Contacts of the helix formed by residues 43 - 58 (chain B) in PDB entry 2X7X
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 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 3.8 6.4 - - - -
42B ASP* 1.3 81.0 - - - +
44B SER* 1.3 58.8 + - - +
45B TRP* 2.9 14.0 + - - +
46B ARG* 2.8 34.8 + - - +
47B HIS* 2.8 31.1 + - - +
197B GLU* 4.7 2.0 - - - +
224B ARG* 3.4 32.8 + - - +
1334B FRU 2.8 26.5 + - - -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 1.3 76.2 - - - +
45B TRP* 1.3 62.2 + - - +
47B HIS* 3.9 9.0 - - - +
48B LYS* 3.2 22.2 + - - +
224B ARG* 5.6 7.0 + - - +
250B LEU* 3.3 12.5 - - - +
255B ASN* 2.9 33.3 + - - -
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Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 2.9 9.4 + - - +
44B SER* 1.3 78.2 + - - +
46B ARG* 1.3 102.2 + - - +
48B LYS* 3.2 13.2 + - - +
49B MET* 3.2 43.9 + - + -
120B ASP* 4.1 9.0 - - + -
224B ARG* 4.8 2.9 - - - +
248B ASP* 3.7 25.4 + - + +
250B LEU* 3.6 30.7 - - + -
271B TYR* 3.0 55.2 + + - -
272B PRO 3.7 17.7 - - - -
273B THR* 3.6 10.8 - - + +
1334B FRU 3.8 16.6 - - - +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 2.9 33.0 + - - +
40B CYS* 3.6 21.6 - - - -
41B SER* 3.5 27.4 - - - +
42B ASP* 4.2 1.6 - - - +
43B ASP* 2.8 26.2 + - - +
45B TRP* 1.3 89.6 - - - +
47B HIS* 1.3 51.7 + - - +
49B MET* 3.2 7.0 + - - +
50B ASN* 2.7 47.2 + - - +
95B SER* 3.2 11.1 + - - -
119B VAL* 5.9 0.4 - - - +
120B ASP* 2.5 33.9 + - - +
121B ARG* 3.8 0.4 - - - +
1334B FRU 2.7 49.2 + - - +
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 4.8 6.9 + - - +
43B ASP 2.8 22.6 + - - +
44B SER* 4.0 9.4 - - - +
45B TRP 3.3 0.2 - - - -
46B ARG* 1.3 74.6 - - - +
48B LYS* 1.3 58.4 + - - +
50B ASN* 3.3 12.0 + - - +
51B ASP* 2.8 65.5 + - - +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 3.2 12.2 + - - +
45B TRP 3.2 10.1 + - - +
47B HIS* 1.3 81.8 - - - +
49B MET* 1.3 62.9 + - - +
51B ASP* 3.3 6.9 + - - +
52B GLU* 3.0 48.9 + - - +
250B LEU* 3.8 21.1 - - + +
251B PRO* 4.4 23.0 - - + +
273B THR* 3.2 17.8 + - + +
274B ASN* 5.4 0.6 + - - +
1333B PO4 3.3 33.7 + - - +
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Residues in contact with MET 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 3.5 24.5 - - - +
45B TRP* 3.2 38.7 + - + +
46B ARG* 3.2 9.9 + - - +
48B LYS* 1.3 78.5 - - - +
50B ASN* 1.3 62.8 + - - +
52B GLU* 3.2 11.8 + - - +
53B ILE* 2.9 39.3 + - + +
93B ILE* 6.1 0.9 - - - -
119B VAL* 3.6 34.8 - - + -
120B ASP* 4.9 0.7 - - + -
272B PRO 5.2 0.7 - - - +
273B THR* 3.7 31.5 - - - +
275B GLY* 4.1 5.6 - - - -
278B VAL* 4.9 1.6 - - - -
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.9 0.2 - - - +
39B GLN* 2.9 35.3 + - - +
41B SER 5.6 0.4 + - - -
42B ASP* 4.5 9.1 + - - -
46B ARG* 2.7 32.5 + - - +
47B HIS* 3.5 12.6 + - - +
49B MET* 1.3 72.4 - - - +
51B ASP* 1.3 61.8 + - - +
53B ILE* 3.4 6.9 + - - +
54B LEU* 3.1 31.5 + - + +
67B ILE* 3.6 35.0 - - + +
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 2.8 56.0 + - - +
48B LYS* 3.7 6.2 - - - +
50B ASN* 1.3 73.0 - - - +
52B GLU* 1.3 56.9 + - - +
