Contacts of the helix formed by residues 78 - 92 (chain I) in PDB entry 5A15
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 78 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.9 0.9 - - - +
32I GLY* 5.3 0.2 - - - -
77I ARG* 1.3 75.1 - - - +
79I GLY* 1.3 63.4 + - - +
80I PHE* 3.1 11.0 + - - +
81I LEU* 3.0 31.8 + - + +
82I PHE* 3.4 20.4 + - - +
105I ARG* 4.2 6.2 + - - +
109I GLU* 4.3 17.2 + - - +
36J TYR* 5.7 1.2 - - - -
83J ARG* 2.7 54.6 + - - +
87J ASP* 4.4 10.7 + - - +
90J ARG* 3.6 10.2 + - - +
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Residues in contact with GLY 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I VAL* 3.0 29.0 + - - -
32I GLY* 4.4 5.3 + - - -
34I GLN* 3.5 15.9 - - - -
36I TYR* 2.6 34.7 + - - -
77I ARG 3.2 4.4 + - - -
78I ASP* 1.3 72.1 + - - +
80I PHE* 1.3 60.3 + - - +
82I PHE 3.5 3.8 + - - -
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Residues in contact with PHE 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I GLN* 3.6 33.7 - - - -
36I TYR* 4.2 2.2 - - - -
78I ASP* 3.1 14.6 + - - +
79I GLY* 1.3 79.1 - - - +
81I LEU* 1.3 60.4 + - + +
82I PHE 3.5 0.2 + - - -
83I ARG* 3.5 20.3 - - - +
84I TYR* 3.8 10.8 - - - -
34J GLN* 5.3 12.3 - - + -
36J TYR* 5.5 11.0 - + - -
83J ARG* 3.9 28.0 - - - +
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Residues in contact with LEU 81 (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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78I ASP* 3.0 21.5 + - + +
79I GLY 3.4 0.2 - - - -
80I PHE* 1.3 72.8 - - - +
82I PHE* 1.3 64.9 + - - +
83I ARG 3.1 3.2 + - - -
84I TYR* 3.3 13.9 + - + -
85I ILE* 3.5 13.5 + - - +
100I PHE* 3.7 30.3 - - + -
102I GLU* 3.5 19.1 - - + +
105I ARG* 3.7 43.7 - - + +
106I LEU* 3.8 19.9 - - + +
109I GLU* 3.8 30.3 - - + +
83J ARG* 4.0 1.6 - - - +
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Residues in contact with PHE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I LEU* 3.9 26.7 - - + -
31I VAL* 3.7 41.5 - - + -
36I TYR* 3.7 16.4 - + + -
43I LEU* 5.4 0.2 - - + -
51I LEU* 4.2 20.4 - - + -
75I ILE* 5.3 2.5 - - + -
78I ASP 3.4 5.3 + - - +
79I GLY 3.7 11.2 - - - +
80I PHE 3.3 0.8 - - - -
81I LEU* 1.3 76.7 - - - +
83I ARG* 1.3 59.4 + - - +
85I ILE* 3.5 13.6 - - + +
86I LEU* 2.8 53.8 + - + +
113I PHE* 3.7 40.6 - + + -
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Residues in contact with ARG 83 (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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78H ASP* 2.7 39.3 + - - +
80H PHE* 3.7 32.3 - - + +
81H LEU* 4.0 2.8 - - - +
102H GLU* 2.7 41.8 + - - -
105H ARG* 2.9 11.3 - - - +
36I TYR* 3.4 33.8 + - + +
80I PHE 3.5 11.4 - - - +
81I LEU 3.1 0.2 - - - -
82I PHE* 1.3 77.7 - - - +
84I TYR* 1.3 79.3 + - + +
86I LEU* 3.6 4.0 + - - +
87I ASP* 3.3 34.3 + - - +
90I ARG* 5.3 0.5 + - - -
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Residues in contact with TYR 84 (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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102H GLU* 4.2 0.5 + - - -
105H ARG* 3.9 29.8 - - - -
80I PHE 3.8 17.0 - - - -
81I LEU* 3.3 16.7 + - + +
82I PHE 3.2 0.6 - - - -
83I ARG* 1.3 97.5 + - + +
85I ILE* 1.3 65.6 + - - +
86I LEU 3.3 0.4 - - - -
87I ASP* 4.5 2.2 - - - +
88I TYR* 3.2 15.2 + - - +
94I VAL* 3.4 34.4 - - + +
95I VAL 4.8 0.2 - - - -
96I LEU* 5.0 2.0 - - + -
97I PRO* 3.4 40.5 - - + +
100I PHE* 3.8 28.4 - + - -
106I LEU* 4.0 17.0 - - + -
118I LEU* 5.0 1.0 - - - +
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Residues in contact with ILE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 4.9 1.1 - - + -
81I LEU 3.5 13.6 + - - +
82I PHE* 3.1 26.4 + - + +
84I TYR* 1.3 79.3 - - - +
86I LEU* 1.3 61.9 + - - +
88I TYR* 3.1 15.6 + - - +
89I LEU* 3.1 20.4 + - + +
