Contacts of the helix formed by residues 350 - 356 (chain D) in PDB entry 1FM6
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 350 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LYS* 3.5 28.6 + - - +
337D ASP* 2.6 21.7 + - - +
338D GLY* 3.9 0.2 - - - -
348D MET 3.8 0.8 + - - -
349D THR* 1.3 69.4 - - - +
351D GLU* 1.3 61.1 + - - +
353D LEU* 3.4 2.8 + - - +
354D LYS* 2.9 36.3 + - + +
365D GLU* 2.5 41.4 + - - +
368D PHE* 3.6 47.4 - - + +
369D GLU* 4.0 19.6 - - - +
372D VAL* 4.2 18.6 - - - +
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Residues in contact with GLU 351 (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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250D TYR 5.6 1.6 - - - +
349D THR* 3.3 7.7 + - - +
350D ARG* 1.3 79.4 - - - +
352D PHE* 1.3 63.4 + - - +
354D LYS* 3.4 9.4 + - - +
355D SER* 3.1 23.8 + - - -
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Residues in contact with PHE 352 (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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249D ILE* 4.0 22.0 - - + +
250D TYR* 3.4 24.9 + - - +
251D ASP* 3.5 26.7 - - + -
252D MET* 3.8 3.6 - - + -
255D LEU* 4.1 6.5 - - + -
277D VAL* 4.0 24.0 - - + -
281D ILE* 3.7 20.6 - - + -
348D MET* 3.9 21.8 - - + -
349D THR* 3.1 23.1 + - - +
350D ARG 3.3 0.2 - - - -
351D GLU* 1.3 76.2 - - - +
353D LEU* 1.3 64.6 + - - +
355D SER* 2.8 27.4 + - - -
356D LEU* 3.6 14.2 + - + +
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Residues in contact with LEU 353 (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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281D ILE* 3.8 21.1 - - + -
339D VAL* 4.4 3.1 - - + -
348D MET* 3.5 37.9 - - + +
349D THR 3.2 15.3 + - - +
350D ARG* 3.8 5.4 - - - +
352D PHE* 1.3 76.7 - - - +
354D LYS* 1.3 62.4 + - - +
356D LEU* 3.2 26.4 + - + +
360D PHE 4.0 1.0 - - - +
361D GLY* 3.4 9.9 - - - +
363D PHE* 4.1 13.7 - - + -
364D MET* 4.1 22.2 - - + -
368D PHE* 4.1 18.6 - - + -
503D BRL 3.9 22.2 - - - -
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Residues in contact with LYS 354 (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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350D ARG* 2.9 22.9 + - + +
351D GLU* 3.7 9.6 - - - +
352D PHE 3.2 0.2 - - - -
353D LEU* 1.3 78.0 - - - +
355D SER* 1.3 57.8 + - - +
356D LEU 3.4 0.9 - - - +
361D GLY* 3.1 23.5 - - - +
365D GLU* 3.7 42.1 + - + +
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Residues in contact with SER 355 (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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351D GLU* 3.1 14.4 + - - -
352D PHE* 2.8 30.0 + - - -
354D LYS* 1.3 76.0 - - - +
356D LEU* 1.3 68.8 + - - +
357D ARG* 3.5 2.1 + - - -
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Residues in contact with LEU 356 (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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277D VAL* 4.1 15.3 - - + -
278D ALA* 4.4 13.9 - - + +
281D ILE* 3.9 34.1 - - + -
352D PHE* 3.8 18.4 - - + +
353D LEU* 3.2 23.4 + - + +
354D LYS 3.4 1.1 - - - +
355D SER* 1.3 83.7 + - - +
357D ARG* 1.3 70.3 + - - +
360D PHE* 3.8 20.2 - - + +
361D GLY* 3.1 21.2 - - - +
363D PHE* 4.0 17.3 - - + -
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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