Contacts of the strand formed by residues 213 - 218 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ASN 3.3 5.3 + - - +
178C ILE* 3.7 14.1 - - + +
179C HIS 3.1 23.0 + - - -
211C PRO* 3.7 3.3 - - - +
212C ASP* 1.4 89.3 - - + +
214C VAL* 1.3 63.6 + - - +
215C VAL* 4.0 0.8 + - + -
239C GLU* 4.7 2.2 - - + +
240C GLN* 3.7 24.9 - - - +
242C ILE* 3.7 25.8 - - + -
262C VAL* 4.6 6.7 - - + -
265C TYR* 3.6 39.7 - - + -
266C PHE* 3.6 35.9 - - + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C HIS* 3.2 18.2 - - + +
181C SER* 4.6 0.9 - - - -
197C THR* 4.5 18.2 - - + -
201C VAL* 4.7 8.3 - - + -
211C PRO* 3.6 26.5 - - + -
213C LEU* 1.3 78.0 - - - +
215C VAL* 1.3 69.9 + - - +
216C CYS* 3.6 14.5 + - - -
230C ILE* 5.9 2.7 - - + -
234C CYS* 5.3 7.6 - - + -
236C VAL* 5.0 18.2 - - + -
240C GLN* 3.0 13.4 + - + +
241C VAL* 5.2 3.1 - - + -
242C ILE* 3.0 28.1 + - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 4.2 27.4 - - + -
178C ILE* 3.9 26.2 - - + -
179C HIS 2.7 7.5 + - - +
180C VAL* 3.9 22.4 - - + -
181C SER* 2.8 27.7 + - - -
214C VAL* 1.3 76.0 - - - +
216C CYS* 1.3 65.7 + - - +
217C ARG* 4.6 1.1 - - - +
242C ILE* 3.8 17.3 - - + -
244C VAL* 3.6 29.2 - - + -
257C LEU* 6.0 2.2 - - + -
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Residues in contact with CYS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C SER* 4.1 4.0 - - - -
183C VAL* 3.8 19.7 - - + -
197C THR* 5.3 7.0 - - - -
214C VAL* 3.9 19.7 - - - -
215C VAL* 1.3 81.2 - - - +
217C ARG* 1.3 60.4 + - - +
218C CYS* 3.0 12.8 + - - -
222C LEU* 4.6 1.3 - - + -
230C ILE* 4.6 15.0 - - - -
241C VAL* 4.2 20.4 - - - -
242C ILE 2.7 22.3 + - - +
243C CYS* 4.2 0.7 - - - -
244C VAL* 2.8 28.9 + - - +
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Residues in contact with ARG 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 3.2 17.8 + - - -
14C ILE* 2.6 49.7 + - + +
180C VAL* 5.1 2.0 - - + -
181C SER 2.9 22.3 + - - +
182C LEU* 3.6 15.8 - - + +
183C VAL* 2.7 33.1 + - - +
215C VAL* 3.9 3.3 + - + +
216C CYS* 1.3 69.7 - - - +
218C CYS* 1.3 57.0 + - - +
244C VAL* 3.7 5.8 - - - -
246C ASP* 2.8 27.7 + - - +
601C ATP 3.4 42.8 + - - -
186D PRO* 5.4 3.6 - - - +
188D SER* 3.1 28.9 + - - -
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Residues in contact with CYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LEU* 6.2 0.2 - - - -
183C VAL* 4.2 7.4 - - - -
216C CYS* 3.0 19.5 + - - -
217C ARG* 1.3 74.5 - - - +
219C SER* 1.3 60.1 + - - +
220C ASN 3.2 11.7 - - - +
222C LEU* 3.5 20.0 - - + -
243C CYS* 2.1 51.4 - - - -
244C VAL 3.0 5.9 + - - -
245C HIS* 3.5 4.7 - - - -
246C ASP* 3.0 29.9 + - - +
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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