Contacts of the strand formed by residues 208 - 218 (chain A) 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 PRO 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TYR* 3.5 15.7 - - - +
148A MET* 3.5 18.2 - - - +
200A ILE* 3.6 19.5 - - + -
201A GLU 3.7 0.9 - - - +
203A THR* 4.4 0.6 - - - +
207A PHE* 1.3 102.4 - - + +
209A PHE* 1.3 58.9 + - - +
210A PHE* 4.2 4.3 - - + -
529A PHE* 3.6 32.3 - - + -
538A TYR* 3.9 18.6 - - + -
559A ILE* 3.7 20.4 - - + -
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Residues in contact with PHE 209 (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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148A MET* 4.4 3.8 - - + -
149A PRO* 3.9 46.7 - - + -
200A ILE* 3.3 4.5 - - - -
201A GLU* 2.8 56.0 + - + +
203A THR* 3.6 18.2 - - + -
208A PRO* 1.3 73.6 - - - +
210A PHE* 1.3 76.8 + - - +
211A ARG* 3.4 30.0 + - + -
194B PHE* 4.5 9.4 - + - -
215B THR* 3.9 17.9 - - + -
217B TYR* 3.4 34.3 - + + -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.6 30.7 - - + -
149A PRO 4.8 1.4 + - - +
151A PHE* 3.6 35.8 - + + +
167A PHE* 3.7 24.9 - + - -
169A LEU* 5.0 2.5 - - + -
174A TRP* 3.4 30.5 - + + +
199A ILE 3.5 2.9 - - - -
200A ILE* 3.8 18.4 - - + +
208A PRO* 4.3 4.3 - - + -
209A PHE* 1.3 89.0 - - - +
211A ARG* 1.3 61.1 + - - +
212A THR* 3.7 3.1 + - - -
529A PHE* 3.7 39.0 - + - -
540A ILE* 4.3 15.3 - - + -
559A ILE* 4.3 9.2 - - + -
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Residues in contact with ARG 211 (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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116A ALA* 5.7 4.4 + - - +
174A TRP* 3.7 2.0 - - - -
198A GLY* 3.1 4.7 - - - -
199A ILE* 2.6 60.6 + - + +
201A GLU* 3.7 32.0 + - - -
209A PHE* 3.4 21.9 + - + +
210A PHE* 1.3 72.0 - - - +
212A THR* 1.3 60.3 + - - +
213A LEU* 3.7 17.7 - - + +
214B LYS* 4.0 21.4 - - - +
215B THR* 2.8 38.4 + - + -
216B LEU* 4.0 14.8 - - - +
268B ASP* 4.4 8.5 + - - +
270B ILE* 5.7 2.4 - - - +
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.8 19.2 + - - +
174A TRP* 3.6 16.2 - - + -
196A SER* 4.2 5.8 + - - -
197A MET 3.8 5.6 - - - +
210A PHE 3.7 1.8 + - - -
211A ARG* 1.3 71.3 - - - +
213A LEU* 1.3 65.1 + - - +
214A LYS 3.6 22.9 - - - +
215A THR* 3.7 21.1 - - + -
212B THR* 4.6 8.1 - - + -
214B LYS 4.0 0.7 - - - -
215B THR* 3.1 42.7 + - - +
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Residues in contact with LEU 213 (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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116A ALA* 3.9 10.3 - - + -
117A LEU* 3.7 43.5 - - + +
197A MET 2.8 10.9 + - - +
198A GLY* 4.0 2.2 - - - -
199A ILE* 3.8 21.1 - - + -
211A ARG* 3.5 41.7 + - - +
212A THR* 1.3 81.4 - - - +
214A LYS* 1.3 65.0 + - - +
266A TYR* 3.7 26.1 + - + +
213B LEU 2.8 26.0 - - - +
214B LYS* 4.6 10.3 - - + +
268B ASP* 5.8 0.9 - - - +
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Residues in contact with LYS 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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196A SER* 3.2 5.9 - - - -
197A MET* 3.0 44.7 + - + +
212A THR* 3.6 2.8 - - - +
213A LEU* 1.3 80.2 + - - +
215A THR* 1.3 73.6 - - - +
216A LEU* 4.2 16.3 - - + +
265A TYR 3.7 8.7 - - - +
266A TYR* 2.9 48.0 + - + +
268A ASP* 2.7 31.1 + - - +
112B SER* 3.6 9.5 + - - -
116B ALA* 5.8 0.2 - - - +
211B ARG* 4.0 12.3 - - - +
212B THR 4.1 5.6 - - - -
213B LEU* 4.4 9.8 - - + +
266B TYR* 4.1 8.3 + - - -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 3.6 34.3 - - + -
195A VAL 3.3 4.5 - - - -
196A SER* 4.0 0.7 - - - -
212A THR* 3.7 17.5 - - + -
214A LYS* 1.3 80.1 - - - +
216A LEU* 1.3 63.8 + - - +
209B PHE* 4.2 3.5 - - - -
211B ARG* 2.8 38.2 + - - +
212B THR* 2.8 47.3 + - - +
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Residues in contact with LEU 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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193A GLN 4.6 0.2 - - - -
194A PHE* 3.6 6.9 - - - -
195A VAL* 2.7 61.2 + - + +
197A MET* 4.2 13.9 - - + -
214A LYS* 4.2 19.3 - - + +
215A THR* 1.3 81.5 - - - +
217A TYR* 1.3 64.0 + - - +
218A LEU* 4.1 8.5 - - + -
264A MET* 3.8 23.8 - - + -
270A ILE* 3.5 32.5 - - + -
201B GLU* 5.5 0.2 - - - -
209B PHE* 4.4 3.4 - - - -
211B ARG* 4.0 17.7 - - - +
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Residues in contact with TYR 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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180A VAL* 3.6 28.0 - - + +
182A LEU* 4.0 6.1 - - - +
192A ASN* 3.2 36.0 + - + +
193A GLN 3.6 10.5 - - - -
194A PHE* 4.1 7.0 - + - -
216A LEU* 1.3 74.5 - - - +
218A LEU* 1.3 64.6 + - - +
219A SER* 3.2 21.9 + - - -
147B ASN 4.6 2.6 + - - -
148B MET* 5.4 1.6 - - + -
149B PRO* 3.5 35.0 - - + +
201B GLU* 4.4 9.8 + - - +
203B THR* 3.7 26.2 - - + -
207B PHE* 6.1 0.8 - + - -
209B PHE* 3.3 43.9 - + + -
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 3.4 7.1 - - - +
193A GLN* 2.8 41.9 + - + +
195A VAL* 4.7 7.0 - - + -
216A LEU* 5.0 13.2 - - + -
217A TYR* 1.3 70.6 - - - +
219A SER* 1.3 59.7 + - - +
220A ASP 3.9 1.3 - - - -
222A VAL 5.5 0.7 - - - +
224A ARG* 3.7 42.2 + - - +
238A MET* 3.6 31.6 - - + -
262A ILE* 4.2 20.0 - - + -
264A MET* 5.1 4.3 - - - -
270A ILE* 5.5 8.5 - - + -
272A GLU* 5.5 2.0 - - - +
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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