Contacts of the helix formed by residues 303 - 313 (chain D) in PDB entry 1FBA
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 ARG 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D GLU* 5.2 1.9 + - - +
41D LYS* 4.5 3.8 - - - +
42D ARG* 3.3 54.8 - - - +
45D ASP* 4.7 10.9 + - - -
271D SER* 5.5 1.9 + - - +
302D GLY* 1.3 72.6 - - - +
304D ALA* 1.3 56.7 + - - +
305D LEU 3.0 0.2 - - - -
306D GLN* 3.1 7.4 + - - +
307D ALA* 2.9 38.1 + - - +
355D SER 5.5 0.2 + - - -
356D LEU* 3.2 64.8 + - + +
358D VAL* 3.5 22.1 - - - +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D SER* 3.6 27.6 + - - +
274D GLN 4.8 1.6 - - - +
276D GLU* 3.2 34.4 - - - +
279D ALA* 4.1 10.3 - - + -
301D TYR* 3.9 23.3 - - + -
302D GLY 3.2 1.2 - - - +
303D ARG* 1.3 77.1 - - - +
305D LEU* 1.3 58.4 + - - +
330D ARG* 4.5 6.2 - - - -
334D ASN* 4.5 6.4 + - - -
356D LEU* 4.1 7.8 - - + +
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE 3.8 14.8 - - - +
30D LEU* 3.7 26.0 - - + -
73D ILE* 4.2 4.9 - - + -
276D GLU* 4.2 5.2 - - - +
299D PHE* 3.9 13.9 - - + -
301D TYR* 3.5 28.5 - - + +
302D GLY 3.0 9.9 + - - +
304D ALA* 1.3 79.8 - - - +
306D GLN* 1.3 56.7 + - - +
307D ALA 3.9 0.7 - - - -
309D VAL* 3.6 16.1 - - - +
327D LEU* 3.9 15.4 - - + +
330D ARG* 3.9 13.7 - - + +
331D ALA* 3.9 29.4 - - + +
334D ASN* 3.8 21.1 - - - +
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.1 15.6 - - + +
31D ALA 3.1 26.5 + - - -
32D ALA* 4.3 2.7 - - - +
34D GLU* 3.2 22.6 + - - +
39D MET* 5.6 0.3 - - - +
58D TYR* 2.8 39.2 + - - +
59D ARG* 5.8 0.2 + - - -
62D LEU* 3.7 16.0 - - + +
302D GLY* 3.2 18.2 + - - +
303D ARG* 3.1 4.7 + - - +
305D LEU* 1.3 82.3 - - - +
307D ALA* 1.3 67.6 + - - +
308D SER 3.3 2.5 - - - -
309D VAL* 3.0 17.8 + - + +
310D LEU* 3.0 22.6 + - + +
327D LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D GLU* 3.3 9.9 + - - +
303D ARG* 2.9 12.7 + - - +
306D GLN* 1.3 77.0 - - - +
308D SER* 1.3 62.7 + - - +
310D LEU* 3.4 10.0 + - - +
311D ARG* 3.2 27.5 + - - +
353D SER* 3.7 15.0 - - - -
356D LEU* 3.5 31.9 - - + -
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D GLU* 2.8 35.3 + - - -
307D ALA* 1.3 70.6 - - - +
309D VAL* 1.3 61.0 + - - +
311D ARG* 3.4 8.7 + - - +
312D ALA* 2.9 32.1 + - - +
326D GLU* 3.7 28.0 + - - +
330D ARG* 5.5 4.9 - - - -
352D GLY* 4.1 11.6 - - - -
353D SER* 4.1 3.3 + - - -
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TYR* 4.2 9.4 - - + +
61D LEU* 4.1 22.9 - - + -
62D LEU* 4.2 14.4 - - + -
305D LEU 3.6 21.5 - - - +
306D GLN* 3.0 11.5 + - + +
308D SER* 1.3 75.6 - - - +
310D LEU* 1.3 59.5 + - - +
312D ALA* 3.2 2.8 + - - +
313D TRP* 2.9 33.2 + - + +
323D GLY* 3.6 14.7 - - - +
326D GLU* 4.0 9.0 - - + -
327D LEU* 3.6 36.6 - - + +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D MET* 4.4 10.5 - - + -
42D ARG* 4.2 31.4 - - + +
43D LEU* 4.5 3.6 - - + -
46D ILE* 3.6 36.5 - - + +
58D TYR* 3.5 42.2 - - + +
306D GLN* 3.0 23.5 + - + +
307D ALA* 3.7 9.9 - - - +
309D VAL* 1.3 76.6 - - - +
311D ARG* 1.3 57.9 + - - +
313D TRP* 3.7 5.6 - - + +
314D ALA* 2.8 30.5 + - - -
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Residues in contact with ARG 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 5.9 5.7 + - - +
46D ILE* 4.4 16.2 - - + +
307D ALA* 3.2 17.9 + - - +
308D SER* 3.7 7.9 - - - +
309D VAL 3.2 0.4 - - - -
310D LEU* 1.3 80.7 - - - +
312D ALA* 1.3 62.2 + - - +
314D ALA* 3.8 13.2 + - - +
353D SER* 6.3 0.8 - - - +
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Residues in contact with ALA 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D SER 2.9 18.4 + - - +
309D VAL 3.8 2.7 - - - +
311D ARG* 1.3 76.5 - - - +
313D TRP* 1.3 62.2 + - - +
314D ALA* 4.4 0.5 - - - +
319D ASN* 3.3 22.7 + - - +
322D ALA* 4.0 23.1 - - + +
323D GLY 4.6 0.2 - - - -
326D GLU* 3.7 23.6 - - + +
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Residues in contact with TRP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.0 12.3 - - + -
46D ILE* 3.8 20.9 - - + -
48D VAL* 4.8 6.1 - - + -
54D ASN* 4.2 8.3 - - - -
57D ALA* 4.6 11.6 + - + -
58D TYR* 3.7 49.4 - + + -
61D LEU* 3.1 36.0 - - + +
309D VAL* 2.9 19.1 + - + +
310D LEU* 3.7 4.5 - - + +
312D ALA* 1.3 77.4 - - - +
314D ALA* 1.3 64.1 + - - +
315D GLY* 3.1 34.3 + - - -
316D LYS 3.1 37.0 + - - +
317D LYS* 4.6 4.6 - - + +
319D ASN* 3.0 33.2 + - - +
320D ILE* 4.6 3.2 - - - +
323D GLY* 4.4 2.4 - - - -
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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