Contacts of the strand formed by residues 216 - 224 (chain A) in PDB entry 2F24
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 THR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A TYR* 4.2 0.2 - - - +
192A PRO* 3.0 20.9 + - - +
193A SER* 3.3 5.7 + - - -
194A ALA 2.8 25.5 + - - -
212A VAL* 3.3 8.7 - - + +
213A ALA* 2.7 29.4 + - + +
214A GLN 4.2 3.4 - - - +
215A ASP* 1.3 82.3 - - - +
217A LEU* 1.3 63.5 + - - +
236A ALA* 4.1 14.4 - - + -
237A ARG 3.4 4.5 - - - +
244A VAL* 3.9 38.8 - - + -
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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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179A TYR* 3.7 31.0 - - + +
181A TYR* 3.7 23.1 - - + +
192A PRO* 3.7 13.7 - - + -
194A ALA* 3.8 3.6 - - - +
215A ASP 4.0 8.5 - - - +
216A THR* 1.3 80.2 - - - +
218A GLU* 1.3 73.7 + - + +
219A CYS* 3.1 10.2 + - - +
236A ALA* 4.2 0.7 - - - +
237A ARG* 3.0 51.3 + - + +
238A SER* 4.4 1.3 - - - -
239A HIS* 3.5 37.7 - - + +
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Residues in contact with GLU 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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86A ASN* 5.3 0.9 - - - +
160A GLY 3.9 4.9 - - - +
161A PRO* 3.6 15.3 - - + +
179A TYR* 3.6 34.9 + - + -
217A LEU* 1.3 78.1 - - - +
219A CYS* 1.3 59.9 + - - +
235A ASN 4.3 0.3 - - - +
236A ALA* 3.6 0.3 - - - -
237A ARG* 2.8 63.6 + - + +
243A ARG* 4.5 2.8 + - - -
273A GLN* 3.5 21.2 - - + +
274A GLY 5.7 0.2 - - - +
334A TYR* 2.5 36.8 + - - -
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Residues in contact with CYS 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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160A GLY* 4.0 12.4 + - - +
177A PRO* 3.4 30.5 - - - +
178A ALA 3.6 26.0 - - - -
179A TYR* 5.0 0.6 - - - -
194A ALA* 3.8 10.3 - - - -
217A LEU 3.1 2.5 + - - +
218A GLU* 1.3 75.4 - - - +
220A GLN* 1.3 71.2 + - - +
234A LEU* 3.8 21.5 - - + -
235A ASN 3.3 15.7 - - - +
236A ALA* 3.6 16.2 - - + -
243A ARG* 5.3 0.7 - - - +
273A GLN* 5.7 0.6 - - - +
274A GLY 5.5 1.6 - - - -
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Residues in contact with GLN 220 (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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161A PRO 3.0 24.3 + - - +
162A GLY* 3.6 5.3 - - - -
163A HIS* 3.1 23.0 + - - +
177A PRO* 3.8 7.9 - - + -
219A CYS* 1.3 80.6 - - - +
221A VAL* 1.3 66.2 + - - +
233A THR 3.9 0.2 - - - +
234A LEU* 3.5 2.9 - - - +
235A ASN 3.0 29.8 + - - +
273A GLN* 3.7 12.3 - - + +
274A GLY 4.0 8.5 - - - +
275A SER* 2.8 28.7 + - - -
276A VAL* 3.1 25.1 + - + +
336A ASP* 2.9 22.1 + - - -
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Residues in contact with VAL 221 (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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163A HIS* 4.5 10.7 + - - +
164A CYS 5.3 0.7 - - - -
165A LEU* 3.8 34.0 - - + +
175A VAL* 3.9 14.8 - - + -
177A PRO* 4.1 20.3 - - + +
196A CYS* 3.6 25.6 - - - -
220A GLN* 1.3 81.3 - - - +
222A ALA* 1.3 61.6 + - - +
232A VAL* 3.8 13.2 - - + -
233A THR 3.2 12.3 - - - +
234A LEU* 3.8 17.0 - - + -
276A VAL* 4.3 9.3 - - - +
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Residues in contact with ALA 222 (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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165A LEU* 3.8 11.7 - - - -
221A VAL* 1.3 74.6 - - - +
223A GLU* 1.3 60.0 + - - +
232A VAL* 3.4 5.0 - - - +
233A THR* 2.8 38.7 + - + +
276A VAL* 4.5 6.1 - - + -
277A ILE* 4.1 8.5 - - - -
278A SER* 4.0 15.0 - - - +
293A LEU* 3.8 28.3 - - + -
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Residues in contact with GLU 223 (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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165A LEU* 4.0 10.7 - - + +
166A GLN 4.6 0.3 - - - +
167A LEU* 3.4 34.8 - - + +
168A ASN* 2.8 40.5 + - - +
222A ALA* 1.3 74.0 - - - +
224A VAL* 1.3 77.9 + - - +
230A ARG* 3.0 42.1 + - + +
231A VAL 3.3 11.2 - - - +
232A VAL* 5.3 1.1 - - + +
278A SER* 3.3 20.4 + - - +
291A GLN* 4.2 5.6 - - - +
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Residues in contact with VAL 224 (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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223A GLU* 1.3 82.8 - - - +
229A GLN 3.9 5.3 - - - +
230A ARG* 3.4 13.4 - - - -
231A VAL* 2.7 45.5 + - + +
233A THR* 5.0 4.9 - - + -
278A SER* 4.3 4.0 - - - -
290A ALA* 6.4 0.9 - - - -
291A GLN* 3.6 25.4 - - + +
293A LEU* 3.7 29.4 - - + -
315A PRO* 3.9 25.4 - - + +
316A PRO* 3.7 35.0 - - + -
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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