Contacts of the helix formed by residues 44 - 60 (chain B) in PDB entry 1X2W
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 SER 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.8 15.3 - - - -
10B GLU* 5.1 4.9 + - - -
42B PHE* 3.5 2.2 - - - +
43B GLN* 1.3 83.1 - - - +
45B SER* 1.3 63.8 + - - +
46B GLU* 3.8 15.2 + - - +
47B GLU* 3.2 27.6 + - - +
48B ALA* 3.3 20.3 + - - +
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Residues in contact with SER 45 (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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91A TYR* 3.6 26.7 - - - -
44B SER* 1.3 71.2 - - - +
46B GLU* 1.3 76.2 + - - +
48B ALA* 3.4 2.9 + - - +
49B ASP* 3.0 38.0 + - - +
104B ASN* 4.2 5.9 + - - +
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Residues in contact with GLU 46 (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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9B TYR* 3.1 21.9 + - - +
10B GLU* 5.9 0.2 - - - +
44B SER* 3.9 15.7 + - - +
45B SER* 1.3 87.2 + - - +
47B GLU* 1.3 65.4 + - - +
49B ASP* 3.2 13.3 + - - +
50B PHE* 2.9 23.4 + - - +
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Residues in contact with GLU 47 (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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9B TYR* 3.6 21.2 + - + -
10B GLU* 5.4 0.7 - - - +
12B HIS* 5.3 2.4 - - - -
14B TYR* 2.8 33.9 + - + +
41B SER* 3.0 21.6 + - - +
42B PHE* 4.0 9.6 - - + -
43B GLN* 2.7 35.8 + - - +
44B SER* 3.2 17.0 + - - +
46B GLU* 1.3 78.7 - - - +
48B ALA* 1.3 63.3 + - - +
50B PHE* 3.2 4.9 + - - +
51B VAL* 3.0 23.1 + - + +
120B GLU* 3.8 5.7 - - - +
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Residues in contact with ALA 48 (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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91A TYR* 4.2 8.7 - - - +
42B PHE* 3.7 39.7 - - + -
44B SER 3.3 8.9 + - - +
45B SER 3.7 7.4 - - - +
46B GLU 3.3 0.2 - - - -
47B GLU* 1.3 80.6 - - - +
49B ASP* 1.3 63.8 + - - +
51B VAL* 3.1 2.6 + - - +
52B VAL* 2.9 29.9 + - - +
104B ASN* 4.1 18.8 - - + -
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Residues in contact with ASP 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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45B SER* 3.0 25.0 + - - +
46B GLU* 3.2 13.2 + - - +
48B ALA* 1.3 75.9 - - - +
50B PHE* 1.3 63.5 + - - +
52B VAL* 3.3 7.3 + - - +
53B LYS* 3.0 36.8 + - - +
104B ASN* 3.0 26.1 + - - +
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Residues in contact with PHE 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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7B SER* 4.0 20.6 - - - -
8B SER 3.6 20.0 - - - -
9B TYR* 3.4 46.2 - + + -
14B TYR* 3.8 24.2 - + - -
46B GLU 2.9 13.1 + - - +
47B GLU 3.4 6.7 - - - +
49B ASP* 1.3 77.3 - - - +
51B VAL* 1.3 67.4 + - + +
53B LYS* 3.5 9.0 + - + +
54B LEU* 3.0 36.9 + - + +
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Residues in contact with VAL 51 (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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14B TYR* 3.9 31.6 - - + -
40B VAL* 4.0 1.6 - - + -
42B PHE* 3.6 25.6 - - + -
47B GLU* 3.0 15.7 + - + +
48B ALA 3.6 6.3 - - - +
50B PHE* 1.3 80.5 - - + +
52B VAL* 1.3 66.0 + - - +
54B LEU* 3.3 7.2 + - + +
55B ALA* 2.9 22.5 + - - +
99B PHE* 3.7 24.2 - - + -
118B VAL* 4.1 22.3 - - + +
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Residues in contact with VAL 52 (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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42B PHE* 5.5 2.0 - - + -
