Contacts of the helix formed by residues 79 - 101 (chain I) in PDB entry 5T0G
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 ILE 79 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H PHE* 6.3 4.0 - - + -
17H GLY 5.7 4.0 - - - +
19H LEU* 5.1 20.0 - - + -
119H GLN* 4.1 13.7 - - - +
152H SER* 4.7 14.4 - - - +
154H ALA* 5.7 2.9 - - + -
27I ALA* 5.3 13.0 - - + -
76I VAL* 4.9 0.6 - - - +
78I GLY* 1.3 75.8 - - - -
80I THR* 1.3 69.4 + - - +
81I SER* 4.0 3.8 - - - +
82I ASP* 3.3 32.1 - - + +
83I ALA* 3.2 16.3 + - - +
128I ARG* 6.2 2.0 - - - +
131I GLY* 5.4 5.2 - - - +
132I VAL* 3.4 9.0 - - + +
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Residues in contact with THR 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H ALA* 3.3 32.7 - - + +
155H TYR* 4.4 8.9 + - - +
156H PHE* 5.6 7.4 - - + -
63I GLU* 4.0 19.7 - - - +
64I LYS* 5.6 6.5 - - - +
66I TYR* 5.0 9.2 + - + +
76I VAL* 5.6 6.3 - - + -
78I GLY 3.6 5.1 + - - +
79I ILE* 1.3 72.7 - - - +
81I SER* 1.3 71.0 + - - +
83I ALA* 3.0 11.6 + - - +
84I ASN* 2.9 28.2 + - - +
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Residues in contact with SER 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H ALA* 4.1 9.1 - - - +
116H SER* 5.9 1.5 - - - -
119H GLN* 3.5 31.6 - - - -
152H SER 4.3 0.2 - - - -
153H GLY* 2.4 34.6 + - - -
154H ALA* 3.6 2.2 + - - -
155H TYR* 4.3 3.5 - - - -
79I ILE* 3.6 2.0 - - - +
80I THR* 1.3 80.8 + - - +
82I ASP* 1.3 58.2 + - - +
84I ASN* 2.7 33.5 + - - +
85I VAL* 3.0 17.0 + - - +
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Residues in contact with ASP 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H PHE* 5.8 0.3 - - - -
119H GLN* 3.7 14.2 - - - +
123H GLN* 5.1 0.2 - - - +
79I ILE* 3.3 29.0 + - + +
81I SER* 1.3 78.1 - - - +
83I ALA* 1.3 63.1 + - - +
85I VAL* 3.6 10.4 + - - +
86I LEU* 3.7 14.1 + - - +
128I ARG* 3.8 28.2 + - - +
130I PHE* 3.3 28.2 - - - -
131I GLY* 3.4 20.1 + - - -
132I VAL* 3.3 19.4 - - + +
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Residues in contact with ALA 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I TYR* 5.6 2.7 - - + -
76I VAL* 3.5 33.4 - - + -
79I ILE 3.2 4.2 + - - +
80I THR 3.0 10.3 + - - +
82I ASP* 1.3 78.4 - - - +
84I ASN* 1.3 55.7 - - - +
86I LEU* 2.4 39.8 + - - +
87I THR* 2.8 21.3 + - + -
132I VAL* 4.0 7.5 - - + +
134I LEU* 5.0 4.5 - - + -
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Residues in contact with ASN 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H GLN* 4.2 10.5 + - - +
116H SER* 5.6 9.1 - - - -
155H TYR* 3.3 30.1 + - + -
66I TYR* 3.1 37.2 + - - -
80I THR* 2.9 25.9 + - - +
81I SER* 2.7 19.4 + - - +
83I ALA* 1.3 70.0 - - - +
85I VAL* 1.3 60.8 + - - +
87I THR* 3.1 18.2 + - - +
88I ASN* 3.6 18.6 + - - +
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Residues in contact with VAL 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H SER* 4.8 20.2 - - - +
119H GLN* 4.4 18.2 - - + -
120H GLU* 5.4 4.9 - - + +
123H GLN* 5.6 4.5 - - - +
81I SER 3.0 12.0 + - - +
