Contacts of the helix formed by residues 426 - 431 (chain A) in PDB entry 5FN3
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 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A ALA* 4.5 0.2 - - - -
330A PHE* 3.1 32.8 - - - -
333A GLU* 3.2 26.3 + - - +
337A TYR* 4.1 5.3 - - - -
340A SER* 3.2 16.9 - - - -
362A PHE* 3.8 11.0 - - - -
364A GLU* 4.0 16.1 + - - -
425A SER* 1.3 69.6 + - - +
427A LEU* 1.3 65.6 + - - +
429A ARG* 3.1 20.3 + - - +
430A PHE* 3.7 6.2 + - - -
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Residues in contact with LEU 427 (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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362A PHE* 3.3 46.7 - - + -
422A LEU* 3.8 21.3 - - + -
425A SER* 2.8 15.4 + - - +
426A SER* 1.3 74.7 - - - +
428A GLN* 1.3 54.5 - - + +
430A PHE* 2.6 36.7 + - + +
431A LEU* 3.4 32.6 + - + +
436A ILE* 5.1 1.8 - - + -
438A GLY* 3.6 37.2 - - - +
439A VAL 3.9 2.7 - - - +
440A VAL* 3.8 20.4 - - + -
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Residues in contact with GLN 428 (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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141A PRO 5.8 0.4 + - - -
142A ASN 5.3 1.0 + - - -
143A ASP* 6.1 1.2 - - - +
146A GLY* 3.0 15.8 - - - -
147A VAL* 2.8 66.7 + - + +
148A TYR* 3.6 15.0 - - - -
337A TYR* 3.1 24.3 + - + +
422A LEU* 4.1 18.5 + - + -
423A PRO 3.5 17.1 + - - +
424A PRO* 3.7 6.3 - - - +
425A SER 2.6 22.0 + - - +
427A LEU* 1.3 72.5 - - - +
429A ARG* 1.3 56.1 + - - +
431A LEU* 4.2 14.4 - - + -
432A ARG* 4.4 0.9 - - - +
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Residues in contact with ARG 429 (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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145A PHE* 2.6 48.4 + - - +
336A ASP 4.3 1.2 + - - -
337A TYR* 3.8 23.6 - - + +
340A SER* 3.9 8.1 - - - +
341A SER* 3.3 49.4 - - - +
344A VAL* 4.1 14.9 - - + +
425A SER 4.0 0.4 + - - -
426A SER 3.1 14.2 + - - +
427A LEU 2.9 0.2 + - - -
428A GLN* 1.3 78.9 - - - +
430A PHE* 1.3 65.7 + - + +
432A ARG* 3.0 47.2 + - - +
644A GLU 3.7 19.0 + - - -
645A TYR* 4.4 10.1 - - - +
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Residues in contact with PHE 430 (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* 4.7 12.8 - - + -
326A MET* 6.2 1.1 - - + -
328A VAL* 5.9 0.2 - - + -
330A PHE* 4.3 22.7 - + - -
340A SER* 4.6 6.1 - - - -
343A MET* 4.8 11.9 - - + -
344A VAL* 3.4 26.5 - - + -
347A MET* 4.0 25.1 - - + -
356A LEU* 3.9 17.8 - - + +
359A VAL* 5.0 4.3 - - + -
362A PHE* 3.3 40.8 - + + -
426A SER* 3.8 10.8 - - - -
427A LEU 2.6 13.9 + - - +
429A ARG* 1.3 75.8 - - + +
431A LEU* 1.3 57.0 + - + +
433A ALA* 2.8 24.9 + - - +
434A ARG 3.3 9.4 + - - +
436A ILE* 3.8 17.8 - - + +
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Residues in contact with LEU 431 (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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147A VAL* 3.4 29.2 - - + +
152A TYR* 3.8 19.4 + - - +
381A ASP* 3.7 35.7 - - + +
384A SER* 4.8 0.2 - - - +
422A LEU* 4.4 11.4 - - + -
427A LEU* 3.4 35.0 - - + +
428A GLN* 4.2 10.8 - - - +
429A ARG 3.1 0.8 + - - -
430A PHE* 1.3 77.7 - - - +
432A ARG* 1.3 60.0 + - - +
433A ALA 3.1 2.1 + - - -
434A ARG 3.3 16.2 + - - +
435A ASN 3.9 20.2 - - - +
436A ILE* 4.3 9.6 - - + +
438A GLY* 5.5 0.7 - - - -
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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