Contacts of the helix formed by residues 314 - 319 (chain A) in PDB entry 4FDI
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 PHE 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LEU* 3.5 31.2 - - + +
308A CYS* 3.6 19.7 - - - -
312A THR* 3.3 13.9 - - - +
313A THR* 1.3 83.9 - - - +
315A GLU* 1.3 67.6 + - - +
316A GLY 3.2 0.7 - - - -
317A GLY* 2.9 15.6 + - - -
318A MET* 3.6 4.7 + - - +
399A LYS* 3.6 2.0 - - - +
401A HIS* 3.6 26.7 - + - -
404A THR* 4.4 10.8 - - + -
405A TRP 4.0 12.6 - - - -
406A THR* 3.8 24.0 - - + -
427A VAL* 3.2 46.2 - - + -
428A THR* 4.2 3.6 - - + -
450A GLU* 3.5 10.5 - - - +
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Residues in contact with GLU 315 (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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73A TYR* 2.5 30.1 + - - -
306A PHE* 3.5 30.7 - - + -
314A PHE* 1.3 70.5 - - - +
316A GLY* 1.3 57.8 + - - +
317A GLY 3.1 0.2 + - - -
318A MET 4.8 0.2 - - - +
319A ARG* 2.9 53.6 + - - +
384A TYR* 2.8 26.0 + - - -
399A LYS* 2.9 19.0 + - - +
444A LEU* 3.6 19.6 - - + +
448A PRO 4.1 2.0 - - - +
450A GLU* 2.9 29.4 + - - +
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 6.4 0.4 - - - -
290A GLY* 3.3 13.3 - - - -
303A ASN* 3.2 29.6 + - - +
306A PHE* 3.5 15.4 - - - +
307A LEU 3.0 20.4 + - - -
308A CYS 3.7 7.6 - - - -
309A GLY* 3.4 6.5 - - - -
315A GLU* 1.3 78.5 - - - +
317A GLY* 1.3 57.3 + - - +
319A ARG 4.7 3.0 - - - +
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Residues in contact with GLY 317 (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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77A PRO* 4.0 5.4 - - - +
289A ASN* 3.9 8.0 - - - +
290A GLY* 3.0 20.0 + - - -
309A GLY* 3.1 28.5 + - - +
310A LYS* 3.9 1.1 - - - -
312A THR* 3.5 11.6 + - - -
314A PHE 2.9 6.7 + - - -
316A GLY* 1.3 79.6 - - - +
318A MET* 1.3 66.8 + - - +
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Residues in contact with MET 318 (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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73A TYR* 3.2 8.7 - - + -
74A SER* 2.8 52.1 + - - +
75A ALA* 3.5 6.3 - - - +
76A ASN* 3.4 40.2 - - - +
77A PRO* 3.9 3.4 - - + -
312A THR 4.2 2.5 - - - +
313A THR* 3.8 29.6 - - - -
314A PHE 3.6 3.2 + - - +
315A GLU 3.3 1.8 + - - -
317A GLY* 1.3 86.0 - - - +
319A ARG* 1.3 61.0 + - - +
320A GLU* 3.3 8.9 - - - +
382A ILE* 5.7 1.1 - - + -
383A PHE 4.3 5.2 - - - +
384A TYR* 3.9 42.2 - - + -
385A TYR 4.3 1.6 - - - +
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Residues in contact with ARG 319 (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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43A TRP* 3.4 40.9 + - + +
70A PRO 2.8 28.3 + - - -
71A ASN* 3.6 18.1 - - - +
72A PHE 3.3 18.8 - - - +
73A TYR* 3.3 26.0 + - + -
290A GLY* 4.9 1.0 - - - -
306A PHE* 3.3 35.5 - - + -
315A GLU* 2.9 46.4 + - + +
316A GLY* 4.7 5.5 - - - +
318A MET* 1.3 78.7 + - - +
320A GLU* 1.3 66.4 + - - +
444A LEU* 3.9 22.6 + - - +
448A PRO* 5.5 0.2 - - - +
52B PRO* 4.1 10.1 - - - +
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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