Contacts of the strand formed by residues 212 - 217 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D GLY* 3.2 5.4 - - - -
49D VAL* 3.1 38.8 + - + +
51D LYS* 3.4 38.0 - - + +
64D LYS* 3.2 32.0 - - - +
65D ARG* 3.0 28.5 + - - +
66D LEU* 3.7 23.8 + - + +
210D GLU* 5.5 1.6 - - - +
211D LEU* 1.3 73.5 - - - +
213D LEU* 1.3 67.9 + - - +
226D ILE* 4.6 10.5 - - + +
232D ARG* 5.3 0.9 - - - +
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 5.2 1.1 - - + -
47D PHE 3.4 13.2 - - - +
48D GLY* 3.7 9.6 - - - -
66D LEU* 3.7 4.5 - - - +
190D VAL* 4.0 26.2 - - + +
193D VAL* 4.0 17.5 - - + -
194D ALA* 5.0 4.5 - - + -
211D LEU* 4.0 27.3 + - + -
212D GLU* 1.3 84.9 - - - +
214D SER* 1.3 61.0 + - - +
226D ILE* 3.3 14.2 - - - +
227D VAL* 3.1 36.4 + - + -
232D ARG* 4.1 37.4 - - + +
235D ALA* 5.2 0.9 - - + -
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Residues in contact with SER 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL 3.7 0.2 - - - +
46D VAL* 3.3 17.0 - - - +
47D PHE* 2.9 51.3 + - - -
66D LEU* 3.9 13.0 - - - +
213D LEU* 1.3 76.5 + - - +
215D TRP* 1.3 58.9 + - - +
224D HIS* 2.5 37.8 + - - -
225D GLU 3.8 3.8 + - - -
226D ILE* 5.1 0.5 - - - -
227D VAL* 3.4 6.5 - - - +
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Residues in contact with TRP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL 3.6 0.9 - - - -
46D VAL* 4.1 7.4 - - + -
47D PHE* 6.0 0.2 - - - -
186D CYS* 3.7 24.0 - - + -
187D ARG* 3.9 16.8 - - - -
190D VAL* 3.1 35.2 - - + -
214D SER* 1.3 77.0 - - - +
216D VAL* 1.3 64.3 + - - +
219D LEU* 3.2 37.2 - - + +
220D THR* 3.8 28.0 - - + -
224D HIS* 3.0 32.0 - - - -
225D GLU* 2.8 18.2 + - + +
226D ILE 3.6 21.3 - - - -
227D VAL* 3.8 18.1 - - + +
228D PRO* 3.5 20.8 - - + +
231D ILE* 4.7 7.1 - - + +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLY* 3.1 0.9 - - - -
45D VAL* 2.6 60.7 + - + +
47D PHE* 5.6 1.3 - - + -
72D HIS 4.1 4.5 - - - +
138D GLY 4.1 5.6 - - - +
139D SER* 3.8 26.5 - - - +
140D TYR* 3.7 13.5 - - + +
186D CYS* 4.3 3.0 - - - -
215D TRP* 1.3 79.5 - - - +
217D GLY* 1.3 59.4 + - - +
220D THR* 3.7 6.7 - - - -
222D GLY 3.2 28.3 - - - +
223D ARG 3.6 1.6 - - - +
224D HIS* 3.6 19.3 - - + +
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASP* 3.0 15.7 - - - -
44D GLY* 3.6 4.0 - - - -
140D TYR* 3.5 13.2 - - - -
186D CYS* 5.0 0.4 - - - -
216D VAL* 1.3 79.1 - - - +
218D GLU* 1.3 64.0 + - - -
219D LEU* 3.0 6.7 - - - +
220D THR* 3.0 20.5 + - - -
222D GLY 3.1 18.0 + - - -
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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