Contacts of the helix formed by residues 339 - 350 (chain A) in PDB entry 5FN2
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 GLY 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ASN* 3.0 28.0 + - - -
331A GLN 4.1 4.7 - - - -
332A GLY* 3.6 5.0 - - - -
337A TYR 3.0 0.4 - - - -
338A ILE* 1.3 82.8 - - - +
340A SER* 1.3 61.0 + - - +
341A SER 3.2 1.3 - - - -
342A ARG* 3.2 2.8 + - - +
343A MET* 2.9 24.4 + - - +
630A ALA* 3.7 15.9 - - - -
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Residues in contact with SER 340 (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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255A ASN* 3.8 2.2 + - - -
330A PHE* 3.4 18.8 - - - +
333A GLU* 2.8 29.5 + - - -
337A TYR* 3.3 25.1 - - - +
339A GLY* 1.3 73.4 - - - +
341A SER* 1.3 54.5 + - - +
343A MET* 3.2 4.5 + - - +
344A VAL* 2.9 31.9 + - - +
426A SER* 3.3 17.0 - - - -
429A ARG* 3.7 12.1 - - - -
430A PHE* 4.8 1.3 - - - -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP 5.1 0.2 - - - -
337A TYR 2.3 29.8 + - - -
338A ILE* 3.8 4.9 - - - -
340A SER* 1.3 77.6 + - - +
342A ARG* 1.3 58.6 + - - +
344A VAL* 3.2 5.0 + - - +
345A TYR* 2.9 29.9 + - - +
429A ARG* 3.4 43.4 - - - +
633A PRO* 3.8 8.3 - - - +
645A TYR* 3.6 21.1 + - - -
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Residues in contact with ARG 342 (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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338A ILE 3.6 9.2 - - - +
339A GLY 3.2 9.7 + - - +
341A SER* 1.3 82.7 + - - +
343A MET* 1.3 56.0 + - - +
345A TYR* 3.2 6.4 + - - +
346A ASP* 2.9 56.3 + - - +
629A ARG* 3.2 46.6 + - - +
630A ALA* 3.0 26.8 + - - +
631A LEU* 4.2 10.3 - - - +
632A SER 2.4 26.6 + - - +
633A PRO* 4.1 7.4 - - - -
636A GLU* 3.3 38.3 + - - +
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Residues in contact with MET 343 (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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255A ASN* 3.3 29.2 - - + +
257A TRP* 4.0 11.9 - - + -
326A MET* 3.5 28.5 - - + -
328A VAL* 4.6 0.7 - - + -
330A PHE* 3.7 23.6 - - + -
339A GLY 2.9 6.9 + - - +
340A SER 3.3 9.0 - - - +
342A ARG* 1.3 78.1 - - - +
344A VAL* 1.3 56.3 + - - +
346A ASP* 3.2 10.2 + - - +
347A MET* 2.9 44.0 + - - +
352A PHE* 3.4 45.3 - - + -
430A PHE* 4.9 4.0 - - + -
628A ALA* 4.2 8.7 - - + -
629A ARG 5.5 0.7 - - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER 2.9 16.6 + - - +
341A SER* 3.3 11.7 - - - +
343A MET* 1.3 75.1 - - - +
345A TYR* 1.3 58.0 + - - +
347A MET* 3.2 10.7 + - - +
348A GLU* 2.9 44.5 + - - +
356A LEU* 5.4 3.4 - - + +
429A ARG* 3.9 16.6 - - + +
430A PHE* 3.5 50.7 - - + +
432A ARG* 6.0 0.9 - - + -
433A ALA* 4.5 14.4 - - + +
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Residues in contact with TYR 345 (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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341A SER 2.9 12.9 + - - +
342A ARG* 3.2 11.7 - - - +
344A VAL* 1.3 79.7 - - - +
346A ASP* 1.3 64.3 + - - +
348A GLU* 3.2 13.7 + - + +
349A LYS* 2.9 70.7 + - + +
351A LYS* 5.9 0.4 - - - -
633A PRO* 4.0 18.6 - - + -
636A GLU* 3.2 35.6 + - - -
637A LEU* 3.3 39.2 - - + +
645A TYR* 3.9 36.1 - + + -
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Residues in contact with ASP 346 (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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342A ARG* 2.9 51.2 + - - +
343A MET* 3.4 12.3 - - - +
345A TYR* 1.3 83.0 - - - +
347A MET* 1.3 56.8 + - - +
349A LYS* 3.2 6.4 + - - +
350A GLY* 2.9 26.5 + - - -
351A LYS* 3.3 19.2 + - - +
352A PHE* 3.7 29.9 - - + +
628A ALA* 5.8 1.9 - - - +
629A ARG 4.3 5.7 + - - +
636A GLU* 4.3 2.3 - - - +
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Residues in contact with MET 347 (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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277A VAL* 5.9 1.6 - - + -
326A MET* 5.5 3.1 - - + -
343A MET* 2.9 35.5 + - + +
344A VAL* 3.4 8.5 - - - +
346A ASP* 1.3 77.5 - - - +
348A GLU* 1.3 62.0 + - - +
350A GLY* 3.3 10.0 + - - -
352A PHE* 3.4 21.5 - - + -
354A VAL* 3.1 34.5 - - - +
355A GLN* 3.6 22.2 - - - +
356A LEU* 3.6 32.1 - - + +
359A VAL* 3.5 31.2 - - + -
430A PHE* 3.7 15.9 - - + -
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Residues in contact with GLU 348 (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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344A VAL* 2.9 25.9 + - - +
345A TYR* 3.2 15.1 + - + +
347A MET* 1.3 78.9 - - - +
349A LYS* 1.3 68.0 - - + +
355A GLN* 4.5 8.4 + - - -
356A LEU* 4.7 8.5 - - + -
433A ALA* 3.8 30.5 - - + +
645A TYR* 5.6 2.3 + - - -
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Residues in contact with LYS 349 (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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345A TYR* 2.9 62.8 + - + +
346A ASP* 3.2 8.0 + - - +
348A GLU* 1.3 83.7 - - + +
350A GLY* 1.3 59.5 + - - +
351A LYS* 3.4 44.7 - - + +
355A GLN* 4.8 4.4 + - - -
637A LEU* 6.2 0.4 - - - +
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Residues in contact with GLY 350 (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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268A THR* 5.0 9.5 + - - -
346A ASP 2.9 6.6 + - - -
347A MET 3.3 9.4 + - - -
349A LYS* 1.3 79.6 - - - +
351A LYS* 1.3 59.1 + - - +
352A PHE 3.2 17.7 + - - -
355A GLN* 4.8 11.2 - - - -
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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