Contacts of the strand formed by residues 322 - 330 (chain U) in PDB entry 3FKS
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 SER 322 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146U GLU* 4.7 0.2 + - - -
163U ARG* 3.4 41.2 - - - +
164U GLY* 3.9 2.2 + - - -
201U LEU* 5.7 0.3 - - - +
260U ARG* 3.5 14.2 + - - +
264U LYS 3.3 1.6 + - - -
265U HIS* 3.3 24.7 + - - +
266U ALA* 3.3 19.6 + - - -
312U ALA 3.6 6.5 - - - -
313U LYS* 3.7 13.0 - - - -
321U GLY* 1.3 74.4 - - - -
323U LEU* 1.3 62.3 + - - +
324U THR* 4.2 0.9 + - - -
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Residues in contact with LEU 323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164U GLY* 3.4 9.7 - - - -
253U ALA* 4.3 6.1 - - + +
256U GLY* 4.0 19.3 - - - +
257U GLU* 3.6 36.8 - - + +
260U ARG* 4.1 11.2 - - + -
266U ALA* 3.2 20.2 - - + +
268U ILE* 3.7 27.1 - - + -
270U TYR* 5.8 1.8 - - - +
310U ARG* 4.1 2.5 - - + +
311U ALA* 3.1 45.0 - - + +
312U ALA 3.3 14.8 + - - +
322U SER* 1.3 76.9 - - - +
324U THR* 1.3 57.3 + - - +
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Residues in contact with THR 324 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL* 4.1 3.5 - - + +
161U ILE* 4.2 14.6 - - + -
162U GLY 2.8 25.8 + - - +
163U ARG* 2.9 9.0 - - - +
164U GLY 2.8 12.6 + - - +
165U GLN 3.4 13.7 - - - +
201U LEU* 5.2 2.4 - - - +
266U ALA 3.1 7.4 + - - -
267U LEU* 3.5 31.0 - - + +
268U ILE* 2.9 31.1 + - - +
322U SER* 4.2 0.7 + - - -
323U LEU* 1.3 72.3 - - - +
325U ALA* 1.3 67.0 + - - +
326U LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 325 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165U GLN 2.8 11.6 + - - +
166U ARG* 3.6 24.2 - - + -
167U GLU 3.0 24.9 + - - -
268U ILE* 3.5 11.2 - - + +
270U TYR* 4.5 11.2 - - + -
308U LEU* 4.5 5.4 - - + -
311U ALA* 3.8 14.4 - - + -
323U LEU 3.8 0.8 + - - -
324U THR* 1.3 74.1 - - - +
326U LEU* 1.3 66.6 + - - +
327U PRO* 3.5 6.3 - - + -
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Residues in contact with LEU 326 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U THR* 5.9 2.0 - - + -
161U ILE* 4.3 17.9 - - + -
167U GLU* 3.4 30.7 - - + +
169U ILE* 4.3 20.9 - - + -
181U ALA* 4.8 7.6 - - + +
184U THR* 4.9 13.2 - - + +
185U ILE* 6.1 0.2 - - + -
267U LEU* 3.9 22.9 - - + -
268U ILE 3.1 8.5 + - - -
269U VAL* 3.6 32.6 - - + +
270U TYR* 3.4 19.1 + - - -
324U THR* 4.7 1.3 - - + -
325U ALA* 1.3 84.0 - - - +
327U PRO* 1.3 65.7 - - - +
328U VAL* 3.4 3.7 + - - +
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Residues in contact with PRO 327 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166U ARG* 4.9 1.3 - - + -
167U GLU 3.2 21.1 - - - +
168U LEU* 3.1 15.1 - - + +
169U ILE 2.8 27.4 + - - -
270U TYR* 4.3 8.1 - - + +
273U LEU* 3.4 25.8 - - + -
308U LEU* 3.6 27.1 - - + -
325U ALA* 3.5 7.4 - - + +
326U LEU* 1.3 86.9 - - - +
328U VAL* 1.3 60.0 + - - +
344U VAL* 4.4 0.4 - - + -
348U THR* 3.7 17.5 - - + -
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Residues in contact with VAL 328 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169U ILE* 3.4 28.3 - - + +
177U LYS* 4.0 30.3 - - + +
178U THR* 5.8 0.9 - - - -
181U ALA* 5.3 1.1 - - + -
269U VAL* 4.1 11.4 - - + -
270U TYR 3.0 20.4 + - - +
271U ASP* 3.8 22.0 - - + +
272U ASP* 3.2 14.1 - - - +
273U LEU* 3.0 31.4 + - - +
326U LEU 3.8 7.9 - - - +
327U PRO* 1.3 75.2 - - - +
329U ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 329 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168U LEU* 3.7 20.9 - - + -
169U ILE 3.0 7.6 + - - +
170U ILE* 3.5 45.3 - - + +
171U GLY 3.6 4.9 + - - -
177U LYS* 3.8 4.7 - - - +
272U ASP* 3.9 0.4 - - - -
273U LEU* 4.9 5.4 - - + -
274U SER* 2.9 21.3 - - - +
327U PRO 4.0 0.2 + - - -
328U VAL* 1.3 74.6 - - - +
330U GLU* 1.3 75.6 + - - +
331U THR* 4.1 1.8 - - + +
340U ILE* 4.4 15.7 - - + -
341U PRO* 3.7 35.9 - - + -
344U VAL* 5.1 7.6 - - + -
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Residues in contact with GLU 330 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171U GLY 3.6 5.2 - - - +
173U ARG* 3.6 27.8 - - - +
177U LYS* 4.0 17.7 - - - +
272U ASP* 3.7 13.8 + - - +
274U SER* 2.9 19.6 + - - +
275U LYS* 3.5 22.5 + - - -
329U ILE* 1.3 80.7 - - - +
331U THR* 1.3 72.3 + - - +
332U GLN* 3.1 26.1 + - - +
341U PRO* 5.3 0.5 - - - +
323X ALA* 4.2 12.3 - - - +
326X PHE* 6.1 0.2 - - - +
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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