Contacts of the helix formed by residues 328 - 343 (chain A) in PDB entry 2FY5
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 ASP 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A TRP* 4.3 5.9 - - - -
85A TYR* 4.4 0.2 + - - -
154A GLN* 3.2 16.2 + - - +
324A HIS* 3.2 19.9 - - - -
327A PHE* 1.3 81.0 - - - +
329A GLY* 1.3 66.7 + - - +
330A ILE* 3.2 5.8 + - + +
331A VAL* 3.2 6.2 + - - +
332A LEU* 3.2 18.0 + - - +
448A ARG* 2.9 40.7 + - - +
449A VAL* 3.6 27.2 - - + +
2000A SOP 3.8 16.3 - - + +
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 1.3 73.8 - - - +
330A ILE* 1.3 63.1 + - - +
332A LEU* 3.6 11.4 - - - +
333A VAL* 2.9 29.7 + - - +
542A VAL* 4.5 9.9 - - - -
550A CYS* 5.3 0.9 - - - -
2000A SOP 3.4 39.1 - - - +
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Residues in contact with ILE 330 (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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154A GLN* 6.1 0.2 - - - +
328A ASP* 3.2 4.2 + - + +
329A GLY* 1.3 75.5 - - - +
331A VAL* 1.3 64.6 + - + +
333A VAL* 3.4 4.0 + - - +
334A GLN* 3.0 42.7 + - + +
440A SER* 5.4 3.8 - - - -
442A ARG* 3.7 27.1 - - - +
541A GLN 4.0 7.6 - - - +
542A VAL* 4.6 3.6 - - + -
543A PRO* 4.1 20.0 - - + +
2000A SOP 3.5 50.9 - - - +
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Residues in contact with VAL 331 (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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151A CYS 5.7 0.2 - - - +
154A GLN* 3.6 39.3 - - + +
155A TYR* 3.8 48.4 - - + +
158A LEU* 4.3 11.2 - - + -
327A PHE* 4.8 2.2 - - + -
328A ASP 3.2 7.8 + - - +
330A ILE* 1.3 75.9 - - + +
332A LEU* 1.3 65.8 + - - +
334A GLN* 3.2 16.6 + - - +
335A CYS* 3.3 10.7 + - - +
442A ARG* 4.2 25.4 - - - +
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Residues in contact with LEU 332 (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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98A PRO* 5.4 5.8 - - + -
100A VAL* 3.2 25.6 - - + -
158A LEU* 4.5 12.1 - - + +
308A LEU* 3.8 20.4 - - + -
310A PHE* 6.0 1.1 - - + -
320A VAL* 4.4 4.7 - - + -
322A CYS* 3.0 41.5 - - + -
327A PHE* 4.2 11.9 - - + -
328A ASP 3.2 11.6 + - - +
329A GLY* 3.6 13.9 - - - +
331A VAL* 1.3 80.7 - - - +
333A VAL* 1.3 57.5 + - - +
335A CYS* 3.3 5.2 + - + +
336A THR* 2.9 42.5 + - - +
550A CYS* 5.6 1.1 - - - -
2000A SOP 6.0 0.4 - - + -
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Residues in contact with VAL 333 (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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100A VAL* 4.7 19.1 - - + -
329A GLY* 2.9 20.0 + - - +
330A ILE* 3.9 4.3 - - - +
331A VAL 3.2 0.2 - - - -
332A LEU* 1.3 74.2 - - - +
334A GLN* 1.3 61.3 + - - +
336A THR* 3.6 5.1 - - - -
337A GLU* 2.7 49.6 + - + +
542A VAL* 3.6 23.1 - - + -
543A PRO 4.1 7.0 - - - +
544A THR* 3.5 29.2 - - + -
548A MET* 4.6 7.2 - - - -
550A CYS* 5.3 1.6 - - + +
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Residues in contact with GLN 334 (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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127A TYR* 4.7 1.3 - - - +
139A ASP* 5.0 11.7 + - - +
155A TYR* 4.0 22.0 - - + +
330A ILE* 3.0 34.9 - - + +
331A VAL* 3.2 5.8 + - - +
333A VAL* 1.3 81.0 - - - +
335A CYS* 1.3 58.1 + - - +
337A GLU* 3.6 16.4 + - - +
338A HIS* 3.0 29.3 + - - +
442A ARG* 5.7 1.3 - - - +
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Residues in contact with CYS 335 (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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127A TYR* 3.4 45.9 + - - +
158A LEU* 3.8 24.2 - - + -
159A PHE* 4.1 12.3 - - - -
308A LEU* 5.4 4.0 - - - -
310A PHE* 5.6 1.1 - - - -
331A VAL 3.3 5.8 + - - +