82I ASP* 3.8 8.1 - - - +
83I ALA 3.1 0.2 - - - -
84I ASN* 1.3 78.3 - - - +
86I LEU* 1.3 66.5 + - + +
88I ASN* 3.5 2.7 + - - +
89I GLU* 3.0 26.7 + - + +
130I PHE* 5.1 14.6 - - + -
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Residues in contact with LEU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ASP 3.7 15.9 - - - +
83I ALA* 2.4 27.7 + - - +
85I VAL* 1.3 72.8 - - + +
87I THR* 1.3 54.3 + - + -
89I GLU* 3.4 6.8 - - + +
90I LEU* 2.9 33.8 + - - +
114I LEU* 4.1 29.5 - - + +
117I ILE* 5.4 4.7 - - + -
118I LYS* 4.4 13.2 - - + -
130I PHE* 3.9 51.4 - - + -
132I VAL* 4.9 7.0 - - + +
134I LEU* 4.5 19.3 - - + -
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Residues in contact with THR 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I TYR* 4.2 30.1 - - + -
68I LEU* 5.1 7.0 - - - +
74I CYS* 5.0 7.9 - - - -
76I VAL* 6.3 0.7 - - + -
83I ALA* 2.8 25.6 + - + +
84I ASN* 3.1 23.2 + - - -
86I LEU* 1.3 74.6 - - + +
88I ASN* 1.3 72.1 + - - +
90I LEU* 3.9 2.9 - - - +
91I ARG* 2.8 46.4 + - - +
134I LEU* 5.8 4.9 - - + -
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Residues in contact with ASN 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H GLN* 5.8 6.1 - - - +
116H SER* 5.8 5.5 - - - -
84I ASN* 3.6 17.4 + - - +
85I VAL* 3.5 3.7 + - - +
86I LEU 3.5 0.4 - - - -
87I THR* 1.3 84.2 + - - +
89I GLU* 1.3 63.7 + - - +
91I ARG* 3.5 29.4 + - - +
92I LEU* 2.9 23.9 + - - +
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Residues in contact with GLU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I VAL* 3.0 24.4 + - + +
86I LEU* 3.4 11.0 - - + +
87I THR 3.2 0.2 - - - -
88I ASN* 1.3 74.9 - - - +
90I LEU* 1.3 65.4 + - - +
92I LEU* 2.9 16.7 + - - +
93I ILE* 3.0 33.2 + - + +
114I LEU* 4.9 5.6 - - + -
117I ILE* 4.0 30.6 - - + +
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Residues in contact with LEU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I LEU* 3.6 44.6 - - + -
86I LEU 2.9 17.8 + - - +
87I THR* 4.4 2.5 - - - +
89I GLU* 1.3 74.7 - - - +
91I ARG* 1.3 56.1 + - - +
93I ILE* 3.2 10.3 + - + +
94I ALA* 2.9 26.7 + - + +
110I LEU* 3.9 33.7 - - + +
114I LEU* 3.6 42.1 - - + +
117I ILE* 6.2 0.7 - - - -
136I TYR* 4.1 15.0 - - + +
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Residues in contact with ARG 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I TYR* 4.8 12.3 - - - +
67I LYS 3.6 25.9 + - - +
68I LEU* 4.0 24.0 - - + +
87I THR* 2.8 37.3 + - - +
88I ASN* 3.5 27.4 + - - +
89I GLU 3.1 0.2 - - - -
90I LEU* 1.3 79.6 - - - +
92I LEU* 1.3 57.3 + - - +
94I ALA* 3.5 3.4 + - - +
95I GLN* 2.9 32.9 + - + +
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Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I ASN 2.9 11.1 + - - +
89I GLU* 2.9 12.7 + - - +
91I ARG* 1.3 74.0 - - - +
93I ILE* 1.3 62.6 + - + +
95I GLN* 3.7 6.8 - - + +
96I ARG* 2.9 62.6 + - + +
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Residues in contact with ILE 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I GLU* 3.0 44.9 + - + +
