Contacts of the helix formed by residues 79 - 94 (chain e) in PDB entry 5XTD
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 ASP 79 (chain e).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77e ASP* 3.2 2.1 - - + +
78e LYS* 1.3 80.8 - - - +
80e PRO* 1.3 73.1 - - + +
81e VAL* 4.5 2.5 - - + +
82e LEU* 3.3 38.2 + - + +
83e ASP* 2.9 24.1 + - - +
21r HIS* 4.9 10.9 + - - -
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Residues in contact with PRO 80 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70e ASN* 3.7 33.7 - - + +
78e LYS 3.4 6.5 - - - +
79e ASP* 1.3 85.3 - - + +
81e VAL* 1.3 61.4 + - + +
83e ASP* 3.3 6.1 + - + +
84e VAL* 3.0 36.1 + - + +
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Residues in contact with VAL 81 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79e ASP* 3.2 3.2 - - + +
80e PRO* 1.3 80.5 - - + +
82e LEU* 1.3 68.2 + - + +
84e VAL* 3.1 6.0 + - - +
85e TRP* 3.0 53.6 + - + +
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Residues in contact with LEU 82 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77e ASP* 3.8 20.9 - - + +
79e ASP* 3.3 37.6 + - + +
81e VAL* 1.3 81.2 - - + +
83e ASP* 1.3 61.0 + - - +
85e TRP* 4.6 4.5 - - + +
86e ASN* 2.9 32.2 + - - +
21r HIS* 4.0 27.6 - - + +
22r MET* 4.1 16.4 - - + -
25r ILE* 3.8 22.1 - - + +
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Residues in contact with ASP 83 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70e ASN* 4.1 8.7 + - - -
72e ASP 5.2 2.7 - - - +
73e SER* 2.7 35.7 - - - +
74e HIS* 4.8 4.3 - - + +
75e GLY 3.6 0.4 - - - +
76e TYR* 3.1 6.3 - - + +
77e ASP 2.6 48.4 + - - +
78e LYS 4.4 0.5 - - - +
79e ASP 2.9 13.4 + - - +
80e PRO* 3.4 9.6 - - + +
82e LEU* 1.3 74.3 - - - +
84e VAL* 1.3 68.5 - - + +
86e ASN* 3.2 4.3 + - - +
87e MET* 2.9 29.5 + - - +
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Residues in contact with VAL 84 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72e ASP 5.8 2.2 - - - +
74e HIS* 4.9 13.9 - - + -
80e PRO* 3.0 19.0 + - + +
81e VAL* 3.1 5.3 + - - +
83e ASP* 1.3 78.0 - - + +
85e TRP* 1.3 61.9 + - + +
87e MET* 3.4 6.6 - - - +
88e ARG* 3.0 65.7 + - + +
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Residues in contact with TRP 85 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81e VAL* 3.0 45.6 + - + +
82e LEU* 4.3 5.4 - - + +
84e VAL* 1.3 79.1 - - + +
86e ASN* 1.3 65.9 + - - +
88e ARG* 3.2 38.9 + - + +
89e LEU* 2.9 47.0 + - + +
25r ILE* 5.2 7.4 - - + -
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Residues in contact with ASN 86 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76e TYR* 3.0 43.3 - - + +
77e ASP* 5.1 5.8 + - - +
82e LEU 2.9 20.6 + - - +
83e ASP 3.8 2.5 - - - +
85e TRP* 1.3 75.4 - - - +
87e MET* 1.3 63.1 - - - +
89e LEU* 3.9 4.4 - - - +
90e VAL* 3.0 31.3 + - - +
24r TRP* 5.0 2.7 - - - +
25r ILE* 4.2 28.6 - - + +
28r THR* 4.2 12.6 + - - +
29r THR* 5.8 0.2 - - - +
81r GLN* 3.7 14.1 + - - +
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Residues in contact with MET 87 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70a LEU* 3.8 15.3 - - + -
