Contacts of the helix formed by residues 46 - 57 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLY 3.6 2.4 + - - -
45B ALA* 1.3 75.1 - - - +
47B LEU* 1.3 65.4 + - - -
48B SER 3.2 2.9 - - - -
49B GLN* 2.9 17.4 + - - -
50B ILE* 3.1 23.8 + - - +
303B GLU* 3.6 17.9 - - - +
340B THR* 5.0 2.7 - - - -
342B ILE* 3.8 15.3 - - - -
343B PRO* 4.6 0.4 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.0 34.8 - - + +
71A LEU* 3.6 42.4 - - + -
340A THR* 3.9 2.7 - - - +
341A LEU* 3.5 30.3 - - + +
343A PRO* 4.2 7.2 - - + -
46B GLY* 1.3 72.1 - - - -
48B SER* 1.3 52.3 + - - +
50B ILE* 3.4 14.8 + - + -
51B SER* 2.6 43.9 + - - +
71B LEU* 6.3 0.4 - - + -
340B THR* 5.8 1.0 - - - +
341B LEU 5.4 0.6 + - - -
343B PRO* 3.9 26.3 - - + +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 5.7 0.9 + - - -
303A GLU* 6.0 0.3 - - - +
338A SER* 5.6 0.7 + - - -
340A THR* 3.7 26.3 + - - +
46B GLY 3.2 0.6 - - - -
47B LEU* 1.3 78.6 - - - +
49B GLN* 1.3 65.9 + - - +
51B SER* 3.1 13.5 + - - -
52B SER 3.2 9.4 + - - -
303B GLU* 5.7 1.1 - - - -
307B PHE* 3.1 40.4 + - - -
308B THR* 4.6 6.4 - - - +
309B LEU* 4.0 4.9 - - - +
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Residues in contact with GLN 49 (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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44B GLY 3.3 14.7 + - - +
45B ALA* 3.9 14.6 - - + -
46B GLY* 2.9 28.3 + - - +
48B SER* 1.3 74.3 + - - +
50B ILE* 1.3 62.7 + - - +
52B SER* 2.6 26.3 + - - -
53B THR 4.0 0.3 + - - -
258B ILE* 4.7 1.8 - - + -
262B GLY* 5.5 0.2 - - - -
270B LEU* 3.6 32.1 - - + +
274B ILE* 3.6 12.6 - - + +
303B GLU* 3.0 25.8 + - - +
304B THR 3.0 16.6 + - - -
307B PHE* 3.3 23.4 - - + +
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Residues in contact with ILE 50 (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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341A LEU* 4.9 2.9 - - + -
357A ILE* 6.2 0.2 - - + -
42B SER* 5.4 0.9 - - - +
45B ALA* 4.4 9.0 - - + +
46B GLY 3.1 20.5 + - - +
47B LEU* 3.6 16.2 - - + +
49B GLN* 1.3 75.6 - - - +
51B SER* 1.3 59.0 + - - +
53B THR* 2.8 29.3 + - - -
54B PHE* 3.7 9.5 - - + -
63B TYR* 3.6 46.0 - - + +
274B ILE* 3.7 11.0 - - + +
300B SER* 5.0 4.0 - - - +
343B PRO* 3.8 30.7 - - + +
345B PHE* 3.8 20.0 - - + -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA 4.6 1.3 - - - -
340A THR* 3.3 4.4 + - - -
341A LEU* 2.8 43.7 + - - +
47B LEU* 2.6 25.2 + - - +
48B SER 3.4 6.5 - - - -
49B GLN 3.1 0.4 - - - -
50B ILE* 1.3 73.9 - - - +
52B SER* 1.3 60.0 + - - +
54B PHE* 2.8 35.1 + - - +
55B TYR* 3.5 8.2 - - - -
309B LEU* 3.7 14.4 - - - -
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 3.2 4.8 + - - -
49B GLN* 2.6 21.2 + - - -
51B SER* 1.3 76.9 - - - +
53B THR* 1.3 57.2 + - - +
55B TYR 3.0 4.6 + - - +
56B PHE* 2.8 40.4 + - - +
270B LEU* 4.6 0.7 - - - +
271B ILE* 4.0 17.9 - - - +
274B ILE* 3.7 14.7 - - - +
275B ASN* 5.2 0.2 - - - -
307B PHE* 3.8 27.5 - - - -
309B LEU* 4.1 9.0 - - - -
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Residues in contact with THR 53 (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 ILE 2.8 20.7 + - - +
52B SER* 1.3 76.4 + - - +
54B PHE* 1.3 68.5 + - - +
55B TYR 3.2 1.7 + - - -
57B LYS* 3.3 25.7 + - - +
59B GLY 4.7 0.5 - - - +
61B PRO* 3.3 26.8 - - - +
63B TYR* 3.9 11.1 - - + -
274B ILE* 4.0 34.8 - - + +
275B ASN* 3.5 26.9 - - - +
278B ASP* 4.5 3.8 - - + -
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Residues in contact with PHE 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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73A LYS* 3.3 36.6 + - + +
341A LEU* 3.8 29.8 - - + -
357A ILE* 4.0 18.2 - - + -
50B ILE* 3.7 13.2 - - + -
51B SER* 2.8 16.0 + - - +
53B THR* 1.3 93.6 - - - +
55B TYR* 1.3 69.7 + - + +
57B LYS 5.2 2.0 - - - -
60B THR* 5.9 0.2 - - + -
61B PRO* 3.6 24.9 - - + -
63B TYR* 4.0 17.5 - - + -
64B THR* 3.5 30.5 - - + -
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Residues in contact with TYR 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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73A LYS* 3.5 33.8 - - + +
74A THR 4.4 1.4 + - - -
75A SER* 2.7 33.3 + - - -
80A ASP* 4.1 17.5 - - + +
339A ALA* 3.4 34.7 + - + +
341A LEU* 5.4 2.0 - - + -
51B SER* 3.5 19.5 - - - -
52B SER 3.0 1.4 + - - -
54B PHE* 1.3 85.2 - - + +
56B PHE* 1.3 80.7 + - + +
57B LYS 3.7 3.1 - - - -
309B LEU* 4.0 7.0 - - + -
328B ILE* 3.5 26.2 - - + -
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Residues in contact with PHE 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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52B SER* 2.8 22.2 + - - +
55B TYR* 1.3 95.3 - - + +
57B LYS* 1.3 60.3 + - - +
58B SER 4.3 0.2 + - - -
271B ILE* 3.7 39.1 - - + +
275B ASN* 3.3 14.8 + - - -
309B LEU* 4.2 20.0 - - + -
328B ILE* 4.1 28.9 - - + -
330B PRO* 4.3 12.6 - - + -
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Residues in contact with LYS 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 THR* 3.3 23.9 + - - +
54B PHE 5.6 1.0 - - - -
55B TYR 5.0 2.1 - - - -
56B PHE* 1.3 80.9 + - - +
58B SER* 1.3 76.1 + - - +
59B GLY 3.4 10.6 + - - +
60B THR 5.2 2.5 + - - +
61B PRO* 4.8 7.1 - - + +
62B ASN* 4.2 4.0 - - - +
275B ASN* 3.4 42.5 + - + +
278B ASP* 2.6 36.9 + - + +
279B ASP* 2.8 30.7 + - - +
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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