Contacts of the helix formed by residues 71 - 88 (chain B) in PDB entry 4XYN
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 PHE 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A THR* 3.6 20.9 - - + -
83A THR* 4.0 14.6 - - + -
86A HIS* 3.7 47.1 - + + +
11B LEU 4.2 2.7 - - - -
12B ILE* 3.8 31.9 - - + -
15B PHE* 3.5 42.3 - + + -
26B HIS 4.2 1.6 + - - +
70B ASP* 1.3 72.3 - - - +
72B GLN* 1.3 66.6 + - - +
74B PHE* 3.1 4.9 + + - +
75B MET* 2.9 56.3 + - + +
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Residues in contact with GLN 72 (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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83A THR* 4.3 29.9 - - + +
70B ASP* 3.0 14.5 + - - +
71B PHE* 1.3 78.6 - - - +
73B GLU* 1.3 64.2 + - + +
75B MET* 3.3 5.9 + - + +
76B ALA* 3.2 19.9 + - - +
65P SER 4.8 14.3 + - - -
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Residues in contact with GLU 73 (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 LEU* 3.2 28.8 - - - +
62B ASP* 4.0 0.9 - - - -
63B ASN* 2.9 28.1 + - + +
64B ASP* 3.1 10.4 + - - +
69B CYS* 3.2 15.5 - - - -
70B ASP* 2.7 48.9 + - - +
72B GLN* 1.3 75.4 - - + +
74B PHE* 1.3 64.9 + - - +
76B ALA* 3.4 8.2 + - - +
77B PHE* 3.1 20.1 + - - +
501B CA 2.7 26.2 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.5 7.4 - - + -
11B LEU* 4.0 14.8 - - + -
14B VAL* 4.3 12.1 - - + -
15B PHE* 3.5 36.3 - + + -
28B LEU* 4.1 14.6 - - + -
33B LEU* 5.5 0.9 - - + -
36B LEU* 3.8 32.8 - - + -
69B CYS* 3.7 7.2 - - - -
70B ASP 2.9 14.2 + - - +
71B PHE* 3.1 16.4 + + - +
73B GLU* 1.3 77.1 - - - +
75B MET* 1.3 62.0 + - - +
77B PHE* 3.2 27.2 + + - +
78B VAL* 2.8 49.2 + - + +
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Residues in contact with MET 75 (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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75A MET* 5.9 2.7 - - + -
78A VAL* 4.7 4.5 - - + -
79A ALA* 3.8 40.7 - - + +
82A THR* 4.0 12.8 - - - +
83A THR* 4.0 10.5 - - - +
11B LEU* 3.8 30.1 - - + -
71B PHE* 2.9 52.2 + - + +
72B GLN* 3.6 8.5 - - + +
74B PHE* 1.3 81.0 - - - +
76B ALA* 1.3 62.9 + - - +
78B VAL* 3.4 10.9 + - + +
79B ALA* 3.1 24.0 + - + +
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Residues in contact with ALA 76 (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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79A ALA* 5.3 1.1 - - - +
61B LEU* 5.6 0.7 - - + -
63B ASN* 6.2 2.2 - - - +
72B GLN 3.2 12.9 + - - +
73B GLU* 3.5 11.9 - - - +
74B PHE 3.1 0.4 - - - -
75B MET* 1.3 78.3 - - - +
77B PHE* 1.3 59.2 - - - +
79B ALA* 3.5 5.9 + - - +
80B MET* 3.1 37.2 + - + +
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Residues in contact with PHE 77 (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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8A MET* 6.2 0.4 - - + -
33B LEU* 4.5 6.7 - - + -
36B LEU* 4.9 0.7 - - + -
37B ILE* 3.9 19.3 - - + -
41B LEU* 3.6 33.2 - - + -
45B LEU* 3.9 16.4 - - + -
57B VAL* 4.5 9.6 - - + -
61B LEU* 3.5 38.4 - - + -
73B GLU 3.1 8.7 + - - +
74B PHE* 3.3 32.5 - + - +
76B ALA* 1.3 74.3 - - - +
78B VAL* 1.3 66.4 + - + +
80B MET* 3.2 15.0 + - + +
81B VAL* 3.1 41.1 + - + +
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Residues in contact with VAL 78 (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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4A LEU* 4.6 0.7 - - + -
8A MET* 4.0 21.5 - - + +
11A LEU* 4.7 6.3 - - + -
75A MET* 4.9 2.5 - - + -
11B LEU* 3.9 35.2 - - + -
74B PHE* 2.8 55.3 + - + +
75B MET* 3.4 14.1 + - + +
77B PHE* 1.3 72.5 - - + +
79B ALA* 1.3 51.0 + - - +
81B VAL* 3.5 1.6 + - - +
82B THR* 2.6 49.8 + - - +
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Residues in contact with ALA 79 (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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72A GLN* 6.4 0.7 - - + -
75A MET* 3.8 39.9 - - + +
76A ALA 5.5 0.2 - - - +
79A ALA* 5.8 2.0 - - + -
75B MET 3.1 16.3 + - - +
