Contacts of the strand formed by residues 224 - 232 (chain D) in PDB entry 4JF7
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 ARG 224 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ASN* 3.2 23.9 + - - -
191D SER* 3.7 2.6 + - - -
192D ASN 5.6 0.5 - - - -
193D GLN* 3.8 10.9 - - + +
218D LEU* 3.8 39.5 + - - +
220D ASP* 2.4 42.8 + - - +
222D VAL* 2.9 31.0 + - + +
223D ASN* 1.3 69.5 - - - +
225D LYS* 1.3 61.0 + - - +
227D CYS* 4.3 4.0 - - - -
238D MET* 5.3 0.2 - - - -
240D CYS* 4.0 22.9 - - + -
241D PHE 3.6 5.6 - - - +
242D VAL* 4.7 5.4 - - + +
260D ARG* 3.7 11.7 - - - +
262D ILE* 4.1 15.3 - - - -
272D GLU* 2.8 48.8 + - - +
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Residues in contact with LYS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ASN* 2.9 29.5 + - - +
181D ILE* 3.8 16.0 - - - +
187D ASP 4.6 3.4 + - - -
188D HIS* 3.6 20.4 + - - +
191D SER* 3.5 10.4 + - - -
193D GLN* 5.4 0.2 - - - -
223D ASN* 3.5 31.2 - - - +
224D ARG* 1.3 78.7 - - - +
226D SER* 1.3 72.3 + - - +
227D CYS* 3.2 5.5 + - - -
240D CYS* 3.9 1.7 - - - -
241D PHE* 2.8 51.4 + - + +
243D SER* 3.6 15.9 - - - -
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Residues in contact with SER 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ILE* 4.5 10.5 - - - +
179D ASN* 5.7 2.2 - - - +
193D GLN* 5.8 0.2 + - - -
225D LYS* 1.3 77.1 - - - +
227D CYS* 1.3 63.9 + - - +
241D PHE* 3.6 21.5 - - - -
288D ASN* 4.1 8.8 + - - +
289D PRO* 3.0 38.4 + - - +
291D THR* 3.3 23.1 - - - +
306D TYR* 4.7 4.3 + - - -
390D GLU* 4.9 1.4 + - - -
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Residues in contact with CYS 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 4.8 8.8 - - - +
166D SER* 3.7 12.7 - - - -
177D THR* 4.6 1.6 - - + +
193D GLN* 3.6 40.1 - - - +
224D ARG 4.3 1.3 - - - -
225D LYS 3.9 12.3 - - - -
226D SER* 1.3 77.2 - - - +
228D SER* 1.3 59.4 + - - +
238D MET* 3.9 10.1 - - + -
239D TYR 3.2 6.7 - - - +
240D CYS* 2.1 45.5 - - - -
291D THR* 3.6 12.0 - - - -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 3.5 4.7 - - - -
226D SER 3.6 1.0 + - - -
227D CYS* 1.3 72.7 - - - +
229D ILE* 1.3 60.7 + - - +
238D MET* 3.3 5.3 - - - +
239D TYR 2.8 32.6 + - - -
289D PRO* 4.0 9.4 - - - -
290D GLY 3.8 5.4 + - - -
291D THR 2.9 21.5 + - - -
292D GLY 2.6 23.5 + - - -
303D PHE* 3.6 23.4 - - - -
304D PRO* 4.0 4.2 - - - +
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Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 3.1 41.3 + - - +
167D PHE 4.1 1.6 - - - +
168D SER* 3.6 3.5 - - - +
175D CYS* 3.9 33.4 - - + +
176D TYR 3.9 8.5 - - - +
177D THR* 3.8 14.4 - - + -
195D VAL* 3.9 28.3 - - + -
228D SER* 1.3 75.8 - - - +
230D SER* 1.3 62.5 + - - +
236D CYS* 4.0 10.8 - - + -
237D MET 3.6 12.6 - - - +
238D MET* 4.3 10.3 - - + -
293D SER* 3.2 11.1 - - - -
294D GLY 2.9 18.6 + - - -
303D PHE* 4.1 0.9 - - - -
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D SER* 3.5 8.2 + - - -
175D CYS* 4.3 3.8 - - - -
229D ILE* 1.3 77.2 - - - +
231D THR* 1.3 75.1 + - - +
232D VAL* 4.1 0.5 - - - +
236D CYS* 3.4 2.8 - - - +
237D MET 2.9 32.1 + - - -
294D GLY* 3.5 28.3 + - - -
295D VAL* 3.6 7.3 - - - -
296D TYR 3.8 0.3 + - - -
301D VAL* 3.6 25.0 - - - +
303D PHE* 4.0 3.8 - - - -
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D SER* 2.9 41.1 + - - +
170D THR* 2.9 34.1 + - - +
173D HIS* 3.6 31.0 - - - +
175D CYS* 3.7 17.0 - - - +
230D SER* 1.3 87.7 + - - +
232D VAL* 1.3 63.9 + - - +
235D GLY 3.6 5.2 - - - -
296D TYR* 3.8 12.1 + - - +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D HIS* 3.2 11.9 - - - -
230D SER 4.1 0.2 - - - +
231D THR* 1.3 82.4 - - - +
233D PRO* 1.3 86.4 - - + +
234D GLY 3.1 2.4 + - - -
235D GLY* 2.9 34.4 + - - +
236D CYS* 3.7 8.1 - - - +
237D MET* 3.8 18.6 - - + -
263D ILE* 4.8 2.2 - - + -
265D TYR* 4.6 8.5 - - + -
296D TYR* 4.6 4.9 - - + -
301D VAL* 3.8 27.6 - - + -
367D LEU* 4.0 19.7 - - + -
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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