Contacts of the strand formed by residues 212 - 217 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I GLY* 3.3 5.7 - - - -
49I VAL* 3.1 38.7 + - + +
51I LYS* 3.4 39.5 + - + +
64I LYS* 3.2 32.6 - - - +
65I ARG* 3.0 27.9 + - - +
66I LEU* 3.7 23.9 + - + +
210I GLU* 5.5 1.3 - - - +
211I LEU* 1.3 73.3 - - - +
213I LEU* 1.3 67.2 + - - +
226I ILE* 4.6 10.6 - - + +
232I ARG* 5.3 0.9 - - - +
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Residues in contact with LEU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I VAL* 5.2 1.1 - - + -
47I PHE 3.4 14.1 - - - +
48I GLY* 3.7 9.2 - - - -
66I LEU* 3.7 5.7 - - - +
190I VAL* 3.9 26.5 - - + +
193I VAL* 4.0 16.8 - - + -
194I ALA* 5.0 4.5 - - + -
211I LEU* 4.0 26.9 + - + -
212I GLU* 1.3 83.0 - - - +
214I SER* 1.3 60.6 + - - +
226I ILE* 3.3 15.1 - - - +
227I VAL* 3.1 35.3 + - + -
232I ARG* 4.1 38.5 - - + +
235I ALA* 5.2 0.7 - - + -
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Residues in contact with SER 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I VAL* 3.2 17.2 - - - +
47I PHE* 2.9 51.4 + - - -
66I LEU* 3.9 12.9 - - - +
213I LEU* 1.3 76.3 + - - +
215I TRP* 1.3 57.9 - - - +
224I HIS* 2.5 37.2 + - - -
225I GLU 3.8 2.8 + - - -
226I ILE* 5.1 0.9 - - - -
227I VAL* 3.4 7.1 - - - +
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Residues in contact with TRP 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I VAL 3.7 0.7 - - - -
46I VAL* 4.1 8.1 - - + -
186I CYS* 3.7 23.3 - - + -
187I ARG* 4.0 16.6 - - - -
190I VAL* 3.1 35.0 - - + -
214I SER* 1.3 78.5 - - - +
216I VAL* 1.3 64.2 + - - +
219I LEU* 3.2 37.0 - - + +
220I THR* 3.8 28.2 - - + +
224I HIS* 2.9 32.7 - - - -
225I GLU* 2.8 16.4 + - + +
226I ILE 3.6 21.3 - - - -
227I VAL* 3.8 17.9 - - + +
228I PRO* 3.4 21.2 - - + +
231I ILE* 4.7 7.6 - - + +
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Residues in contact with VAL 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLY* 3.1 0.5 - - - -
45I VAL* 2.5 61.9 + - + +
47I PHE* 5.6 1.3 - - + -
72I HIS 4.1 4.9 - - - +
138I GLY 4.1 5.6 - - - +
139I SER* 3.8 26.9 - - - +
140I TYR* 3.7 13.9 - - + +
186I CYS* 4.3 3.2 - - - -
215I TRP* 1.3 80.2 - - - +
217I GLY* 1.3 59.6 + - - +
220I THR* 3.7 6.1 - - - -
222I GLY 3.3 27.6 - - - +
223I ARG 3.6 7.9 - - - +
224I HIS* 3.7 13.5 - - + +
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Residues in contact with GLY 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ASP* 3.0 16.2 - - - -
44I GLY* 3.6 4.3 - - - -
140I TYR* 3.5 13.0 - - - -
186I CYS* 5.0 0.4 - - - -
216I VAL* 1.3 78.7 - - - +
218I GLU* 1.3 63.4 + - - -
219I LEU* 3.0 7.1 - - - +
220I THR* 3.0 19.9 + - - -
222I GLY 3.1 17.5 + - - -
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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