332A LEU* 3.5 11.2 - - + +
334A GLN* 1.3 77.3 - - - +
336A THR* 1.3 55.7 + - - +
338A HIS* 3.1 3.3 + - - +
339A LEU* 2.7 51.1 + - - +
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Residues in contact with THR 336 (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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100A VAL* 4.2 3.4 - - + +
102A PHE* 3.2 29.1 - - + -
310A PHE* 5.1 3.6 - - - -
320A VAL* 4.2 7.4 - - - +
332A LEU* 2.9 36.6 + - - +
333A VAL* 3.6 8.1 - - - -
335A CYS* 1.3 77.3 - - - +
337A GLU* 1.3 62.5 + - - +
339A LEU* 3.0 13.1 + - - +
340A LEU* 3.0 22.8 + - + +
548A MET* 3.1 31.6 - - + -
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Residues in contact with GLU 337 (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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333A VAL* 2.7 28.6 + - + +
334A GLN* 3.8 18.3 - - - +
336A THR* 1.3 73.2 - - - +
338A HIS* 1.3 61.5 + - - +
340A LEU* 3.5 3.6 + - - +
341A LYS* 3.0 25.5 + - - +
544A THR* 2.8 34.4 - - - -
545A THR* 2.9 24.5 + - - +
546A THR* 2.9 25.0 + - - +
548A MET* 4.0 14.4 - - + -
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Residues in contact with HIS 338 (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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123A GLY 5.8 1.1 - - - -
126A SER* 5.8 1.3 - - - -
127A TYR* 3.5 37.4 - + + +
130A LEU* 3.6 25.3 - - + +
136A ILE* 6.2 1.1 - - + -
334A GLN 3.0 20.5 + - - +
335A CYS 3.1 4.9 + - - +
337A GLU* 1.3 73.6 - - - +
339A LEU* 1.3 71.1 + - - +
341A LYS* 3.3 8.2 + - + +
342A HIS* 3.1 32.7 + + + +
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Residues in contact with LEU 339 (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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102A PHE* 5.6 2.2 - - + -
120A LEU* 4.3 10.5 - - + +
123A GLY* 3.5 36.6 - - - +
124A VAL* 3.7 15.5 - - + +
127A TYR* 4.1 13.7 - - + -
159A PHE* 5.5 1.1 - - + -
310A PHE* 3.4 40.4 - - + -
335A CYS* 2.7 32.6 + - - +
336A THR* 3.2 14.6 - - + +
338A HIS* 1.3 78.1 + - - +
340A LEU* 1.3 66.4 + - + +
342A HIS* 3.1 18.8 + - - +
343A MET* 3.3 12.1 + - - +
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Residues in contact with LEU 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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102A PHE* 3.8 42.0 - - + -
105A GLN* 6.2 1.1 - - - +
116A PHE* 4.4 9.9 - - + -
120A LEU* 5.5 2.0 - - + -
336A THR* 3.0 9.7 + - + +
337A GLU* 4.1 4.7 - - - +
339A LEU* 1.3 76.3 - - + +
341A LYS* 1.3 65.7 + - - +
343A MET* 3.2 41.1 + - + +
546A THR* 5.1 10.8 - - + -
548A MET* 3.2 33.2 - - + -
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A GLU 3.0 18.3 + - - +
338A HIS* 3.7 8.5 - - + +
340A LEU* 1.3 74.1 - - - +
342A HIS* 1.3 65.3 + - - +
343A MET 3.3 4.7 + - - -
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Residues in contact with HIS 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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119A SER* 4.4 8.1 - - - -
122A SER* 4.1 9.7 + - - -
123A GLY* 3.7 27.8 - - - -
126A SER* 3.4 25.9 + - - -
205A ARG* 4.8 3.0 + - - -
208A GLU* 5.5 3.1 - - - -
338A HIS* 3.1 25.2 + + + +
339A LEU* 3.2 14.0 + - - +
341A LYS* 1.3 78.9 - - - +
343A MET* 1.3 66.1 + - - +
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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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116A PHE* 3.3 57.2 - - + +
119A SER* 3.4 29.7 + - - +
120A LEU* 3.9 22.9 - - - +
123A GLY* 5.8 0.4 - - - -
339A LEU 3.7 11.2 - - - +
340A LEU* 3.2 40.5 + - + +
341A LYS 3.1 5.0 - - - -
342A HIS* 1.3 87.9 - - - +
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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