76B ALA* 3.7 7.0 - - - +
78B VAL* 1.3 75.2 - - - +
80B MET* 1.3 59.7 + - - +
83B THR* 2.8 37.1 + - - +
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Residues in contact with MET 80 (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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72A GLN* 6.3 0.2 - - - +
60B THR* 4.5 17.7 - - + +
61B LEU* 3.6 31.6 - - + -
76B ALA* 3.1 34.7 + - + +
77B PHE* 3.2 13.0 + - + +
79B ALA* 1.3 75.3 - - - +
81B VAL* 1.3 59.2 - - + +
83B THR* 3.6 4.8 - - - +
84B ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 81 (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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8A MET* 3.8 27.4 - - + -
41B LEU* 4.4 4.3 - - + -
44B PHE* 4.0 24.2 - - + +
45B LEU* 4.3 18.6 - - + -
77B PHE* 3.1 45.8 + - + +
78B VAL 3.8 3.8 - - - +
80B MET* 1.3 72.7 - - + +
82B THR* 1.3 60.2 + - - +
84B ALA* 3.0 10.9 + - + +
85B CYS* 2.9 26.0 + - - +
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Residues in contact with THR 82 (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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8A MET* 3.2 45.7 - - + +
11A LEU* 4.5 3.4 - - + +
12A ILE* 3.8 4.9 - - + +
71A PHE* 3.7 22.4 - - + -
75A MET* 3.8 19.8 - - + +
78B VAL* 2.6 33.3 + - - +
79B ALA 4.2 0.2 - - - -
81B VAL* 1.3 73.8 - - - +
83B THR* 1.3 57.3 + - - +
85B CYS* 3.4 6.0 + - - +
86B HIS* 2.9 28.1 + - - +
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Residues in contact with THR 83 (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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71A PHE* 4.0 13.1 - - + -
72A GLN* 3.3 44.7 - - + +
75A MET* 3.8 12.6 - - - +
79B ALA 2.8 23.2 + - - -
80B MET* 3.6 5.8 - - - +
82B THR* 1.3 74.6 - - - +
84B ALA* 1.3 70.1 + - - +
86B HIS* 3.6 2.4 + - + +
87B GLU* 3.3 31.6 + - + +
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Residues in contact with ALA 84 (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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80B MET 2.9 13.6 + - - +
81B VAL* 3.1 14.4 - - + +
83B THR* 1.3 77.6 - - - +
85B CYS* 1.3 55.4 + - - +
87B GLU* 2.8 40.1 + - - +
88B PHE* 3.4 3.8 + - - +
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Residues in contact with CYS 85 (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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8A MET* 5.7 0.9 - - + -
9A VAL* 4.7 5.4 - - - -
12A ILE* 3.3 21.5 - - + -
44B PHE* 4.5 32.3 - - + -
81B VAL 2.9 13.7 + - - +
82B THR* 3.7 9.9 - - + +
84B ALA* 1.3 72.0 - - - +
86B HIS* 1.3 62.2 + - - +
88B PHE* 3.2 25.1 + - - +
89B PHE* 3.6 24.4 + - - -
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Residues in contact with HIS 86 (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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12A ILE* 3.7 12.5 - - + +
15A PHE* 4.3 7.1 - + - -
16A HIS* 3.6 30.7 - + - -
26A HIS 5.8 0.4 + - - -
71A PHE* 3.5 59.1 - + + +
82B THR 2.9 18.0 + - - +
83B THR* 3.9 5.2 - - + +
84B ALA 2.9 0.2 + - - -
85B CYS* 1.3 75.8 - - - +
87B GLU* 1.3 67.1 + - + +
89B PHE* 2.8 25.9 + - + +
90B GLU* 3.5 29.2 + - + -
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Residues in contact with GLU 87 (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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83B THR* 3.3 25.9 - - + +
84B ALA* 2.8 14.8 + - - +
86B HIS* 1.3 79.3 - - + +
88B PHE* 1.3 55.9 + - - +
89B PHE 2.8 14.9 + - - -
90B GLU* 3.0 24.1 + - + +
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Residues in contact with PHE 88 (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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84B ALA 3.4 4.3 + - - +
85B CYS* 3.2 16.5 + - - +
86B HIS 3.2 0.2 - - - -
87B GLU* 1.3 77.1 - - - +
89B PHE* 1.3 83.8 + + - +
90B GLU 3.7 0.4 - - - -
91B HIS 4.6 7.4 - - - +
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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