Contacts of the helix formed by residues 55 - 72 (chain B) in PDB entry 4XZC
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 1.3 89.6 + - - +
56B ASP* 1.3 64.2 + - - +
57B ARG* 3.1 44.9 + - + +
58B GLU* 3.3 13.1 + - - +
59B LYS* 3.2 28.7 + - - +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 1.3 75.4 - - - +
57B ARG* 1.3 61.5 + - + +
58B GLU 3.3 0.2 - - - -
59B LYS* 3.6 23.8 + - - +
60B ASP* 2.8 40.2 + - - +
441B GLY 4.6 0.9 - - - +
442B PHE* 3.3 27.9 - - + -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 3.1 19.5 + - + +
56B ASP* 1.3 78.6 - - + +
58B GLU* 1.3 52.0 + - - +
60B ASP* 3.2 10.8 - - - +
61B SER* 2.8 34.2 + - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 4.7 9.9 + - - +
53B ALA* 4.3 10.8 - - + -
54B THR* 3.4 22.9 + - - -
55B ASP* 3.3 16.2 + - - +
56B ASP 3.3 0.4 - - - -
57B ARG* 1.3 76.9 - - - +
59B LYS* 1.3 63.9 + - - +
60B ASP 3.1 1.6 - - - -
61B SER* 3.4 9.1 + - - +
62B ILE* 3.0 49.5 + - + +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET* 3.3 27.8 - - - +
53B ALA* 3.5 34.0 + - + -
54B THR 3.9 10.4 + - - -
55B ASP 3.2 17.9 + - - +
56B ASP* 3.6 21.4 + - - +
57B ARG 3.4 0.2 - - - -
58B GLU* 1.3 76.3 - - - +
60B ASP* 1.3 62.8 + - - +
62B ILE* 4.4 1.3 - - - -
63B TYR* 3.1 22.2 + - - +
441B GLY* 3.2 36.0 + - - +
442B PHE* 3.6 18.2 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP* 2.8 27.8 + - - +
57B ARG* 3.2 9.8 - - - +
58B GLU 3.1 0.2 - - - -
59B LYS* 1.3 79.4 - - - +
61B SER* 1.3 63.0 + - - +
63B TYR* 3.4 4.9 + - - +
64B ALA* 3.1 22.6 + - - +
442B PHE* 4.3 13.1 - - - -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG 2.8 17.2 + - - -
58B GLU* 3.6 11.6 - - - -
60B ASP* 1.3 74.2 - - - +
62B ILE* 1.3 58.3 + - - +
64B ALA* 3.2 9.3 + - - +
65B CYS* 2.9 35.0 + - - -
339B PRO* 4.0 13.9 - - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.5 40.7 - - + +
49B LYS* 3.8 48.7 - - + +
50B MET* 3.8 11.2 - - + +
53B ALA* 3.8 12.1 - - + -
58B GLU* 3.0 42.0 + - + +
59B LYS* 3.9 4.0 - - - +
61B SER* 1.3 73.0 - - - +
63B TYR* 1.3 67.7 + - - +
65B CYS* 3.1 10.3 + - - +
66B ALA* 2.9 21.3 + - - +
437B ILE* 5.2 0.2 - - + -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET* 3.8 11.6 - - + +
59B LYS 3.1 15.9 + - - +
60B ASP* 3.8 5.4 - - - +
62B ILE* 1.3 78.8 - - - +
64B ALA* 1.3 66.2 + - - +
66B ALA* 3.0 7.2 + - + +
67B MET* 2.9 51.1 + - + +
434B LEU* 3.5 38.3 - - + +
437B ILE* 4.1 16.4 - - + -
438B GLN* 4.1 26.6 + - + -
442B PHE* 5.0 7.2 - + + -
451B ALA* 3.5 21.2 - - + +
452B SER* 4.6 2.1 + - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP 3.1 13.9 + - - +
61B SER* 3.3 11.9 - - - +
63B TYR* 1.3 81.1 - - - +
65B CYS* 1.3 60.4 + - - +
67B MET* 3.5 7.4 + - - +
68B VAL* 3.1 28.4 + - + +
339B PRO* 4.2 20.0 - - + -
341B GLY 6.3 0.7 - - - +