106I LEU* 3.8 16.4 - - + -
109I GLU* 4.1 11.9 - - + -
110I ALA* 4.0 22.4 - - - +
113I PHE* 4.0 20.4 - - + -
115I LEU* 4.0 16.4 - - + -
118I LEU* 3.8 23.6 - - + -
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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
----------------------------------------------------------
36I TYR* 4.0 31.6 - - + -
37I PHE 4.2 8.5 - - - +
38I THR* 3.8 30.1 - - + +
42I THR* 4.3 3.8 - - + -
43I LEU* 5.1 1.3 - - + -
82I PHE* 2.8 31.2 + - + +
83I ARG* 3.8 5.8 - - - +
85I ILE* 1.3 78.7 - - - +
87I ASP* 1.3 61.0 + - - +
89I LEU* 3.3 20.7 + - + +
90I ARG* 3.2 52.9 + - - +
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Residues in contact with ASP 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ARG* 5.3 2.7 - - - -
78H ASP* 4.3 13.5 + - - +
105H ARG* 2.2 37.3 + - - +
109H GLU* 4.5 7.6 - - - +
83I ARG* 3.3 16.5 + - - +
84I TYR* 4.0 6.5 - - - +
85I ILE 3.3 0.6 - - - -
86I LEU* 1.3 75.0 - - - +
88I TYR* 1.3 64.8 + - - +
90I ARG* 3.0 33.3 + - - +
91I ASP* 3.0 24.9 + - - +
93I GLN 3.5 8.8 - - - +
94I VAL* 4.7 7.6 - - + -
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Residues in contact with TYR 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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46I ILE* 3.7 26.6 - - + +
84I TYR 3.2 7.4 + - - +
85I ILE 3.1 10.2 + - - +
87I ASP* 1.3 77.8 - - - +
89I LEU* 1.3 57.5 + - - +
92I ARG* 2.6 60.2 + - - +
93I GLN* 3.5 19.5 - - - -
94I VAL* 3.4 21.7 - - + +
115I LEU* 4.1 23.8 - - + -
117I ASP* 3.3 29.8 + - - +
118I LEU* 3.7 39.6 + - + -
121I LEU* 4.5 8.1 - - + -
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Residues in contact with LEU 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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92D ARG* 4.7 2.4 + - - -
42I THR* 3.5 35.4 - - + +
43I LEU* 4.8 7.9 - - + +
45I SER* 3.6 17.8 + - - +
46I ILE* 3.9 26.9 - - + -
49I SER* 5.6 2.2 - - - +
51I LEU* 3.6 30.7 - - + -
82I PHE* 5.3 0.4 - - + -
85I ILE* 3.1 17.2 + - + +
86I LEU* 3.5 22.7 - - + +
87I ASP 3.3 0.4 - - - -
88I TYR* 1.3 79.5 - - + +
90I ARG* 1.3 62.3 + - - +
92I ARG* 4.3 7.8 + - - -
115I LEU* 4.1 18.6 - - + -
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Residues in contact with ARG 90 (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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92D ARG* 3.0 27.2 + - - -
32H GLY* 4.3 2.6 - - - -
76H ASP* 2.7 46.1 + - - +
77H ARG* 3.4 28.0 + - - +
78H ASP* 3.4 18.8 - - - +
37I PHE 3.4 11.9 + - - -
38I THR* 4.5 0.2 + - - -
42I THR* 4.1 15.0 - - + +
83I ARG 5.3 0.4 + - - -
86I LEU* 3.2 46.2 + - - +
87I ASP* 3.0 33.3 + - - +
88I TYR 3.1 0.8 - - - -
89I LEU* 1.3 77.8 - - - +
91I ASP* 1.3 68.2 + - - +
92I ARG 3.7 0.2 - - - -
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Residues in contact with ASP 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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92D ARG* 4.2 18.5 + - - +
77H ARG* 2.8 44.2 + - - -
108H ARG* 3.2 30.6 + - - +
112H TYR* 4.6 1.9 - - - -
87I ASP* 3.0 14.3 + - - +
90I ARG* 1.3 77.6 - - - +
92I ARG* 1.3 73.1 + - - +
93I GLN* 3.2 33.6 + - + +
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Residues in contact with ARG 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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45D SER* 5.5 4.0 - - - -
89D LEU 4.5 7.3 + - - -
90D ARG 2.8 30.7 + - - -
91D ASP* 3.8 13.8 + - - +
92D ARG* 3.2 39.2 - - + +
45I SER* 3.1 39.2 + - - -
46I ILE* 3.6 29.6 - - - +
47I PRO* 5.6 0.4 - - - +
88I TYR* 2.6 53.7 + - + +
89I LEU 4.3 4.6 + - - -
91I ASP* 1.3 73.5 - - - +
93I GLN* 1.3 58.5 + - - +
121I LEU* 5.2 3.3 - - - +
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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