Contacts of the helix formed by residues 78 - 98 (chain T) in PDB entry 5A0Q
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 THR 78 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159S SER 5.8 0.2 + - - -
160S GLY 4.7 1.8 - - - +
161S THR* 3.8 34.4 + - + +
162S PHE* 5.9 1.3 - - + +
74T ILE* 4.1 23.4 - - + +
76T GLY 4.4 3.3 + - - -
77T LEU* 1.3 73.3 - - - +
79T ALA* 1.4 65.0 + - - +
81T ALA* 3.1 15.8 + - - +
82T ARG* 3.1 35.6 + - + +
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Residues in contact with ALA 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LEU* 4.4 22.4 - - + -
159S SER 3.9 18.9 + - - +
160S GLY 4.5 0.8 + - - -
77T LEU* 3.2 9.5 - - + +
78T THR* 1.4 79.9 - - - +
80T ASP* 1.3 64.5 + - - +
82T ARG* 3.3 25.5 + - - +
83T LEU* 3.1 32.4 + - + +
126T ARG* 6.0 1.1 - - - +
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Residues in contact with ASP 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S PHE* 4.3 1.7 - - - -
77T LEU* 2.8 39.5 - - + +
79T ALA* 1.3 73.8 - - - +
81T ALA* 1.4 56.6 + - - +
83T LEU* 3.7 16.0 - - - +
84T LEU* 3.0 33.4 + - - +
126T ARG* 4.8 12.6 + - - +
127T PRO 3.8 5.8 - - - +
128T TYR* 3.7 23.3 - - + -
129T GLY 3.1 21.8 + - - +
130T VAL* 3.8 16.2 - - + -
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Residues in contact with ALA 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T LEU* 5.4 1.3 - - + -
72T ILE* 4.2 4.7 - - - +
74T ILE* 3.4 41.1 - - + -
77T LEU 3.8 2.6 + - - +
78T THR 3.1 15.0 + - - +
80T ASP* 1.4 77.6 - - - +
82T ARG* 1.3 57.4 + - + +
84T LEU* 3.7 2.5 + - - +
85T CYS* 3.0 28.6 + - - +
130T VAL* 3.6 19.7 - - + +
132T LEU* 4.5 3.1 - - + +
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Residues in contact with ARG 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S GLN* 4.1 5.7 + - - +
117S SER* 2.9 25.4 + - - -
118S ASN* 3.2 50.4 + - - +
121S LEU 5.8 0.8 - - - +
160S GLY* 3.0 25.1 + - - -
162S PHE* 4.5 20.2 - - - -
64T LEU* 5.4 9.0 - - + -
78T THR* 3.1 28.8 + - + +
79T ALA* 3.3 23.9 + - - +
81T ALA* 1.3 75.5 - - + +
83T LEU* 1.3 65.5 + - - +
85T CYS* 3.7 6.0 - - - +
86T ASN* 2.8 31.9 + - - +
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Residues in contact with LEU 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S ASN* 4.4 17.5 - - + +
121S LEU* 4.4 10.8 - - + +
122S GLN* 3.2 34.5 - - - +
79T ALA* 3.1 20.6 + - + +
80T ASP* 3.4 22.4 + - - +
82T ARG* 1.3 78.3 - - - +
84T LEU* 1.3 62.9 + - - +
86T ASN* 3.5 6.6 + - + +
87T PHE* 3.4 18.2 + - - +
115T LYS* 3.9 8.8 + - - +
126T ARG* 5.7 2.0 - - - +
128T TYR* 4.3 14.6 - - + -
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Residues in contact with LEU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T ASP 3.0 16.2 + - - +
81T ALA* 4.0 4.0 - - - +
83T LEU* 1.3 75.7 - - - +
85T CYS* 1.4 57.2 + - - +
87T PHE* 3.3 7.7 - - + +
88T MET* 3.0 35.8 + - + +
112T ILE* 4.5 17.7 - - + -
115T LYS* 4.0 22.9 - - + +
116T THR* 4.0 16.2 - - - +
