Contacts of the strand formed by residues 210 - 216 (chain D) in PDB entry 2HU4
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 ILE 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B TYR* 4.6 8.3 - - - +
129B CYS* 5.5 2.9 - - - -
412B GLN* 3.4 65.5 - - + +
413B THR* 3.9 22.4 - - + +
419B ARG* 5.0 0.9 - - - +
206D LYS* 4.0 2.0 - - - -
207D TYR* 3.1 33.7 + - + +
208D ASN* 4.5 11.2 - - + +
209D GLY* 1.3 81.0 - - - +
211D ILE* 1.3 66.9 + - - +
212D THR* 3.4 9.9 + - + +
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Residues in contact with ILE 211 (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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98B ALA* 4.0 17.5 - - + +
99B VAL 3.9 17.9 - - - +
100B TYR* 3.9 21.9 - - + -
412B GLN* 5.4 0.4 + - - +
413B THR* 5.8 1.9 - - - +
419B ARG* 2.7 35.7 + - - +
447B CYS* 4.0 18.2 - - + -
449B VAL* 3.5 27.4 - - + -
204D VAL* 3.8 17.5 - - + -
205D LEU 3.6 8.3 - - - +
206D LYS* 3.9 11.8 - - - +
209D GLY 4.1 0.6 + - - -
210D ILE* 1.3 72.6 - - - +
212D THR* 1.3 63.6 + - - +
213D ASP 4.1 14.4 - - - +
214D THR* 4.9 1.6 - - - +
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Residues in contact with THR 212 (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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419B ARG* 5.0 3.6 - - - +
449B VAL* 6.1 0.2 - - - -
205D LEU 3.1 11.4 + - - -
207D TYR* 3.7 17.1 + - + -
210D ILE* 3.4 20.8 + - + +
211D ILE* 1.3 75.5 - - - +
213D ASP* 1.3 65.6 + - - +
259D LYS 3.5 18.8 - - - +
260D GLY* 2.7 29.6 + - - +
261D LYS* 3.6 23.5 + - - +
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Residues in contact with ASP 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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449B VAL* 5.8 0.7 - - - -
451B SER* 3.9 14.6 + - - -
204D VAL* 4.0 1.4 - - - -
205D LEU* 3.1 33.5 + - + +
211D ILE* 3.9 7.7 - - - +
212D THR* 1.3 82.7 + - - +
214D THR* 1.3 82.1 + - - +
260D GLY 3.3 15.5 - - - +
261D LYS* 4.1 5.0 - - - +
262D VAL* 2.7 44.0 + - - +
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Residues in contact with THR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 4.2 14.2 - - - +
449B VAL* 4.1 11.1 - - - +
451B SER* 3.2 25.0 + - - -
452B ASP 2.7 31.9 + - - +
453B THR* 5.3 0.2 - - + -
202D VAL* 3.2 19.9 - - + +
203D ALA 3.2 7.3 + - - -
204D VAL* 4.7 1.9 - - - -
211D ILE* 4.9 0.9 - - - +
213D ASP* 1.3 89.8 + - - +
215D ILE* 1.3 75.8 + - - +
216D LYS* 4.5 1.5 + - - +
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Residues in contact with ILE 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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202D VAL* 3.2 1.2 - - - -
203D ALA* 2.6 45.0 + - + +
205D LEU* 4.3 20.0 - - + -
214D THR* 1.3 84.6 - - - +
216D LYS* 1.3 69.9 + - - +
218D TRP* 4.7 4.7 - - + -
223D LEU* 3.5 12.5 - - + +
239D THR* 6.3 0.9 - - + -
241D MET* 4.3 13.2 - - + -
255D PHE* 3.8 44.6 - - + -
257D MET* 5.8 0.7 - - - -
262D VAL* 4.0 21.8 - - + -
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Residues in contact with LYS 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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451B SER* 4.9 1.6 - - - +
452B ASP* 2.6 59.7 - - + +
453B THR 5.5 2.5 - - - +
454B VAL* 5.6 4.0 - - + -
200D GLY 6.1 0.2 - - - -
201D ALA 3.6 7.2 - - - +
202D VAL* 4.3 8.3 - - + +
214D THR* 4.3 2.2 + - - +
215D ILE* 1.3 78.9 - - - +
217D SER* 1.3 70.8 + - - +
218D TRP* 3.4 14.7 + - - +
223D LEU* 3.9 2.0 - - - -
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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