54B LEU* 3.3 14.4 + - - +
55B ARG* 2.9 42.8 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A HIS* 5.3 2.6 - - - +
48B LYS* 3.0 35.4 + - - +
49B MET* 3.2 3.6 + - - +
51B ASP* 1.3 72.5 - - - +
53B ILE* 1.3 61.4 + - - +
55B ARG* 3.8 19.9 - - - +
56B GLU* 3.0 30.5 + - - +
273B THR* 2.7 29.8 + - - -
274B ASN* 3.1 4.9 + - - +
275B GLY* 2.6 41.0 + - - +
276B ASP* 3.9 11.6 + - + +
1333B PO4 3.0 26.0 + - - +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.7 22.4 - - + -
49B MET* 2.9 40.8 + - + +
50B ASN* 3.7 9.2 - - - +
51B ASP 3.3 0.2 - - - -
52B GLU* 1.3 73.9 - - - +
54B LEU* 1.3 63.7 + - - +
56B GLU* 3.4 4.4 + - - +
57B ALA* 3.2 21.1 + - - +
65B VAL* 3.9 27.8 - - + -
67B ILE* 4.9 3.6 - - + -
93B ILE* 4.8 4.5 - - + -
275B GLY* 3.6 24.2 - - - +
278B VAL* 4.3 17.5 - - + -
279B LEU* 3.8 18.9 - - + +
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Residues in contact with LEU 54 (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 ASN* 3.1 22.2 + - + +
51B ASP* 3.3 14.1 + - - +
53B ILE* 1.3 72.8 - - - +
55B ARG* 1.3 66.5 + - - +
57B ALA* 3.1 16.2 + - + +
58B MET* 3.4 18.4 + - - +
65B VAL* 4.1 33.7 - - + +
67B ILE* 4.1 16.8 - - + -
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Residues in contact with ARG 55 (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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316A HIS* 5.4 1.4 + - - -
320A LEU* 4.6 10.7 - - - +
323A LYS* 5.8 6.8 - - + +
51B ASP* 2.9 35.9 + - - +
52B GLU* 3.8 17.2 - - - +
54B LEU* 1.3 77.8 - - - +
56B GLU* 1.3 60.8 + - - +
57B ALA 3.4 0.5 + - - -
58B MET* 3.4 21.6 - - - +
59B PHE* 3.7 12.5 - - + -
276B ASP* 6.4 0.6 - - - +
321B ASP* 3.5 25.3 + - - +
324B ILE* 3.8 34.0 - - + +
325B GLU* 5.5 7.4 - - - +
328B ASN* 4.1 7.6 + - - +
1333B PO4 2.9 36.8 + - - -
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Residues in contact with GLU 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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323A LYS* 3.0 31.4 + - - -
52B GLU 3.0 17.9 + - - +
53B ILE 3.8 1.6 - - - +
55B ARG* 1.3 76.9 - - - +
57B ALA* 1.3 61.4 + - - +
58B MET 3.3 0.2 - - - -
59B PHE* 3.3 26.2 + - - +
60B TYR* 3.5 15.4 - - + -
276B ASP* 3.3 34.4 - - - +
279B LEU* 3.4 19.1 - - + -
280B GLN* 3.1 31.6 + - + +
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Residues in contact with ALA 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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53B ILE 3.2 12.1 + - - +
54B LEU* 3.1 12.4 + - + +
56B GLU* 1.3 75.1 - - - +
58B MET* 1.3 56.7 + - - +
59B PHE 3.0 5.2 - - - -
60B TYR* 2.9 31.5 + - - +
63B VAL* 4.3 20.3 - - + +
65B VAL* 4.0 21.8 - - + +
279B LEU* 3.3 15.5 - - + +
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 6.1 0.7 - - - +
330A ARG* 4.5 6.9 + - - -
54B LEU* 3.4 15.7 + - - +
55B ARG* 3.4 14.8 - - - +
56B GLU 3.3 0.2 - - - -
57B ALA* 1.3 77.0 - - - +
59B PHE* 1.3 58.8 + - + +
60B TYR 3.6 5.2 + - - +
328B ASN* 3.5 47.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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