Contacts of the strand formed by residues 214 - 219 (chain A) in PDB entry 5ETE
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 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR* 1.3 79.5 - - - +
215A GLU* 1.4 59.7 + - - +
253A GLN* 3.6 17.7 - - - -
280A SER* 3.4 7.4 + - - -
281A TYR* 2.8 37.8 + - - -
284A ALA* 3.5 17.2 - - - +
304A DIO 4.6 2.2 - - - -
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Residues in contact with GLU 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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192A TYR* 4.3 5.4 - - - -
196A TYR* 4.8 0.3 - - - -
207A THR 4.7 0.2 - - - +
208A HIS* 2.9 43.2 + - + +
209A SER* 2.7 44.1 + - - -
210A GLY 5.4 0.2 - - - -
213A TYR 4.4 5.3 - - - +
214A GLY* 1.4 75.1 - - - +
216A ASN* 1.3 70.6 + - - +
217A LEU* 4.0 16.5 - - + +
250A HIS* 5.2 0.7 - - - -
253A GLN* 4.1 4.7 + - - +
278A ILE* 3.7 23.5 - - + +
279A CYS 3.4 6.3 - - - +
280A SER* 4.8 1.8 + - - +
281A TYR* 3.9 4.3 - - - -
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Residues in contact with ASN 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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208A HIS* 5.2 0.7 - - - -
215A GLU* 1.3 79.3 - - - +
217A LEU* 1.4 62.9 + - - +
230A TRP* 3.6 33.9 - - + -
249A GLY 4.3 1.0 - - - +
250A HIS* 3.2 49.9 + - + -
253A GLN* 3.8 12.7 - - - +
254A VAL* 3.9 3.2 - - - +
278A ILE* 3.4 4.0 - - - -
279A CYS 2.9 31.8 + - - +
281A TYR* 3.1 30.1 + - + -
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Residues in contact with LEU 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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196A TYR* 4.9 0.7 - - + -
206A LEU* 4.2 35.3 - - + +
207A THR 3.6 28.0 - - - +
208A HIS* 3.9 29.7 - - + +
215A GLU* 4.0 10.3 - - + +
216A ASN* 1.4 74.4 - - - +
218A ALA* 1.3 60.4 + - - +
230A TRP* 3.1 15.5 + - - -
250A HIS* 4.1 14.8 + - - +
276A TYR* 3.7 17.3 - - + +
277A VAL 3.5 4.0 - - - +
278A ILE* 3.6 36.3 - - + -
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Residues in contact with ALA 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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206A LEU* 4.4 8.5 - - - -
217A LEU* 1.3 77.8 - - - +
219A LEU* 1.3 61.7 + - - +
221A TYR* 4.1 15.7 - - + +
226A ALA* 3.8 28.5 - - + -
229A ALA* 6.3 0.7 - - + -
230A TRP* 3.8 10.5 - - + +
275A ASP 4.4 0.4 - - - -
276A TYR* 3.6 8.0 - - - -
277A VAL* 3.0 32.8 + - + +
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Residues in contact with LEU 219 (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 TYR* 3.6 29.6 - - + +
204A GLY* 3.7 26.0 - - - +
206A LEU* 4.3 16.3 - - + +
218A ALA* 1.3 74.6 - - - +
220A GLY* 1.3 60.6 + - - +
221A TYR* 3.6 15.8 - - - -
269A CYS* 4.9 0.7 - - - -
273A TRP* 3.9 34.1 - - + +
274A GLY 4.4 1.8 - - - +
275A ASP 3.4 16.4 - - - +
276A TYR* 3.9 22.2 - - + -
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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