Contacts of the helix formed by residues 46 - 57 (chain A) in PDB entry 2W5X
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 GLY 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 3.6 1.8 + - - -
45A ALA* 1.3 75.4 - - - +
47A LEU* 1.3 67.0 + - - -
48A SER 3.2 2.9 - - - -
49A GLN* 2.9 18.8 + - - -
50A ILE* 3.0 23.9 + - - +
303A GLU* 3.7 18.9 - - - +
340A THR* 5.0 2.2 - - - -
341A LEU 5.6 0.2 - - - -
342A ILE* 3.9 14.1 - - - -
343A PRO* 4.6 0.2 - - - -
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Residues in contact with LEU 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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46A GLY* 1.3 70.9 - - - -
48A SER* 1.3 57.4 + - - +
50A ILE* 3.4 13.1 + - + -
51A SER* 2.8 33.6 + - - +
340A THR* 5.8 1.0 - - - +
341A LEU 5.5 0.6 + - - -
343A PRO* 4.0 21.7 - - + +
47B LEU* 4.0 37.6 - - + +
71B LEU* 4.0 41.1 - - + -
340B THR* 3.8 3.8 - - - +
341B LEU* 3.4 39.3 - - + +
343B PRO* 4.1 6.1 - - + -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 3.2 0.8 - - - -
47A LEU* 1.3 79.4 - - - +
49A GLN* 1.3 65.4 + - - +
51A SER* 3.1 12.6 + - - -
52A SER 3.2 9.5 + - - -
303A GLU* 5.5 1.5 - - - +
307A PHE* 3.2 40.9 + - - -
308A THR* 4.7 5.0 - - - -
309A LEU* 4.1 4.1 + - - +
48B SER* 5.7 1.2 + - - -
340B THR* 3.7 25.5 + - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.3 15.5 + - - +
45A ALA* 3.8 15.5 - - + -
46A GLY* 2.9 28.5 + - - +
48A SER* 1.3 74.2 + - - +
50A ILE* 1.3 64.7 + - - +
52A SER* 2.6 26.3 + - - -
258A ILE* 4.6 1.8 - - + -
270A LEU* 3.7 29.5 - - + +
274A ILE* 3.4 13.5 - - + +
303A GLU* 2.8 28.6 + - - +
304A THR 3.0 17.8 + - - -
307A PHE* 3.4 20.8 - - + +
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Residues in contact with ILE 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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42A SER* 5.6 0.7 - - - +
45A ALA* 4.4 8.7 - - + +
46A GLY 3.0 20.1 + - - +
47A LEU* 3.5 16.8 - - + +
49A GLN* 1.3 74.9 - - - +
51A SER* 1.3 62.1 + - - +
53A THR* 2.8 30.7 + - - +
54A PHE* 3.8 9.8 - - + -
63A TYR* 3.6 44.9 - - + +
274A ILE* 3.8 10.5 - - + -
300A SER* 5.1 3.6 - - - +
343A PRO* 3.9 31.0 - - + +
345A PHE* 3.9 20.9 - - + -
71B LEU* 5.7 0.2 - - + -
341B LEU* 4.7 3.1 - - + -
357B ILE* 6.1 0.2 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 2.8 23.3 + - - -
48A SER 3.1 8.7 + - - -
50A ILE* 1.3 77.7 - - - +
52A SER* 1.3 62.3 + - - +
54A PHE* 2.8 28.9 + - - +
55A TYR* 3.4 9.0 - - - -
309A LEU* 3.6 17.3 - - - -
339B ALA 4.6 0.9 - - - -
340B THR* 3.3 3.8 + - - -
341B LEU* 2.7 41.6 + - - +
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Residues in contact with SER 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 SER 3.2 4.6 + - - -
49A GLN* 2.6 23.0 + - - -
51A SER* 1.3 75.9 - - - +
53A THR* 1.3 53.9 + - - +
55A TYR 2.9 3.7 + - - +
56A PHE* 2.7 48.1 + - - +
270A LEU* 4.6 0.7 - - - +
271A ILE* 4.0 25.5 - - - +
274A ILE* 3.5 15.8 - - - +
275A ASN* 5.0 0.7 - - - -
307A PHE* 4.0 16.1 - - - -
309A LEU* 4.0 7.1 - - - +
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Residues in contact with THR 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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50A ILE 2.8 19.7 + - - +
52A SER* 1.3 76.6 + - - +
54A PHE* 1.3 64.1 + - - +
55A TYR 3.6 0.3 + - - -
56A PHE 4.2 0.4 - - - -
57A LYS* 3.4 25.7 + - - +
59A GLY 4.6 0.2 - - - +
61A PRO* 3.3 34.0 - - - +
63A TYR* 3.7 12.4 - - + -
274A ILE* 3.9 34.5 - - + +
275A ASN* 3.6 24.0 - - - +
278A ASP* 4.5 4.7 - - + -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.8 12.6 - - + -
51A SER* 2.8 11.9 + - - +
53A THR* 1.3 92.6 - - - +
55A TYR* 1.3 70.2 + - + +
57A LYS 5.2 1.8 - - - -
61A PRO* 3.7 20.9 - - + -
63A TYR* 4.1 15.9 - - + -
64A THR* 3.4 34.3 - - + -
73B LYS* 3.3 36.9 + - + -
341B LEU* 3.6 35.2 - - + -
357B ILE* 4.0 17.5 - - + -
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Residues in contact with TYR 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 SER* 3.4 18.8 - - - -
52A SER 2.9 1.8 + - - -
54A PHE* 1.3 87.1 - - + +
56A PHE* 1.3 77.1 + - + +
57A LYS 3.7 2.9 - - - -
309A LEU* 4.0 9.9 - - + -
328A ILE* 3.5 26.9 - - + -
73B LYS* 3.5 34.2 - - + +
74B THR 4.4 1.4 + - - -
75B SER* 2.6 32.9 + - - -
80B ASP* 4.2 18.2 - - - -
339B ALA* 3.3 34.7 + - + +
341B LEU* 5.7 1.8 - - + -
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 2.7 26.9 + - - +
55A TYR* 1.3 91.3 - - + +
57A LYS* 1.3 58.9 + - - +
271A ILE* 3.6 39.6 - - + +
275A ASN* 3.2 14.9 + - - -
309A LEU* 4.1 12.1 - - + -
328A ILE* 3.9 39.0 - - + -
330A PRO* 4.2 13.7 - - + -
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Residues in contact with LYS 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 THR* 3.4 21.2 + - - +
54A PHE 5.6 1.2 - - - -
55A TYR 3.7 1.9 - - - -
56A PHE* 1.3 79.0 + - - +
58A SER* 1.3 77.6 + - - +
59A GLY 3.3 12.6 + - - +
60A THR 5.3 2.3 + - - +
61A PRO* 4.9 4.6 - - + +
62A ASN* 4.1 5.3 - - - +
275A ASN* 3.4 41.5 + - + +
278A ASP* 2.6 37.1 + - + +
279A ASP* 2.7 32.0 + - - +
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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