128T TYR* 3.6 33.0 - - + -
130T VAL* 3.4 31.2 - - + +
132T LEU* 4.5 18.6 - - + -
147T THR* 5.5 0.7 - - - +
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Residues in contact with CYS 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T LEU* 3.9 13.9 - - + -
66T VAL* 3.6 21.8 - - - -
72T ILE* 3.7 15.0 - - + +
81T ALA 3.0 19.4 + - - +
82T ARG* 3.7 8.1 - - - +
83T LEU 3.3 0.2 - - - -
84T LEU* 1.4 72.1 - - - +
86T ASN* 1.3 59.2 + - - +
87T PHE 3.1 1.8 - - - -
88T MET* 3.0 21.6 + - - +
89T ARG* 3.1 44.0 + - - +
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Residues in contact with ASN 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118S ASN* 4.6 17.9 - - - +
82T ARG 2.8 20.4 + - - +
83T LEU* 3.9 8.6 - - + +
84T LEU 3.5 0.2 - - - -
85T CYS* 1.3 71.8 - - - +
87T PHE* 1.3 60.9 + - - +
89T ARG* 3.9 11.2 + - - +
90T GLN* 3.8 16.8 + - - +
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Residues in contact with PHE 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T LEU 3.4 10.3 + - - +
84T LEU* 3.3 9.6 + - + +
85T CYS 3.1 0.4 - - - -
86T ASN* 1.3 78.1 - - - +
88T MET* 1.4 88.7 + - + +
90T GLN* 3.3 7.4 + - + +
91T GLU* 3.0 57.9 + - + +
111T LEU* 4.1 19.1 - - + -
115T LYS* 3.6 46.9 - - + -
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Residues in contact with MET 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T VAL* 3.7 28.0 - - + -
72T ILE* 4.9 7.2 - - + -
84T LEU* 3.0 25.5 + - + +
85T CYS* 3.0 15.7 + - - +
87T PHE* 1.4 105.3 - - + +
89T ARG* 1.3 58.6 + - - +
91T GLU 3.4 0.3 + - - -
92T CYS* 3.0 33.8 + - - -
108T LEU* 3.6 30.9 - - + +
112T ILE* 3.4 44.9 - - + -
132T LEU* 5.4 1.3 - - + -
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Residues in contact with ARG 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S GLN* 5.6 6.1 + - - +
64T LEU* 3.8 18.2 - - - +
65T HIS* 2.7 43.4 + - - +
66T VAL* 3.5 21.5 - - - +
85T CYS* 3.1 31.1 + - - +
86T ASN* 4.1 10.3 - - - +
87T PHE 3.2 0.2 - - - -
88T MET* 1.3 77.2 - - - +
90T GLN* 1.3 60.8 + - - +
92T CYS* 3.2 4.7 + - - +
93T LEU* 3.1 29.4 + - + +
74a MET* 6.3 1.1 - - + -
77a HIS* 3.3 53.0 + - + +
78a SER* 4.4 2.8 - - - +
80a ASN* 4.9 5.5 + - - +
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Residues in contact with GLN 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T ASN 3.8 10.7 + - - +
87T PHE* 3.3 12.0 + - + +
89T ARG* 1.3 76.8 - - - +
91T GLU* 1.3 66.1 + - - +
93T LEU* 3.4 11.5 + - - +
94T ASP* 3.1 26.8 + - - +
74a MET* 3.6 30.4 - - - +
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Residues in contact with GLU 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T PHE* 3.0 63.8 + - + +
88T MET 3.8 0.2 - - - +
90T GLN* 1.3 83.3 - - - +
92T CYS* 1.4 61.5 + - - +
94T ASP* 3.3 30.2 + - - +
95T SER 3.6 0.9 + - - -
103T LEU* 2.9 17.0 - - - +
108T LEU* 3.5 21.3 - - + -
111T LEU* 3.3 24.0 - - + +