74e HIS* 3.1 46.9 - - + +
76e TYR* 3.3 24.7 - - + -
83e ASP 2.9 17.6 + - - +
84e VAL* 3.4 6.1 - - + +
86e ASN* 1.3 76.7 - - - +
88e ARG* 1.3 65.6 + - + +
90e VAL* 3.1 3.8 + - - +
91e PHE* 2.9 58.4 + - + -
431r THR* 3.5 22.7 - - + -
432r ARG* 4.9 0.7 - - - -
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Residues in contact with ARG 88 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74a TYR* 3.4 29.3 + - + +
84e VAL* 3.0 40.5 + - + +
85e TRP* 3.2 46.3 + - + +
87e MET* 1.3 81.5 - - + +
89e LEU* 1.3 59.3 + - + +
91e PHE* 3.8 0.7 - - - +
92e PHE* 2.9 32.1 + - - +
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Residues in contact with LEU 89 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85e TRP* 2.9 34.7 + - + +
86e ASN* 3.9 4.3 - - - +
88e ARG* 1.3 77.3 - - + +
90e VAL* 1.3 65.0 + - - +
92e PHE* 4.4 4.3 - - + -
93e PHE* 3.0 56.6 + - + +
25r ILE* 3.7 23.1 - - + -
29r THR* 3.6 31.3 - - + +
32r LEU* 4.6 2.0 - - - +
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Residues in contact with VAL 90 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76e TYR* 3.2 29.2 - - + +
86e ASN* 3.0 27.0 + - - +
87e MET* 3.5 7.4 - - - +
89e LEU* 1.3 75.5 - - + +
91e PHE* 1.3 62.9 + - + +
94e GLY* 2.9 32.0 + - - +
95e VAL* 4.4 1.1 - - + +
28r THR* 5.2 8.3 - - + +
32r LEU* 4.9 7.9 - - + -
78r MET* 4.0 22.7 - - + -
435r THR* 3.6 25.6 - - + +
439r MET* 4.2 8.5 - - + -
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Residues in contact with PHE 91 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67a PHE* 3.6 37.9 - + - -
70a LEU* 4.6 6.7 - - + -
71a LEU* 4.5 23.8 - - + -
74a TYR* 3.5 45.1 - + + +
87e MET* 2.9 58.4 + - + +
90e VAL* 1.3 79.4 - - + +
92e PHE* 1.3 63.0 + - - +
95e VAL* 3.2 36.0 - - + +
96e SER* 3.3 4.0 + - - -
431r THR* 3.9 3.4 - - + -
435r THR* 3.9 21.1 - - + -
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Residues in contact with PHE 92 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74a TYR* 4.4 13.0 - + + -
77a LEU* 5.0 11.2 - - + -
78a THR* 4.8 10.3 - - + -
88e ARG 2.9 20.9 + - - +
89e LEU* 4.0 5.2 - - + +
90e VAL 3.1 0.2 - - - -
91e PHE* 1.3 76.5 - - - +
93e PHE* 1.3 94.1 + + + +
96e SER* 2.4 48.7 + - - -
97e ILE* 3.3 31.1 + - + -
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Residues in contact with PHE 93 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89e LEU* 3.0 45.3 + - + +
92e PHE* 1.3 95.7 - + - +
94e GLY* 1.3 61.7 + - - +
95e VAL 3.4 0.5 + - - -
97e ILE* 3.7 27.2 - - + +
98e ILE* 3.5 28.2 + - - +
29r THR* 4.8 12.1 - - - +
32r LEU* 4.1 20.6 - - + -
33r ILE* 3.8 36.3 - - + +
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Residues in contact with GLY 94 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89e LEU 3.8 0.6 + - - -
90e VAL 2.9 18.6 + - - -
93e PHE* 1.3 79.3 - - - +
95e VAL* 1.3 65.3 + - - +
98e ILE* 4.5 4.6 - - - +
99e LEU* 3.8 9.0 - - - +
32r LEU* 3.9 17.6 - - - +
71r TRP* 3.7 20.5 - - - -
439r MET* 4.1 12.9 - - - +
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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