Contacts of the helix formed by residues 43 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 3.9 8.1 + - - -
42A ASP* 1.3 81.8 + - - +
44A SER* 1.3 54.4 + - - +
45A TRP* 3.1 7.4 + - - +
46A ARG* 2.9 34.1 + - - +
47A HIS* 2.8 35.5 + - - +
197A GLU* 4.7 2.4 - - - +
224A ARG* 3.5 37.7 + - - +
1335A FRU 2.7 22.8 + - - -
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Residues in contact with SER 44 (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 ASP* 1.3 75.3 - - - +
45A TRP* 1.3 57.8 + - - +
47A HIS* 3.8 8.7 - - - +
48A LYS* 3.1 26.0 + - - +
224A ARG* 5.6 6.6 + - - +
250A LEU* 3.5 10.0 - - - +
255A ASN* 3.0 33.1 + - - -
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Residues in contact with TRP 45 (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 ASP* 3.1 9.9 + - - +
44A SER* 1.3 78.3 + - - +
46A ARG* 1.3 109.7 + - - +
48A LYS* 3.3 5.5 + - - +
49A MET* 3.2 35.0 + - + -
119A VAL* 5.6 0.9 - - + -
120A ASP* 4.2 12.1 - - + -
224A ARG* 4.7 5.1 - - - +
248A ASP* 3.8 19.7 + - + +
250A LEU* 3.6 30.7 - - + +
271A TYR* 2.9 55.7 + + - -
272A PRO 3.8 17.0 - - - -
273A THR* 3.5 16.5 - - + +
1335A FRU 3.6 17.0 - - - +
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Residues in contact with ARG 46 (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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39A GLN* 3.1 40.3 + - + +
40A CYS* 3.3 20.9 - - - -
41A SER* 3.3 28.1 + - - +
42A ASP* 4.4 2.2 - - - +
43A ASP* 2.9 25.2 + - - +
45A TRP* 1.3 93.0 - - - +
47A HIS* 1.3 67.1 + - - +
49A MET* 3.0 7.3 + - - +
50A ASN* 2.8 34.1 + - - +
95A SER* 3.2 8.7 + - - -
120A ASP* 2.9 30.7 + - - +
121A ARG* 3.5 1.2 - - - +
1335A FRU 2.8 41.6 + - - +
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Residues in contact with HIS 47 (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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42A ASP* 5.1 8.2 + - - +
43A ASP 2.8 22.3 + - - +
44A SER* 3.8 11.0 - - - +
46A ARG* 1.3 71.5 - - - +
48A LYS* 1.3 65.6 + - - +
50A ASN* 3.7 9.0 + - - +
51A ASP* 3.1 62.4 + - - +
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Residues in contact with LYS 48 (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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44A SER 3.1 16.2 + - - +
45A TRP 3.6 5.4 - - - +
46A ARG 3.2 0.2 - - - -
47A HIS* 1.3 81.9 - - - +
49A MET* 1.3 61.2 + - - +
51A ASP* 4.0 5.2 - - - +
52A GLU* 3.2 30.9 + - - +
250A LEU* 3.7 24.0 - - + +
251A PRO* 4.8 18.5 - - + +
272A PRO* 6.0 0.2 - - - +
273A THR* 3.1 24.4 + - + +
1333A PO4 3.4 36.3 + - - +
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Residues in contact with MET 49 (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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37A VAL* 5.9 0.2 - - + -
39A GLN* 4.0 24.5 - - - +
45A TRP* 3.2 30.4 + - + +
46A ARG* 3.0 9.2 + - - +
48A LYS* 1.3 73.6 - - - +
50A ASN* 1.3 68.8 + - - +
52A GLU* 3.0 22.7 + - - +
53A ILE* 3.0 28.7 + - + +
93A ILE* 4.9 4.0 - - + -
119A VAL* 3.3 43.7 - - + -
273A THR* 3.9 25.0 - - + +
275A GLY* 4.3 3.8 - - - -
278A VAL* 4.0 14.1 - - + -
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Residues in contact with ASN 50 (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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37A VAL* 4.7 0.5 - - - +
39A GLN* 2.9 31.1 + - - +
42A ASP* 5.1 6.5 + - - -
46A ARG* 2.8 29.8 + - - +
47A HIS* 3.7 9.9 + - - +
49A MET* 1.3 70.4 - - - +
51A ASP* 1.3 58.4 + - - +
53A ILE* 2.7 30.5 + - - +
54A LEU* 3.0 19.8 + - + +
67A ILE* 3.9 38.0 - - + +
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Residues in contact with ASP 51 (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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47A HIS* 3.1 47.0 + - - +
