Contacts of the strand formed by residues 207 - 215 (chain A) in PDB entry 4FO9
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 VAL 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.9 17.7 - - + -
190A GLU* 3.9 12.6 - - + +
191A ILE* 3.5 39.7 - - + +
194A SER* 3.1 16.9 + - - -
205A TYR* 3.5 7.6 - - - +
206A THR* 1.3 81.5 - - - +
208A GLN* 1.3 61.9 + - - +
264A THR* 4.2 0.3 - - - +
295A LEU* 4.1 9.9 - - + -
296A VAL 3.3 8.5 - - - +
297A ARG* 3.8 28.9 - - + +
507A UNX 3.7 22.2 - - - -
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Residues in contact with GLN 208 (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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154A TYR* 3.7 15.0 + - - -
191A ILE* 5.4 0.2 - - - -
198A LEU* 4.1 6.5 - - - +
205A TYR 3.0 28.5 + - - +
206A THR* 4.0 3.0 - - - +
207A VAL* 1.3 75.1 - - - +
209A VAL* 1.3 62.7 + - - +
210A GLN 4.0 0.2 - - - -
262A ASN* 3.3 20.3 + - - +
264A THR* 3.3 17.5 - - - +
295A LEU* 3.4 9.2 - - - +
296A VAL* 2.9 36.2 + - + +
298A GLN* 2.9 35.7 + - - +
506A UNX 2.7 31.9 - - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.2 15.0 - - + -
181A PHE* 4.1 14.4 - - + -
183A LEU* 4.7 2.0 - - + -
191A ILE* 4.5 9.4 - - + -
208A GLN* 1.3 74.9 - - - +
210A GLN* 1.3 59.7 + - - +
262A ASN* 3.7 2.3 - - - +
263A ILE* 3.0 46.1 + - + +
264A THR* 3.0 11.0 + - + +
267A VAL* 4.0 28.9 - - + -
293A VAL* 3.7 24.2 - - + -
294A TYR 3.5 4.5 - - - -
295A LEU* 4.4 8.5 - - + -
506A UNX 4.2 0.9 - - - -
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Residues in contact with GLN 210 (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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151A LEU* 3.8 6.1 - - - +
154A TYR* 3.7 41.6 - - - +
156A VAL* 5.8 0.9 - - - +
209A VAL* 1.3 72.8 - - - +
211A LEU* 1.3 60.3 + - - +
212A ARG* 3.5 21.6 + - + -
260A PRO* 3.6 31.8 - - + +
261A LEU 3.3 6.3 - - - +
293A VAL* 3.4 4.5 - - - -
294A TYR* 2.9 43.3 + - + +
296A VAL* 3.5 26.5 - - + +
506A UNX 3.4 14.0 - - - -
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Residues in contact with LEU 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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209A VAL 4.2 0.4 - - - -
210A GLN* 1.3 74.5 - - - +
212A ARG* 1.3 77.1 + - - +
213A LEU* 4.7 5.4 - - + -
232A ILE* 3.9 39.0 - - + -
260A PRO* 3.8 0.3 - - - +
261A LEU* 2.9 50.7 + - + +
263A ILE* 4.1 23.5 - - + +
277A ILE* 4.5 13.5 - - + -
279A ILE* 4.6 4.9 - - + -
291A MET* 4.1 20.0 - - + -
292A SER 3.6 12.3 - - - +
293A VAL* 3.8 13.5 - - + -
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Residues in contact with ARG 212 (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 LEU* 3.3 39.3 - - + +
149A LYS* 3.0 33.5 + - - +
150A ASN* 5.0 1.2 - - - +
151A LEU* 3.7 27.8 - - - +
210A GLN* 3.5 30.4 + - + -
211A LEU* 1.3 80.9 - - - +
213A LEU* 1.3 63.5 + - - +
222A GLN 4.6 0.6 + - - -
224A ASP* 3.0 36.6 + - - +
259A ARG 5.4 0.9 - - - -
260A PRO* 4.2 3.1 - - + -
290A SER 4.2 0.2 - - - +
291A MET* 3.4 3.3 - - - -
292A SER* 3.0 35.8 + - - +
294A TYR* 4.1 18.4 - - + -
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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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148A LEU* 3.9 2.2 - - - +
166A LEU* 3.9 20.2 - - + -
211A LEU* 4.7 6.3 - - + -
212A ARG* 1.3 76.3 - - - +
214A CYS* 1.3 65.3 + - - +
224A ASP* 3.4 9.8 + - - +
225A ASN 2.9 33.9 + - - +
226A TYR* 4.0 12.9 - - + -
227A PRO* 4.4 8.3 - - + -
230A LEU* 3.5 37.5 - - + -
232A ILE* 4.5 10.1 - - + -
259A ARG 5.6 1.6 + - - -
261A LEU* 4.7 4.7 - - + -
279A ILE* 4.5 10.5 - - + -
289A TYR* 5.5 1.6 - - + -
290A SER 3.4 5.4 - - - +
291A MET* 3.7 25.1 - - + -
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Residues in contact with CYS 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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146A GLY* 3.6 30.7 - - - -
147A GLN 4.6 0.2 - - - -
148A LEU* 4.0 19.5 - - + -
213A LEU* 1.3 77.8 - - - +
215A LEU* 1.3 75.8 + - - +
222A GLN* 4.0 11.9 - - + -
223A GLU 3.6 16.4 - - - +
225A ASN 3.6 7.4 + - - +
289A TYR* 3.3 10.1 - - - -
290A SER* 2.9 38.1 + - - -
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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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146A GLY* 5.0 2.4 - - - -
214A CYS* 1.3 93.7 - - - +
216A ALA* 1.3 62.5 + - - +
222A GLN* 3.9 27.4 - - - +
223A GLU 4.9 0.4 + - - -
225A ASN* 3.8 26.8 - - - +
287A LYS* 4.2 20.2 - - + -
288A ASN 3.4 25.1 - - - +
289A TYR* 3.8 30.7 - - + +
290A SER* 4.9 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