Contacts of the strand formed by residues 213 - 218 (chain A) in PDB entry 5N4D
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 GLY 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.2 18.6 - - - -
208A THR* 3.0 23.3 + - - -
211A SER 3.4 2.4 + - - -
212A LYS* 1.3 79.0 - - - +
214A PHE* 1.3 62.4 + - - -
238A TYR* 3.3 18.5 + - - -
239A HIS 3.0 15.0 - - - -
241A VAL* 4.2 2.9 - - - -
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Residues in contact with PHE 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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158A ALA* 4.1 6.1 - - + -
171A ILE* 3.8 35.0 - - + -
173A VAL* 3.7 24.9 - - + -
197A VAL* 4.3 4.7 - - + -
205A ILE* 3.9 17.5 - - + -
206A ILE 3.2 14.4 - - - +
207A TRP* 3.8 33.7 - + + +
208A THR 4.4 0.2 - - - +
213A GLY* 1.3 76.5 - - - +
215A LEU* 1.3 63.8 + - - +
216A TYR* 3.9 13.9 - + + -
237A CYS 3.9 0.2 - - - +
238A TYR* 3.4 8.8 - - - -
239A HIS* 2.8 66.2 + + + -
241A VAL* 4.9 1.3 - - + -
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Residues in contact with LEU 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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204A THR 3.8 1.2 - - - +
205A ILE* 3.6 4.0 - - - -
206A ILE* 2.8 49.6 + - + +
208A THR* 4.2 14.8 - - + -
214A PHE* 1.3 75.1 - - - +
216A TYR* 1.3 64.6 + - - +
236A MET* 4.1 16.2 - - + -
237A CYS 3.1 14.8 - - - +
238A TYR* 3.9 9.0 - - + -
251A VAL* 3.8 33.9 - - + -
264A ALA* 4.4 5.6 - - + -
266A THR* 3.9 13.2 - - + -
273A LEU* 3.7 31.6 - - + -
297A VAL* 5.0 1.3 - - + -
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Residues in contact with TYR 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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171A ILE* 3.8 21.1 - - + -
197A VAL* 3.2 23.8 - - + -
198A LYS 4.4 0.9 - - - -
200A PHE* 4.0 13.0 - + + -
203A SER* 3.9 7.9 - - - -
204A THR 4.0 1.8 - - - +
205A ILE* 5.1 1.1 - - + -
214A PHE* 3.9 18.2 - + + -
215A LEU* 1.3 78.0 - - - +
217A GLN* 1.3 69.4 + - - +
218A ARG* 3.5 29.1 + - + -
236A MET* 3.7 7.5 - - - -
237A CYS* 2.9 55.7 + - + +
239A HIS* 3.8 8.7 - - + -
245A GLN* 3.0 15.3 + - - +
248A ASP* 2.5 31.8 + - - +
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Residues in contact with GLN 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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200A PHE* 3.2 22.9 - - - -
201A LYS 3.2 22.1 + - - +
202A PHE* 3.1 34.4 + - - +
203A SER* 3.0 23.9 + - - +
216A TYR* 1.3 73.9 - - - +
218A ARG* 1.3 65.1 + - - +
219A TYR* 3.7 8.9 + - + -
234A ALA* 3.4 25.5 - - + +
235A MET 3.3 11.2 - - - +
236A MET* 4.1 8.3 - - + +
261A ILE* 3.5 7.3 - - - +
262A TYR* 2.8 34.7 + - - +
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Residues in contact with ARG 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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198A LYS 4.1 0.2 - - - +
199A TRP* 3.1 40.0 - - - +
216A TYR* 3.5 29.1 + - + -
217A GLN* 1.3 76.1 - - - +
219A TYR* 1.3 87.7 + - - +
220A PRO* 4.0 2.2 - - - +
221A ALA* 3.5 15.6 - - - +
234A ALA* 3.5 2.8 - - - -
235A MET* 2.8 47.1 + - + +
237A CYS* 3.6 25.5 - - - -
245A GLN* 3.7 23.8 + - - +
248A ASP* 6.2 0.4 - - - +
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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