Contacts of the strand formed by residues 213 - 218 (chain D) in PDB entry 5U03
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 213 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ASN 3.3 5.3 + - - +
178D ILE* 3.7 13.3 - - + +
179D HIS 3.1 23.2 + - - -
211D PRO* 3.7 2.9 - - - +
212D ASP* 1.4 88.4 - - + +
214D VAL* 1.3 64.3 + - - +
215D VAL 4.0 0.7 - - - +
239D GLU* 4.6 1.8 - - + +
240D GLN* 3.7 24.7 - - - +
242D ILE* 3.7 26.0 - - + -
262D VAL* 4.6 6.3 - - + -
265D TYR* 3.6 39.3 - - + -
266D PHE* 3.6 36.6 - - + -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D HIS* 3.2 17.5 - - + +
181D SER* 4.6 0.9 - - - -
197D THR* 4.5 18.6 - - + -
201D VAL* 4.7 7.2 - - + -
211D PRO* 3.6 25.6 - - + -
212D ASP 5.6 0.2 - - - -
213D LEU* 1.3 78.6 - - - +
215D VAL* 1.3 70.4 + - - +
216D CYS* 3.9 14.7 - - - -
230D ILE* 5.9 3.1 - - + -
234D CYS* 5.3 6.7 - - - -
236D VAL* 5.0 18.2 - - + -
240D GLN* 3.0 13.6 + - + +
241D VAL* 5.2 2.2 - - + -
242D ILE* 3.0 27.3 + - - +
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 4.2 29.2 - - + -
178D ILE* 3.9 25.4 - - + -
179D HIS 2.7 7.1 + - - +
180D VAL* 3.9 22.7 - - + -
181D SER* 2.8 28.2 + - - -
213D LEU* 5.4 0.9 - - + -
214D VAL* 1.3 77.6 - - - +
216D CYS* 1.3 65.1 + - - +
217D ARG* 4.6 1.1 - - - +
242D ILE* 3.8 17.0 - - + -
244D VAL* 3.6 28.0 - - + -
257D LEU* 6.0 2.0 - - + -
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Residues in contact with CYS 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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181D SER* 4.1 4.9 - - - -
183D VAL* 3.9 20.2 - - + -
197D THR* 5.3 6.5 - - - -
214D VAL* 3.9 19.5 - - - -
215D VAL* 1.3 80.9 - - - +
217D ARG* 1.3 59.3 + - - +
218D CYS* 3.0 12.6 + - - -
222D LEU* 4.6 1.8 - - + -
230D ILE* 4.6 14.4 - - - -
241D VAL* 4.2 21.1 - - - -
242D ILE 2.7 22.3 + - - +
243D CYS* 4.2 0.4 - - - -
244D VAL* 2.8 28.9 + - - +
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Residues in contact with ARG 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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186C PRO* 5.4 3.4 - - - +
188C SER* 3.1 29.1 + - - -
13D GLY 3.2 18.4 + - - -
14D ILE* 2.6 50.2 + - + +
180D VAL* 5.1 2.0 - - + -
181D SER 2.9 22.5 + - - +
182D LEU* 3.6 15.1 - - + +
183D VAL* 2.7 33.1 + - - +
215D VAL* 3.9 3.4 + - + +
216D CYS* 1.3 68.8 - - - +
218D CYS* 1.3 58.3 + - - +
244D VAL* 3.7 5.4 - - - -
246D ASP* 2.8 27.8 + - - +
601D ATP 3.5 43.0 + - - -
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Residues in contact with CYS 218 (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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183D VAL* 4.2 7.6 - - - -
216D CYS* 3.0 20.3 + - - -
217D ARG* 1.3 75.4 - - - +
219D SER* 1.3 60.9 + - - +
220D ASN 3.2 11.9 - - - +
222D LEU* 3.5 19.7 - - + -
243D CYS* 2.1 51.4 - - - -
244D VAL 3.0 5.9 + - - -
245D HIS* 3.5 4.6 - - - -
246D ASP* 3.0 29.5 + - - +
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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