Contacts of the strand formed by residues 322 - 330 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163J ARG* 3.6 15.7 - - - +
164J GLY 4.0 11.6 + - - -
201J LEU* 5.8 0.3 - - - +
260J ARG* 3.4 19.1 + - - +
264J LYS 3.1 5.1 + - - -
265J HIS* 2.9 27.1 + - - +
266J ALA* 3.3 20.1 + - - +
312J ALA 3.5 11.7 - - - -
313J LYS* 4.0 15.3 - - - -
321J GLY* 1.3 75.2 - - - -
323J LEU* 1.3 61.2 + - - +
324J THR* 4.3 1.6 + - - -
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Residues in contact with LEU 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLY* 3.3 13.8 - - - -
253J ALA* 4.0 26.2 - - + +
256J GLY* 4.1 12.1 - - - +
257J GLU* 4.2 11.9 - - + +
260J ARG* 3.7 16.6 - - + +
266J ALA* 3.2 32.1 - - + +
267J LEU 4.7 0.4 - - - -
268J ILE* 4.1 24.5 - - + -
270J TYR* 5.5 1.1 - - - +
310J ARG* 4.3 8.1 - - + +
311J ALA* 3.2 38.4 - - + +
312J ALA 3.1 7.8 + - - -
322J SER* 1.3 75.4 - - - +
324J THR* 1.3 61.1 + - - +
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Residues in contact with THR 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J VAL* 4.0 11.5 - - + +
161J ILE* 4.3 10.8 - - + -
162J GLY 3.5 15.3 - - - +
163J ARG* 3.3 11.1 - - - +
164J GLY 2.9 16.8 + - - +
165J GLN 3.2 20.0 - - - +
201J LEU* 5.1 4.0 - - - +
266J ALA 2.9 11.8 + - - -
267J LEU* 3.5 24.1 - - + +
268J ILE* 2.8 32.5 + - - +
322J SER* 4.6 1.9 + - - -
323J LEU* 1.3 70.6 - - - +
325J ALA* 1.3 62.8 + - - +
326J LEU* 5.3 0.4 - - + -
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Residues in contact with ALA 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J GLN 3.2 8.4 + - - +
166J ARG* 3.9 13.9 - - + -
167J GLU 3.2 27.2 + - - +
268J ILE* 3.5 5.2 - - + -
270J TYR* 4.2 20.6 - - + -
308J LEU* 4.8 4.0 - - + +
311J ALA* 3.8 21.8 - - + -
323J LEU 4.0 1.0 + - - -
324J THR* 1.3 73.6 - - - +
326J LEU* 1.3 63.6 + - - +
327J PRO* 3.3 8.9 - - + +
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Residues in contact with LEU 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J VAL* 6.1 0.4 - - + -
150J THR* 6.0 1.1 - - + -
161J ILE* 4.6 14.4 - - + -
167J GLU* 3.5 28.3 - - + +
169J ILE* 4.4 17.9 - - + -
181J ALA* 4.8 7.6 - - + -
184J THR* 4.3 20.2 - - + +
267J LEU* 3.7 36.6 - - + -
268J ILE 2.7 9.5 + - - +
269J VAL* 3.2 27.7 - - + +
270J TYR 3.1 19.2 + - - -
324J THR* 5.4 0.2 - - + -
325J ALA* 1.3 77.4 - - - +
327J PRO* 1.3 65.2 - - - +
328J VAL* 4.2 0.9 - - - +
352J ILE* 6.1 0.2 - - + -
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Residues in contact with PRO 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J ARG 5.1 0.2 - - - -
167J GLU 3.1 21.1 - - - +
168J LEU* 3.6 13.7 - - + -
169J ILE* 2.8 29.1 + - - +
270J TYR* 3.7 16.4 - - + +
273J LEU* 3.6 21.3 - - + -
308J LEU* 3.6 28.0 - - + -
325J ALA* 3.3 6.7 - - + +
326J LEU* 1.3 91.1 - - - +
328J VAL* 1.3 60.0 + - - +
344J VAL* 4.5 0.9 - - + -
348J THR* 4.3 9.6 - - + -
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Residues in contact with VAL 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J ILE* 3.3 14.8 - - + +
177J LYS* 3.8 43.5 - - + +
178J THR 5.6 0.2 - - - +
181J ALA* 5.4 2.0 - - + -
269J VAL* 4.2 7.6 - - + -
270J TYR* 2.7 21.2 + - - +
271J ASP* 4.0 22.9 - - + +
272J ASP* 3.0 34.6 - - + +
273J LEU 3.2 11.0 + - - +
326J LEU 4.2 5.2 - - - +
327J PRO* 1.3 79.8 - - - +
329J ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J LEU* 3.7 20.2 - - + -
169J ILE 2.9 9.9 + - - -
170J ILE* 3.4 24.2 - - + +
171J GLY 3.3 24.8 + - - +
177J LYS* 3.8 4.2 - - - +
273J LEU* 3.7 23.1 - - + -
274J SER* 3.4 15.7 - - - +
328J VAL* 1.3 82.7 - - - +
330J GLU* 1.3 63.9 + - - +
340J ILE* 4.3 7.9 - - + -
341J PRO* 4.0 28.7 - - + -
344J VAL* 3.7 25.1 - - + -
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Residues in contact with GLU 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J GLY 3.6 2.5 - - - -
173J ARG* 3.7 30.0 - - + +
177J LYS* 4.0 23.3 + - - +
272J ASP* 4.7 7.3 - - - +
274J SER* 2.9 26.3 + - - +
275J LYS* 4.2 22.5 + - - -
328J VAL* 4.2 1.8 - - - +
329J ILE* 1.3 74.3 - - - +
331J THR* 1.3 70.0 + - - +
332J GLN* 4.5 15.7 + - - +
341J PRO* 5.0 2.9 - - - +
606J PO4 4.6 4.7 + - - -
323M ALA 5.7 0.9 - - - +
327M ALA* 5.7 2.9 - - - +
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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