Contacts of the helix formed by residues 337 - 349 (chain A) in PDB entry 4FUX
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 PRO 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLN* 5.3 2.0 - - + -
335A ASP 3.6 5.3 - - - +
336A LEU* 1.4 91.6 - - + +
338A LYS* 1.3 65.8 + - - +
339A GLU* 3.1 14.6 - - + +
340A LYS* 3.1 37.4 + - + +
341A LEU* 3.1 10.8 + - - +
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Residues in contact with LYS 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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57A PHE 3.8 18.9 - - - +
58A GLU* 3.5 30.1 - - - +
59A HIS* 4.2 4.0 - - - +
60A GLN* 4.1 23.1 - - + +
63A CYS* 4.2 6.3 - - - -
336A LEU 3.8 1.0 + - - -
337A PRO* 1.3 70.5 - - - +
339A GLU* 1.4 85.2 + - - +
341A LEU* 3.4 13.4 + - - +
342A LYS* 2.9 30.9 + - - +
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Residues in contact with GLU 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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93A ILE* 5.2 1.4 - - - +
337A PRO* 3.1 14.9 + - + +
338A LYS* 1.4 111.2 + - - +
340A LYS* 1.3 64.5 + - + +
342A LYS* 3.5 7.9 + - - +
343A GLU* 3.4 20.1 + - - +
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Residues in contact with LYS 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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336A LEU* 4.1 22.9 - - + -
337A PRO* 3.1 28.0 + - + +
339A GLU* 1.3 77.4 - - + +
341A LEU* 1.4 56.9 + - - +
343A GLU* 3.4 27.2 + - - +
344A LEU* 3.1 32.4 + - + +
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Residues in contact with LEU 341 (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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60A GLN* 3.6 25.6 - - + +
63A CYS* 3.6 20.2 - - + +
64A GLN* 4.0 20.9 - - + +
67A LEU* 3.7 26.5 - - + -
334A ASP* 5.6 5.2 - - + -
336A LEU* 3.5 42.0 - - + +
337A PRO 3.1 13.1 + - - +
338A LYS* 3.7 4.9 - - - +
340A LYS* 1.4 74.7 - - - +
342A LYS* 1.4 53.2 + - - +
344A LEU* 3.0 7.7 + - - +
345A ILE* 2.8 39.9 + - - +
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.5 45.6 - - + +
63A CYS* 4.8 0.6 - - - -
93A ILE* 2.8 39.4 + - + +
94A GLU* 4.5 5.1 + - - +
96A MET* 2.9 36.9 + - + +
97A LYS* 5.9 1.2 - - - +
338A LYS 2.9 18.8 + - - +
339A GLU* 3.7 8.5 - - - +
340A LYS 3.4 0.2 - - - -
341A LEU* 1.4 72.6 - - - +
343A GLU* 1.3 52.0 + - - +
345A ILE* 3.3 4.1 + - - +
346A PHE* 2.8 32.9 + - - +
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Residues in contact with GLU 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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93A ILE* 3.6 21.6 - - + +
339A GLU 3.4 9.7 + - - +
340A LYS* 3.4 35.3 + - - +
341A LEU 3.2 0.2 - - - -
342A LYS* 1.3 76.6 - - - +
344A LEU* 1.4 60.0 + - + +
346A PHE* 3.4 3.9 + - + +
347A GLU* 2.9 51.0 + - + +
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Residues in contact with LEU 344 (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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67A LEU* 3.8 29.4 - - + -
71A LYS* 6.1 4.3 - - - -
336A LEU* 3.8 29.8 - - + -
340A LYS* 3.1 19.3 + - + +
341A LEU* 3.0 10.6 + - - +
343A GLU* 1.4 72.1 - - - +
345A ILE* 1.3 55.9 + - - +
347A GLU* 3.4 21.5 + - - +
348A GLU* 2.8 38.3 + - + +
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Residues in contact with ILE 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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56A PRO* 4.6 0.9 - - + -
57A PHE* 3.7 35.4 - - + -
63A CYS* 3.7 32.3 - - + +
66A THR* 4.0 17.7 - - + -
67A LEU* 4.0 25.1 - - + +
70A ILE* 4.4 16.8 - - + -
96A MET* 4.9 1.1 - - + -
99A VAL* 4.1 15.0 - - + -
341A LEU 2.8 17.0 + - - +
342A LYS 3.5 7.0 - - - +
344A LEU* 1.3 70.7 - - - +
346A PHE* 1.3 66.2 + - - +
348A GLU* 3.1 3.9 + - - +
349A THR* 3.0 30.8 + - + +
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Residues in contact with PHE 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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89A ARG* 2.9 57.7 + - - -
90A ALA 3.9 1.8 - - - -
91A PRO 3.3 20.0 - - - -
92A THR* 3.4 8.3 - - - -
93A ILE* 3.4 38.6 - - + -
96A MET* 3.8 22.9 - - + +
342A LYS 2.8 19.7 + - - +
343A GLU* 3.5 12.1 - - + +
345A ILE* 1.3 73.4 - - - +
347A GLU* 1.4 65.5 + - + +
349A THR* 3.0 10.9 + - - -
350A ALA* 3.3 2.9 + - + -
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Residues in contact with GLU 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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343A GLU* 2.9 37.7 + - + +
344A LEU* 3.6 26.7 - - + +
345A ILE 3.3 0.2 - - - -
346A PHE* 1.4 80.3 - - + +
348A GLU* 1.3 61.2 + - + +
349A THR 3.3 0.9 + - - -
350A ALA* 3.3 21.8 + - - +
351A ARG 4.9 0.3 + - - -
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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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67A LEU* 3.7 21.3 - - + -
70A ILE* 4.3 11.2 - - + -
71A LYS* 3.6 44.6 + - + +
74A LEU* 3.5 36.0 - - - +
344A LEU* 2.8 22.9 + - + +
345A ILE* 3.1 6.0 + - - +
347A GLU* 1.3 72.5 - - + +
349A THR* 1.3 58.2 + - - +
350A ALA 3.9 0.2 + - - -
351A ARG* 4.5 12.3 + - - +
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Residues in contact with THR 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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70A ILE* 4.0 18.6 - - + -
87A ILE* 3.6 41.3 - - + +
89A ARG* 2.8 36.4 + - + +
96A MET* 5.1 0.2 - - - -
99A VAL* 4.9 2.2 - - + -
345A ILE* 3.0 19.4 + - + +
346A PHE* 3.0 6.8 + - - -
347A GLU 3.2 0.2 - - - -
348A GLU* 1.3 79.4 - - - +
350A ALA* 1.4 61.5 + - - +
351A ARG 3.3 2.9 - - - -
352A PHE* 3.4 26.6 + - - +
353A GLN* 4.3 3.6 + - - +
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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