90I LEU* 3.2 13.0 + - + +
92I LEU* 1.3 88.1 - - + +
94I ALA* 1.3 63.1 + - - +
96I ARG* 3.0 38.6 - - + +
97I TYR* 3.0 9.8 + - + +
105I ILE* 5.9 2.7 - - + -
110I LEU* 4.3 16.2 - - + -
113I ALA* 4.6 19.7 - - + -
117I ILE* 4.6 12.1 - - + -
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Residues in contact with ALA 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I LEU* 4.7 6.3 - - + +
69I ASN* 4.0 15.4 + - + +
72I MET* 5.2 0.7 - - + -
90I LEU* 2.9 19.7 + - + +
91I ARG* 3.7 6.5 - - - +
93I ILE* 1.3 78.2 - - - +
95I GLN* 1.3 57.0 + - - +
97I TYR* 3.1 6.9 + - - +
98I LEU* 3.0 26.9 + - - +
105I ILE* 3.7 28.9 - - + +
110I LEU* 4.0 10.8 - - + -
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Residues in contact with GLN 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I GLU* 5.5 2.9 - - - +
91I ARG* 2.9 23.1 + - + +
92I LEU* 3.3 8.5 + - + +
94I ALA* 1.3 77.4 - - - +
96I ARG* 1.3 57.9 + - - +
98I LEU* 3.5 29.4 + - - +
99I LEU* 2.9 26.9 + - + +
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Residues in contact with ARG 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I LEU* 2.9 41.6 + - + +
93I ILE* 3.0 38.2 - - - +
95I GLN* 1.3 74.1 - - - +
97I TYR* 1.3 60.2 + - - +
99I LEU* 3.7 16.3 - - + +
100I GLN* 2.9 32.6 + - - +
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Residues in contact with TYR 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ILE* 3.0 13.4 + - + +
94I ALA 3.3 9.2 - - - +
96I ARG* 1.3 77.4 - - - +
98I LEU* 1.3 58.9 + - - +
100I GLN* 3.2 0.4 + - - -
101I TYR* 2.9 65.9 + + - +
102I GLN 3.8 0.2 + - - -
103I GLU* 3.2 49.3 + - + -
105I ILE* 3.3 37.9 - - + -
106I PRO* 3.9 3.2 - - + +
109I GLN* 3.1 31.1 + - - -
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ASN* 6.0 6.1 - - - +
70I GLU* 5.4 8.3 - - - +
94I ALA 3.0 13.9 + - - +
95I GLN* 3.8 31.2 - - - +
97I TYR* 1.3 76.9 - - - +
99I LEU* 1.3 58.3 + - - +
102I GLN* 2.9 45.9 - - - +
103I GLU* 3.5 35.6 + - - +
104I PRO* 4.1 8.7 - - + -
105I ILE 5.7 0.7 - - - +
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Residues in contact with LEU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I GLN* 2.9 19.5 + - + +
96I ARG* 3.7 16.6 - - + +
97I TYR 3.1 0.4 - - - -
98I LEU* 1.3 77.4 - - - +
100I GLN* 1.3 66.7 + - - +
102I GLN* 4.2 14.2 + - - +
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Residues in contact with GLN 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ARG* 2.9 19.8 + - - +
99I LEU* 1.3 80.8 - - + +
101I TYR* 1.3 96.2 + - + +
102I GLN* 5.3 0.9 - - - +
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Residues in contact with TYR 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I TYR* 2.9 50.5 + + + +
100I GLN* 1.3 110.6 + - + +
102I GLN* 1.3 70.8 + - - +
103I GLU* 4.0 15.9 - - + +
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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
------------------------------------------------------------
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