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Residues in contact with CYS 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66T VAL* 3.6 28.0 - - - +
67T ASP* 3.5 35.4 - - - +
70T ILE* 4.7 1.6 - - - -
88T MET 3.0 23.8 + - - -
89T ARG 3.5 8.5 - - - +
91T GLU* 1.4 74.4 - - - +
93T LEU* 1.3 64.6 + - + +
95T SER 3.6 0.9 + - - -
96T ARG* 3.2 28.6 + - - +
103T LEU* 3.3 14.6 - - - +
108T LEU* 3.7 17.5 - - - -
77a HIS* 5.6 0.7 - - - +
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Residues in contact with LEU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67T ASP* 5.4 1.1 - - - +
89T ARG 3.1 17.0 + - - +
90T GLN* 3.7 15.0 - - - +
91T GLU 3.3 0.4 - - - -
92T CYS* 1.3 76.2 - - + +
94T ASP* 1.3 64.8 + - - +
96T ARG* 3.8 17.0 - - + +
97T PHE* 3.0 27.4 + - - +
70a ALA* 3.4 24.6 - - + +
73a LYS* 4.0 24.5 - - + -
74a MET* 3.4 47.1 - - + +
77a HIS* 5.1 8.7 - - + +
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Residues in contact with ASP 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90T GLN* 3.1 15.8 + - - +
91T GLU* 3.3 27.6 - - - +
92T CYS 3.2 0.4 - - - -
93T LEU* 1.3 75.9 - - - +
95T SER* 1.3 59.0 + - - +
97T PHE* 4.8 1.3 - - - -
98T VAL* 2.9 49.8 + - - +
99T PHE* 5.2 5.4 - - - -
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Residues in contact with SER 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91T GLU 3.6 2.6 + - - -
92T CYS 3.6 0.2 + - - -
93T LEU 3.4 0.2 - - - -
94T ASP* 1.3 80.0 + - - +
96T ARG* 1.4 61.0 + - - +
97T PHE 3.3 0.3 + - - -
99T PHE* 3.4 31.2 + - - +
100T ASP 3.7 2.6 + - - -
101T ARG* 3.0 40.0 + - - +
102T PRO 4.3 0.3 + - - -
103T LEU* 3.6 36.0 + - - -
104T PRO* 4.0 0.9 - - - +
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Residues in contact with ARG 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67T ASP* 3.0 29.4 + - - -
68T ASN* 3.7 24.6 - - - +
69T HIS* 2.4 40.2 + - - -
92T CYS 3.2 21.1 + - - +
93T LEU* 4.0 16.6 - - + +
94T ASP 3.3 0.2 - - - -
95T SER* 1.4 76.2 - - - +
97T PHE* 1.3 58.5 + - - +
100T ASP* 3.6 18.4 - - - +
101T ARG 3.0 20.4 + - - +
102T PRO* 3.7 16.3 - - + +
103T LEU 3.9 2.1 - - - +
220T GLU* 5.5 0.6 + - - -
73a LYS* 6.1 2.8 - - - +
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Residues in contact with PHE 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T LEU 3.0 17.6 + - - +
94T ASP* 4.0 2.2 - - - +
96T ARG* 1.3 78.5 - - - +
98T VAL* 1.3 81.5 + - + +
99T PHE 3.3 0.8 + - - -
100T ASP* 3.5 3.9 - - - +
63a THR* 4.6 11.7 - - + -
66a LYS* 3.5 48.8 - - + +
67a ILE* 4.0 20.4 - - + -
70a ALA* 4.8 11.4 - - + -
91b TRP* 5.8 0.9 - + - -
94b ARG* 3.0 48.2 + - - -
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Residues in contact with VAL 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94T ASP* 2.9 34.3 + - - +
97T PHE* 1.3 92.9 - - + +
99T PHE* 1.3 88.1 + - + +
90b SER* 3.5 2.1 + - - -
91b TRP* 3.1 61.9 + - + -
94b ARG* 3.7 5.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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