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Residues in contact with CYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.6 21.3 - - + -
49B LYS* 6.2 2.0 - - - -
61B SER* 2.9 31.3 + - - -
62B ILE* 3.1 8.5 + - - +
64B ALA* 1.3 73.4 - - - +
66B ALA* 1.3 67.7 + - - +
68B VAL* 3.1 9.7 + - - +
69B GLU* 3.0 26.7 + - - +
338B GLY* 6.0 0.2 - - - -
339B PRO* 3.9 30.1 - - - -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.9 7.7 - - + +
46B PHE* 3.7 21.5 - - + -
62B ILE 2.9 12.7 + - - +
63B TYR* 3.0 11.0 + - + +
65B CYS* 1.3 76.7 - - - +
67B MET* 1.3 56.3 + - - +
69B GLU* 3.2 4.0 + - - +
70B ALA* 2.9 28.4 + - - +
434B LEU* 4.3 7.0 - - + -
437B ILE* 3.4 32.8 - - + -
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 2.9 43.9 + - + +
64B ALA* 3.8 9.6 - - - +
66B ALA* 1.3 73.1 - - - +
68B VAL* 1.3 64.5 - - + +
70B ALA* 3.2 1.9 + - - +
71B THR* 2.8 36.6 + - - +
409B GLY 5.8 0.9 - - - +
410B HIS* 4.9 0.9 - - - -
411B SER* 3.6 46.9 - - - +
414B LEU* 4.8 0.2 - - - -
434B LEU* 3.9 28.6 - - + +
451B ALA* 5.1 5.6 - - + -
455B LEU* 4.2 15.9 - - + -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA 3.1 19.5 + - - +
65B CYS* 3.1 9.8 + - - +
67B MET* 1.3 76.5 - - + +
69B GLU* 1.3 67.3 + - - +
71B THR* 3.9 4.9 - - - -
72B LYS* 2.7 48.3 + - + +
335B MET 5.2 0.2 - - - +
336B GLY* 3.7 25.1 - - - +
337B GLN 4.3 12.6 - - - +
338B GLY* 3.9 25.8 - - - +
409B GLY* 4.0 14.4 - - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 3.3 20.7 - - + +
42B ASP 5.8 0.9 - - - +
43B LEU* 4.4 6.1 - - + -
46B PHE* 3.5 35.2 - - + -
65B CYS 3.0 10.4 + - - +
66B ALA 3.7 6.5 - - - +
68B VAL* 1.3 82.2 - - - +
70B ALA* 1.3 62.2 + - - +
71B THR 3.5 0.2 + - - -
72B LYS* 3.4 42.9 + - - +
73B PHE* 5.3 5.5 + - - -
337B GLN 5.6 0.2 - - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 3.7 4.2 - - - +
43B LEU* 4.2 4.9 - - + +
66B ALA 2.9 16.6 + - - +
67B MET 3.2 5.4 + - - +
69B GLU* 1.3 76.7 - - - +
71B THR* 1.3 61.5 + - + +
73B PHE 5.6 0.2 + - - -
414B LEU* 4.7 1.3 - - + -
417B TYR* 2.7 37.1 + - - -
430B GLU* 3.4 25.6 - - + +
434B LEU* 4.0 24.5 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 2.8 33.9 + - - +
70B ALA* 1.3 85.0 - - + +
72B LYS* 1.3 63.5 + - - +
73B PHE 3.0 4.8 + - - -
74B CYS* 3.0 20.7 + - - -
75B ALA* 3.8 4.9 + - - +
408B SER 3.9 5.0 - - - +
409B GLY* 3.2 6.1 - - - -
410B HIS 3.1 41.0 + - - +
411B SER 3.9 11.9 - - - +
413B SER* 4.0 5.3 - - - -
414B LEU* 3.9 16.2 - - + +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 5.5 0.9 - - - -
68B VAL* 2.7 32.2 + - + +
69B GLU* 3.4 39.6 + - - +
70B ALA 3.9 0.6 - - - -
71B THR* 1.3 71.2 + - - +
73B PHE* 1.3 88.5 + - + +
74B CYS 4.1 0.2 + - - -
75B ALA* 5.2 2.4 + - - +
337B GLN* 4.4 18.3 + - - +
406B LEU 4.2 12.8 - - - -
407B GLY* 3.4 19.0 - - - -
408B SER 3.1 33.1 + - - +
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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