Contacts of the helix formed by residues 57 - 65 (chain B) in PDB entry 2XWU
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 GLN 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 5.8 1.6 - - - +
21B PHE* 3.1 49.2 - - + +
55B SER* 2.8 26.9 - - - +
56B PRO* 1.3 86.8 - - - +
58B ALA* 1.3 58.4 + - - +
59B TRP 3.2 0.2 - - - -
60B HIS* 2.8 13.2 + - + +
61B PHE* 2.8 30.8 + - - +
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Residues in contact with ALA 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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52B ALA 3.7 2.9 - - - +
53B GLN* 3.7 20.9 - - - +
55B SER* 3.4 15.1 + - - +
56B PRO 3.1 0.6 - - - -
57B GLN* 1.3 73.7 - - - +
59B TRP* 1.3 56.7 - - - +
60B HIS 2.8 6.7 + - - -
61B PHE* 3.2 26.1 - - + -
62B SER* 2.7 35.3 + - - -
81B ALA* 4.6 7.2 - - + -
85B LYS* 3.7 13.2 - - + -
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Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 3.3 22.2 + - + +
58B ALA* 1.3 78.5 - - - +
60B HIS* 1.3 56.1 + - + +
62B SER* 4.4 1.8 - - - -
63B TRP* 3.2 27.2 + - - +
82B LEU* 4.9 11.2 - - + -
85B LYS* 2.9 64.2 - - + +
86B ILE* 4.1 11.4 - - + -
89B TYR 3.1 22.4 - - - -
92B ASP* 3.3 26.5 + - + +
93B ILE* 3.3 38.6 - - + -
101B LEU* 4.9 9.6 - - + -
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Residues in contact with HIS 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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21B PHE 6.1 1.3 - - - -
22B THR* 6.5 0.9 - - - -
56B PRO 4.2 1.3 + - - +
57B GLN* 2.8 13.7 + - + +
58B ALA 2.8 2.6 - - - -
59B TRP* 1.3 81.7 - - + +
61B PHE* 1.3 61.1 + - + +
62B SER 3.4 2.1 + - - -
63B TRP* 4.0 9.2 + - - +
64B GLN* 3.3 52.5 + - + +
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Residues in contact with PHE 61 (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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21B PHE* 4.0 9.9 - - + +
22B THR* 4.4 1.3 - - - -
23B VAL* 3.7 17.5 - - + +
26B VAL* 3.7 27.6 - - + -
52B ALA 3.3 28.5 - - - -
53B GLN* 4.5 1.3 - - - -
55B SER* 3.9 3.8 - - - -
57B GLN* 2.8 37.5 + - + +
58B ALA* 3.2 25.6 - - + -
60B HIS* 1.3 73.2 - - + +
62B SER* 1.3 68.7 + - - +
63B TRP 3.3 2.0 - - - -
64B GLN* 3.2 19.1 + - - +
65B LEU* 3.1 35.6 + - + +
77B PHE* 3.7 26.2 - + - -
81B ALA* 4.8 3.4 - - + -
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Residues in contact with SER 62 (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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58B ALA* 2.7 22.8 + - - -
61B PHE* 1.3 80.2 - - - +
63B TRP* 1.3 71.1 + - - +
65B LEU 3.2 9.4 + - - -
66B LEU* 3.5 16.1 + - - +
78B GLY* 3.3 36.6 - - - -
81B ALA* 4.1 12.6 - - - -
82B LEU* 3.2 27.6 - - - +
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Residues in contact with TRP 63 (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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59B TRP* 3.2 30.7 + + - +
60B HIS* 4.0 7.2 + - - +
61B PHE 3.3 0.4 - - - -
62B SER* 1.3 87.1 + - - +
64B GLN* 1.3 61.4 + - + +
66B LEU* 3.3 22.4 + - + +
67B GLN* 4.1 4.0 + - - +
82B LEU* 3.7 34.2 - - + +
101B LEU* 3.9 20.4 - - + -
104B GLN* 3.6 24.0 - - + -
105B LEU* 3.5 24.0 - - + -
108B GLN* 3.5 45.5 + - + +
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Residues in contact with GLN 64 (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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22B THR* 5.7 0.3 - - - -
23B VAL* 2.8 43.4 + - + +
24B GLU* 5.8 1.0 + - - -
60B HIS* 3.3 40.3 + - + +
61B PHE* 3.2 14.6 - - - +
62B SER 3.1 0.8 - - - -
63B TRP* 1.3 75.0 - - + +
65B LEU* 1.3 58.1 + - - +
66B LEU 3.1 5.8 - - - -
67B GLN* 3.1 43.5 + - - +
70B LYS* 3.4 8.2 - - - -
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Residues in contact with LEU 65 (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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23B VAL* 4.6 13.7 - - + +
26B VAL* 3.8 5.6 - - + -
27B GLU* 4.5 16.2 - - + -
30B LEU* 4.3 4.0 - - + -
61B PHE* 3.1 36.4 + - + +
62B SER 3.2 6.7 + - - +
64B GLN* 1.3 76.0 - - - +
66B LEU* 1.3 58.0 + - - +
67B GLN 3.3 0.7 - - - -
70B LYS* 3.3 19.2 - - + +
74B ILE* 3.3 33.0 - - + +
75B GLN* 3.2 20.8 - - - +
77B PHE* 3.6 31.2 - - + -
78B GLY* 3.8 16.2 - - - +
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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