48A LYS* 4.0 5.6 - - - +
50A ASN* 1.3 81.7 - - - +
52A GLU* 1.3 57.1 + - - +
54A LEU* 4.0 14.4 - - - +
55A ARG* 3.0 44.3 + - - +
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Residues in contact with GLU 52 (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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48A LYS* 3.2 17.5 + - - +
49A MET* 3.0 9.3 + - - +
51A ASP* 1.3 75.6 - - - +
53A ILE* 1.3 63.8 + - - +
55A ARG* 3.7 16.3 + - - +
56A GLU* 3.3 22.0 + - - +
273A THR* 2.7 31.0 + - - -
274A ASN* 4.2 4.5 + - - +
275A GLY* 2.8 33.1 + - - -
276A ASP* 3.8 13.6 + - + +
1333A PO4 2.8 42.7 + - - +
316B HIS* 4.9 4.8 + - + -
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Residues in contact with ILE 53 (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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37A VAL* 4.7 19.5 - - + -
49A MET* 3.0 46.0 + - + +
50A ASN* 2.7 21.2 + - - +
52A GLU* 1.3 68.9 - - - +
54A LEU* 1.3 65.9 + - - +
56A GLU* 2.9 7.8 + - - +
57A ALA* 2.9 19.3 + - - +
65A VAL* 4.0 25.8 - - + -
67A ILE* 5.1 2.2 - - + -
93A ILE* 5.3 3.8 - - + -
275A GLY* 3.5 21.8 - - - +
278A VAL* 4.5 11.4 - - + -
279A LEU* 3.7 22.4 - - + +
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Residues in contact with LEU 54 (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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50A ASN* 3.0 22.9 + - + +
51A ASP* 4.1 13.7 - - - +
53A ILE* 1.3 76.3 - - - +
55A ARG* 1.3 62.6 + - - +
57A ALA* 3.1 22.2 + - + +
58A MET* 3.5 13.7 + - - +
65A VAL* 3.9 33.4 - - + +
67A ILE* 4.1 20.2 - - + -
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Residues in contact with ARG 55 (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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51A ASP* 3.0 35.1 + - - +
52A GLU* 3.7 25.0 + - - +
53A ILE 3.2 0.2 - - - -
54A LEU* 1.3 76.3 - - - +
56A GLU* 1.3 62.8 + - - +
58A MET* 3.8 9.8 + - - +
59A PHE* 3.4 19.7 - - + -
321A ASP* 3.4 40.3 + - - +
324A ILE* 3.8 36.3 - - + +
325A GLU* 5.0 11.7 - - + +
328A ASN* 4.4 7.1 + - - +
1333A PO4 3.2 24.4 + - - -
320B LEU* 5.1 6.0 - - - +
323B LYS* 5.7 3.4 - - - -
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Residues in contact with GLU 56 (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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52A GLU 3.3 11.3 + - - +
53A ILE 2.9 8.4 + - - +
55A ARG* 1.3 78.9 - - - +
57A ALA* 1.3 65.8 + - - +
59A PHE* 3.2 26.9 + - - +
60A TYR* 3.6 16.0 + - + -
276A ASP* 3.3 23.4 - - - +
279A LEU* 3.4 15.0 - - + -
280A GLN* 2.8 27.8 - - - +
323B LYS* 2.7 38.1 + - - +
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Residues in contact with ALA 57 (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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53A ILE 2.9 10.6 + - - +
54A LEU* 3.1 16.1 + - + +
56A GLU* 1.3 77.0 - - - +
58A MET* 1.3 59.7 + - + +
60A TYR* 2.8 30.0 + - - +
63A VAL* 3.3 21.0 - - + +
65A VAL* 4.0 22.0 - - + +
279A LEU* 3.2 14.6 - - + +
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Residues in contact with MET 58 (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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54A LEU 3.5 12.9 + - - +
55A ARG* 4.2 4.7 - - - +
56A GLU 3.3 1.2 - - - -
57A ALA* 1.3 77.0 - - + +
59A PHE* 1.3 60.7 + - - +
60A TYR 3.3 6.0 + - - +
328A ASN* 3.7 47.8 - - + +
327B LEU* 5.4 3.3 - - - +
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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
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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