48B ALA* 2.9 20.5 + - + +
49B ASP* 3.7 5.8 - - - +
51B VAL* 1.3 76.3 - - + +
53B LYS* 1.3 66.3 + - - +
55B ALA* 3.2 4.0 + - - +
56B PHE* 2.9 22.0 + - - +
99B PHE* 4.1 21.5 - - + -
101B SER* 3.0 31.5 - - - +
102B THR 4.1 2.7 - - - +
103B ASN* 3.6 29.6 - - - +
104B ASN* 3.9 15.7 - - + +
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Residues in contact with LYS 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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49B ASP* 3.0 26.9 + - - +
50B PHE* 3.6 9.9 - - + +
52B VAL* 1.3 78.3 - - - +
54B LEU* 1.3 57.8 + - - +
56B PHE* 3.3 5.7 + - - +
57B GLN* 2.8 54.1 + - + +
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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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7B SER* 3.6 36.6 - - - +
14B TYR* 4.0 21.1 - - + +
16B PRO* 3.9 23.3 - - + -
50B PHE* 3.0 29.3 + - + +
51B VAL* 3.5 7.4 - - - +
53B LYS* 1.3 72.9 - - - +
55B ALA* 1.3 62.7 + - - +
57B GLN* 3.1 19.8 + - + +
58B THR* 2.7 42.1 + - - +
118B VAL* 5.4 3.6 - - + -
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Residues in contact with ALA 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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16B PRO* 4.6 6.1 - - - -
51B VAL 2.9 13.8 + - - +
52B VAL 3.5 7.4 - - - +
54B LEU* 1.3 75.5 - - - +
56B PHE* 1.3 59.0 + - - +
58B THR* 3.5 5.8 - - - -
59B PHE* 2.8 32.7 + - - +
60B GLY 3.7 0.5 + - - -
64B PHE* 3.6 38.1 - - + -
99B PHE* 4.1 13.0 - - + -
101B SER* 4.2 3.6 - - - -
118B VAL* 4.6 4.9 - - + +
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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 VAL 2.9 7.3 + - - +
53B LYS* 3.6 9.2 - - - +
55B ALA* 1.3 74.7 - - - +
57B GLN* 1.3 69.4 + - + +
60B GLY* 2.7 57.8 + - - +
61B HIS* 3.6 34.3 - + - -
101B SER* 3.5 31.6 - - - +
102B THR* 4.6 4.9 - - + -
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Residues in contact with GLN 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 LYS* 2.8 47.6 + - + +
54B LEU* 3.6 23.2 - - + +
56B PHE* 1.3 79.4 - - + +
58B THR* 1.3 62.2 + - - +
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Residues in contact with THR 58 (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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16B PRO* 3.4 22.9 - - + +
54B LEU* 2.7 34.2 + - - +
55B ALA 3.5 3.4 - - - -
57B GLN* 1.3 81.4 - - - +
59B PHE* 1.3 97.0 + - + +
60B GLY 3.8 0.2 - - - -
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Residues in contact with PHE 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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16B PRO* 3.8 6.5 - - + -
17B PHE* 3.5 28.7 - - - -
18B SER* 3.5 31.4 - - - -
55B ALA 2.8 12.8 + - - +
58B THR* 1.3 107.4 - - + +
60B GLY* 1.3 61.5 + - - +
61B HIS 3.7 5.9 + - - +
62B SER* 4.8 1.8 - - - -
64B PHE* 3.7 14.8 - + + -
116B GLN* 3.2 28.7 - - - +
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Residues in contact with GLY 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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55B ALA 3.7 1.3 + - - +
56B PHE* 2.7 43.9 + - - -
58B THR 3.8 0.4 - - - -
59B PHE* 1.3 72.1 - - - +
61B HIS* 1.3 57.7 + - - -
62B SER* 3.2 2.8 + - - -
64B PHE* 4.7 0.2 - - - -
101B SER* 2.6 29.1 + - - -
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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