Contacts of the helix formed by residues 55 - 66 (chain B) in PDB entry 1XHU
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 LYS 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLU* 3.5 29.3 + - - -
39B LYS* 5.3 1.2 - - - +
42B TYR* 3.7 43.4 - - + +
54B PHE* 1.3 75.5 - - - +
56B GLN* 1.3 69.9 + - - +
57B TYR* 3.7 42.4 - - + +
58B GLU* 2.8 25.5 + - + +
59B TYR* 2.7 20.3 + - - +
107B GLU* 4.9 7.0 - - - -
113B ALA 5.7 0.9 - - - +
114B ASP* 3.4 21.5 + - - +
115B ILE* 4.8 1.4 - - - +
116B LEU* 5.0 0.4 - - - -
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Residues in contact with GLN 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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54B PHE 4.2 0.8 + - - -
55B LYS* 1.3 79.0 - - - +
57B TYR* 1.3 63.5 + - + +
59B TYR* 3.1 7.1 + - - +
60B LEU* 3.0 25.9 + - + +
88B LEU 3.5 7.1 + - - -
89B LEU* 3.0 48.0 + - + +
90B SER 4.8 0.8 + - - -
111B ASP* 3.5 34.3 + - - +
112B THR* 3.4 4.8 + - - +
113B ALA* 2.7 48.3 + - + +
114B ASP 4.5 4.6 + - - -
116B LEU* 4.8 13.1 - - + +
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Residues in contact with TYR 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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55B LYS* 3.7 45.2 - - + +
56B GLN* 1.3 79.6 - - + +
58B GLU* 1.3 82.2 + - + +
60B LEU* 3.0 11.3 + - - +
61B ASN* 2.8 30.2 + - - -
91B ARG* 4.7 4.0 - - - +
105B PHE* 4.0 23.3 - - + +
106B GLU* 3.3 31.2 - - + +
107B GLU* 3.8 30.9 + - + +
111B ASP* 4.4 6.7 + - - -
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Residues in contact with GLU 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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42B TYR* 2.3 30.6 + - - -
46B LYS* 2.9 25.0 + - - -
54B PHE* 3.4 19.5 - - + -
55B LYS* 2.8 24.4 + - + +
57B TYR* 1.3 86.0 - - + +
59B TYR* 1.3 62.0 + - - +
61B ASN* 3.9 6.8 - - - +
62B ASP* 3.0 24.1 + - + +
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Residues in contact with TYR 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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54B PHE* 3.9 27.5 - + + -
55B LYS 2.7 14.4 + - - +
56B GLN 3.5 8.5 - - - +
58B GLU* 1.3 71.3 - - - +
60B LEU* 1.3 67.8 + - + +
62B ASP* 3.1 7.4 + - - +
63B LEU* 2.8 58.6 + - + +
80B PHE* 4.5 12.7 - + - -
89B LEU* 4.3 15.5 - - + -
116B LEU* 3.7 20.0 - - + -
118B VAL* 3.6 31.9 - - + -
123B TYR* 2.6 31.5 + + - -
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Residues in contact with LEU 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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56B GLN* 3.0 19.6 + - + +
57B TYR* 3.0 9.9 + - - +
59B TYR* 1.3 85.1 - - + +
61B ASN* 1.3 64.3 + - - +
63B LEU* 3.0 6.2 + - + +
64B PHE* 3.0 31.9 + - + -
80B PHE* 3.2 39.7 - - + -
89B LEU* 3.7 21.1 - - + +
90B SER* 4.2 5.6 - - - -
91B ARG* 4.1 26.7 - - + +
105B PHE* 3.5 29.8 - - + -
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Residues in contact with ASN 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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57B TYR* 2.8 23.5 + - - +
58B GLU* 4.0 6.9 - - - +
60B LEU* 1.3 71.7 - - - +
62B ASP* 1.3 53.7 + - - +
64B PHE 3.5 0.2 + - - -
65B MET* 2.7 45.1 + - - +
99B TRP* 3.1 13.7 + - - +
104B LEU* 3.1 25.5 - - + +
105B PHE* 2.7 72.9 + - - +
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Residues in contact with ASP 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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54B PHE* 4.2 25.4 - - + -
58B GLU 3.0 19.2 + - - +
59B TYR* 3.5 7.6 - - + +
61B ASN* 1.3 73.4 - - - +
63B LEU* 1.3 68.4 + - - +
65B MET* 3.7 13.1 - - - +
66B LYS* 3.2 38.0 + - - +
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Residues in contact with LEU 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 TYR* 2.8 35.6 + - + +
60B LEU* 3.2 10.5 - - + +
62B ASP* 1.3 80.6 + - - +
64B PHE* 1.3 82.8 + - + +
65B MET 3.4 0.2 + - - -
66B LYS* 3.4 19.9 + - - +
67B ASN* 2.9 36.2 + - - +
79B LEU* 4.2 26.9 - - + +
80B PHE* 3.9 32.5 - - + -
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Residues in contact with PHE 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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60B LEU* 3.0 18.0 + - + +
63B LEU* 1.3 101.9 - - + +
65B MET* 1.3 60.2 + - - +
67B ASN* 3.5 22.5 + - - +
68B PRO* 4.1 2.1 - - - +
70B ILE 5.4 0.5 - - - +
76B ARG* 4.0 30.7 + - + +
79B LEU* 4.5 7.4 - - + -
80B PHE* 4.6 9.0 - + - -
96B THR* 3.8 26.9 - - + -
99B TRP* 3.4 57.9 - + + -
105B PHE* 3.4 30.7 - + - -
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Residues in contact with MET 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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61B ASN* 2.7 39.3 + - - +
62B ASP* 3.7 12.8 - - - +
63B LEU 3.3 0.4 - - - -
64B PHE* 1.3 75.7 - - - +
66B LYS* 1.3 56.7 - - - +
67B ASN 3.3 4.2 + - - -
68B PRO* 3.7 15.2 - - - +
99B TRP* 3.6 17.0 - - + -
101B ILE* 3.4 29.6 - - + -
104B LEU* 4.3 14.8 - - + -
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Residues in contact with LYS 66 (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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62B ASP* 3.2 22.8 + - - +
63B LEU* 3.5 32.5 - - - +
64B PHE 3.3 0.2 - - - -
65B MET* 1.3 75.3 - - - +
67B ASN* 1.3 72.0 + - - +
68B PRO* 3.6 6.0 - - - +
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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