - - - -
216L VAL* 1.3 79.9 - - - +
218L GLU* 1.3 61.3 + - - -
219L LEU* 3.0 7.1 - - - +
220L THR* 3.0 19.4 + - - -
222L GLY 3.0 17.2 + - - -
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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