Contacts of the strand formed by residues 213 - 218 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN 3.3 5.5 + - - +
178A ILE* 3.7 13.3 - - + +
179A HIS 3.1 23.2 + - - -
211A PRO* 3.7 2.9 - - - +
212A ASP* 1.4 86.3 - - + +
214A VAL* 1.3 64.5 + - - +
215A VAL 4.0 0.8 + - - +
239A GLU* 4.7 2.2 - - + +
240A GLN* 3.7 24.2 - - - -
242A ILE* 3.7 26.5 - - + -
262A VAL* 4.6 7.2 - - + +
265A TYR* 3.6 40.4 - - + -
266A PHE* 3.6 36.1 - - + -
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A HIS* 3.2 18.8 - - + +
181A SER* 4.6 1.3 - - - -
197A THR* 4.5 19.1 - - + -
201A VAL* 4.7 7.6 - - + -
211A PRO* 3.6 25.1 - - + -
212A ASP 5.6 0.2 - - - -
213A LEU* 1.3 76.7 - - - +
215A VAL* 1.3 70.9 + - - +
216A CYS* 3.6 14.0 + - - -
230A ILE* 5.9 3.1 - - + -
234A CYS* 5.3 6.7 - - - -
236A VAL* 5.0 18.4 - - + -
240A GLN* 3.0 14.0 + - + +
241A VAL* 5.2 2.2 - - + -
242A ILE* 3.0 27.5 + - - +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.2 28.9 - - + -
178A ILE* 3.9 25.1 - - + -
179A HIS 2.7 7.5 + - - +
180A VAL* 3.9 22.0 - - + -
181A SER* 2.8 27.9 + - - -
213A LEU* 5.4 0.4 - - + -
214A VAL* 1.3 76.8 - - - +
216A CYS* 1.3 64.8 + - - +
217A ARG* 4.6 1.1 - - - +
242A ILE* 3.8 17.9 - - + -
244A VAL* 3.6 28.3 - - + -
257A LEU* 6.0 2.2 - - + -
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 4.1 4.5 - - - -
183A VAL* 3.8 19.7 - - + -
197A THR* 5.3 6.7 - - - -
214A VAL* 3.9 19.5 - - - -
215A VAL* 1.3 80.7 - - - +
217A ARG* 1.3 58.6 + - - +
218A CYS* 3.0 12.5 + - - -
222A LEU* 4.6 1.3 - - + -
230A ILE* 4.6 15.0 - - - -
241A VAL* 4.2 20.6 - - - -
242A ILE 2.7 22.3 + - - +
243A CYS* 4.2 0.4 - - - -
244A VAL* 2.8 29.8 + - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY 3.2 18.2 + - - -
14A ILE* 2.6 49.9 + - + +
180A VAL* 5.1 2.0 - - + -
181A SER 2.9 22.1 + - - +
182A LEU* 3.6 15.1 - - + +
183A VAL* 2.7 32.7 + - - +
215A VAL* 3.9 3.6 + - + +
216A CYS* 1.3 69.3 - - - +
218A CYS* 1.3 57.8 + - - +
244A VAL* 3.7 6.1 - - - -
246A ASP* 2.8 27.4 + - - +
601A ATP 3.4 42.2 + - - -
186B PRO* 5.4 3.8 - - - +
188B SER* 3.1 29.5 + - - -
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 6.2 0.2 - - - -
183A VAL* 4.2 7.9 - - - -
216A CYS* 3.0 20.1 + - - -
217A ARG* 1.3 75.9 - - - +
219A SER* 1.3 61.1 + - - +
220A ASN 3.2 10.8 - - - +
222A LEU* 3.5 19.5 - - + -
243A CYS* 2.1 52.7 - - - -
244A VAL 3.0 5.7 + - - -
245A HIS* 3.4 4.8 - - - -
246A ASP* 3.0 29.2 + - - +
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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