Contacts of the helix formed by residues 323 - 337 (chain A) in PDB entry 1F0K
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 5.7 0.4 - - - -
321A GLY 3.9 2.8 + - - -
322A TRP* 1.3 72.8 - - - +
324A ARG* 1.3 59.4 + - - +
325A GLU* 3.5 8.8 + - - +
326A THR* 2.7 34.7 + - - -
327A LEU* 2.8 32.2 + - - +
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Residues in contact with ARG 324 (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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177A LEU* 4.8 4.4 - - - +
180A ARG* 3.6 36.4 + - - +
181A GLU* 3.8 17.0 + - - +
182A GLY 3.1 20.5 + - - +
183A PRO 3.1 21.6 + - - -
184A VAL* 4.6 15.3 - - + +
185A ARG* 4.8 2.2 - - - +
256A ASP* 2.8 44.8 + - - -
323A SER* 1.3 71.4 - - - +
325A GLU* 1.3 61.6 + - - +
327A LEU* 3.2 10.1 + - + +
328A LEU* 2.9 28.9 + - - +
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Residues in contact with GLU 325 (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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323A SER* 3.5 8.2 + - - +
324A ARG* 1.3 78.6 - - - +
326A THR* 1.3 65.3 + - - +
328A LEU* 3.3 19.2 + - - +
329A THR* 3.2 27.2 + - - +
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Residues in contact with THR 326 (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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321A GLY 5.1 2.3 + - - +
322A TRP* 4.3 15.9 - - + -
323A SER* 2.7 33.6 + - - +
325A GLU* 1.3 79.5 - - - +
327A LEU* 1.3 62.5 + - - +
329A THR* 3.0 11.8 + - - -
330A MET* 3.0 39.8 + - + +
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Residues in contact with LEU 327 (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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177A LEU* 4.6 5.6 - - + +
184A VAL* 3.7 39.7 - - + -
256A ASP* 4.3 15.7 - - + +
257A VAL* 4.5 6.3 - - + -
276A PRO* 3.2 32.6 - - + +
322A TRP* 3.7 40.4 - - + +
323A SER 2.8 26.4 + - - +
324A ARG* 3.2 10.7 + - + +
326A THR* 1.3 72.4 - - - +
328A LEU* 1.3 57.4 + - - +
330A MET* 4.3 3.8 - - - -
331A ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PRO* 4.2 15.9 - - + +
174A GLN* 4.3 10.5 - - + +
177A LEU* 3.7 32.7 - - + +
324A ARG 2.9 13.8 + - - +
325A GLU* 3.6 23.6 - - - +
326A THR 3.2 0.2 - - - -
327A LEU* 1.3 75.7 - - - +
329A THR* 1.3 63.5 + - - +
331A ALA* 3.3 1.6 + - - +
332A GLU* 3.0 50.6 + - + +
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Residues in contact with THR 329 (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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325A GLU* 3.2 23.1 + - - +
326A THR* 3.0 13.2 + - - -
328A LEU* 1.3 78.6 - - - +
330A MET* 1.3 65.4 + - + +
332A GLU* 3.0 15.6 + - + +
333A ARG* 2.9 59.5 + - - +
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Residues in contact with MET 330 (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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276A PRO* 3.7 15.3 - - + -
300A GLY 3.6 22.7 - - - +
301A ALA* 3.6 26.9 - - - +
302A ALA* 3.8 8.3 - - - +
322A TRP* 3.6 50.9 - - + +
326A THR* 3.0 31.8 + - + +
327A LEU* 3.7 15.3 - - - +
329A THR* 1.3 76.8 - - + +
331A ALA* 1.3 53.3 + - - +
333A ARG* 3.2 3.4 + - - +
334A ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 331 (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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173A PRO* 3.7 20.6 - - + +
176A ARG* 3.9 7.2 - - - +
177A LEU* 4.2 4.7 - - + -
274A GLY* 3.4 22.1 - - - +
276A PRO* 3.6 15.7 - - + +
327A LEU 2.9 19.2 + - - +
328A LEU 3.4 6.5 - - - +
329A THR 3.1 0.2 - - - -
330A MET* 1.3 76.7 - - - +
332A GLU* 1.3 62.7 + - - +
334A ALA* 3.1 4.6 + - - +
335A ARG 3.0 18.2 + - - -
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Residues in contact with GLU 332 (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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173A PRO* 4.1 20.2 - - + -
174A GLN* 3.1 36.3 - - + +
328A LEU* 3.0 31.7 + - + +
329A THR* 3.0 13.3 + - + +
331A ALA* 1.3 75.0 - - - +
333A ARG* 1.3 64.4 + - + +
335A ARG* 3.3 3.5 + - - +
336A ALA* 2.9 25.3 + - - +
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Residues in contact with ARG 333 (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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299A ALA* 3.4 27.0 + - + +
300A GLY* 2.9 25.9 + - - -
301A ALA* 3.9 9.1 - - + +
329A THR* 2.9 43.3 + - - +
330A MET* 3.3 7.4 - - - +
332A GLU* 1.3 78.0 - - - +
334A ALA* 1.3 61.4 - - - +
336A ALA* 3.2 8.1 + - - +
337A ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 334 (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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270A ILE* 5.2 0.9 - - + -
271A ALA* 3.3 30.4 - - - +
274A GLY* 4.2 0.2 - - - -
275A LEU 3.5 33.0 - - - +
296A LEU* 4.4 7.6 - - + -
301A ALA* 3.4 16.1 - - + +
330A MET 2.8 16.5 + - - +
331A ALA 3.4 8.3 - - - +
333A ARG* 1.3 73.0 - - - +
335A ARG* 1.3 60.9 + - - +
337A ALA* 3.3 9.5 + - - +
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Residues in contact with ARG 335 (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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168A LEU 4.0 11.5 + - - -
170A LEU* 2.9 30.5 + - - +
171A PRO 3.5 11.7 + - - -
172A LEU* 3.5 43.0 - - + +
173A PRO* 4.0 9.9 - - + +
271A ALA 3.3 7.4 + - - -
272A ALA* 3.0 30.4 + - - +
273A ALA* 3.9 11.7 + - - +
274A GLY* 3.8 6.9 - - - -
331A ALA 3.0 14.6 + - - +
332A GLU* 3.7 4.9 - - - +
334A ALA* 1.3 77.0 - - - +
336A ALA* 1.3 63.2 + - - +
338A SER* 3.1 22.2 + - - +
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Residues in contact with ALA 336 (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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332A GLU 2.9 16.9 + - - +
333A ARG* 3.2 9.2 + - - +
335A ARG* 1.3 77.3 - - - +
337A ALA* 1.3 55.6 - - - +
338A SER 3.1 7.9 + - - +
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Residues in contact with ALA 337 (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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271A ALA* 3.9 8.3 - - - +
295A PRO 5.7 1.6 - - - +
296A LEU* 4.2 18.0 - - + +
299A ALA* 4.6 15.7 - - + -
333A ARG 3.1 14.1 + - - +
334A ALA 3.3 7.6 + - - +
335A ARG 3.1 0.8 - - - -
336A ALA* 1.3 75.9 - - - +
338A SER* 1.3 56.5 + - - +
339A ILE* 4.4 3.5 + - - +
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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