Contacts of the helix formed by residues 83 - 102 (chain E) in PDB entry 2Y1M
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 TYR 83 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU* 2.4 35.9 + - + +
395A PRO* 4.0 22.7 - - + -
424A LYS* 3.5 40.6 - - + +
78E LYS 4.7 4.3 - - - -
79E ASN* 2.5 32.8 + - + -
81E PRO* 3.2 32.9 - - + +
82E PRO* 1.3 73.2 - - - +
84E ILE* 1.3 60.4 + - - +
85E LEU* 3.1 4.3 - - + +
86E ASP* 2.9 30.0 + - + +
87E LEU* 2.9 22.0 + - + +
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E VAL* 4.4 11.9 - - + -
67E VAL* 4.8 2.3 - - - +
70E CYS* 3.9 28.7 - - + -
77E LEU* 4.2 16.7 - - + +
82E PRO 3.9 3.0 + - - -
83E TYR* 1.3 68.5 - - - +
85E LEU* 1.3 61.2 + - + +
86E ASP 2.9 11.2 + - - -
87E LEU* 4.3 7.4 - - - +
88E LEU* 3.4 36.0 + - + +
89E PRO* 4.2 0.3 - - - +
129E THR* 4.8 1.6 - - + -
151E LEU* 4.7 13.9 - - + -
154E LEU* 5.0 0.4 - - + -
155E SER* 3.1 30.7 + - - +
158E PHE* 3.6 38.4 - - + -
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 6.2 0.9 - - - +
67E VAL* 3.9 24.4 - - + +
70E CYS* 3.8 23.6 - - + +
71E GLN* 3.8 38.8 - - + +
77E LEU* 4.1 14.4 - - + -
83E TYR* 3.1 3.3 - - + -
84E ILE* 1.3 80.9 - - + +
86E ASP* 1.3 65.2 + - - +
89E PRO* 3.7 17.5 - - - +
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Residues in contact with ASP 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PRO* 5.7 1.9 - - - +
422A GLU* 4.7 5.5 - - - +
424A LYS* 2.3 40.5 + - - +
83E TYR* 2.9 14.5 + - + +
84E ILE 2.9 0.4 - - - -
85E LEU* 1.3 88.0 - - - +
87E LEU* 1.3 69.7 + - + +
88E LEU 3.0 3.4 + - - -
89E PRO* 3.2 4.7 - - - +
90E ASP* 3.1 36.8 + - - +
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Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PRO* 3.7 20.6 - - + -
83E TYR* 2.9 21.5 + - + +
84E ILE* 3.5 8.3 + - - -
86E ASP* 1.3 78.4 - - + +
88E LEU* 1.3 54.3 + - + +
90E ASP* 3.8 5.5 - - - +
91E THR* 2.5 39.6 + - - +
155E SER 3.6 24.0 - - - +
158E PHE* 4.4 15.9 - - + +
159E SER* 3.7 26.7 - - - +
162E LEU* 4.3 17.2 - - + +
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E MET* 3.9 31.8 - - + +
66E VAL* 3.5 39.3 - - + -
67E VAL* 3.7 20.4 - - + -
84E ILE* 3.4 19.8 + - + +
86E ASP 3.0 0.4 + - - -
87E LEU* 1.3 76.7 - - - +
89E PRO* 1.3 76.5 - - + +
91E THR* 3.4 7.9 + - - +
92E TYR* 3.2 19.1 + - - +
122E LEU* 5.9 1.8 - - + -
126E THR* 5.0 1.3 - - + -
158E PHE* 3.9 37.5 - - + -
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Residues in contact with PRO 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E VAL* 4.2 15.5 - - + -
84E ILE 4.2 0.2 - - - +
85E LEU 3.7 19.7 - - - +
86E ASP* 3.2 13.0 - - - +
88E LEU* 1.3 93.4 - - + +
90E ASP* 1.3 63.0 + - - +
92E TYR* 2.9 13.3 + - + +
93E GLN* 2.8 34.6 + - + +
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Residues in contact with ASP 90 (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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86E ASP* 3.1 28.0 + - - +
87E LEU* 3.9 4.5 - - - +
89E PRO* 1.3 81.3 - - - +
91E THR* 1.3 56.3 + - - +
93E GLN* 3.7 11.7 - - - +
94E HIS* 3.1 27.9 + - - +
162E LEU* 3.8 21.6 - - + +
166E LYS* 4.6 11.1 + - - +
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Residues in contact with THR 91 (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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63E MET* 5.1 6.5 - - + -
87E LEU* 2.5 25.5 + - - +
88E LEU* 3.8 11.2 - - + +
89E PRO 3.2 0.4 - - - -
90E ASP* 1.3 74.1 - - - +
92E TYR* 1.3 62.2 + - - +
94E HIS* 3.6 2.6 + - - +
95E LEU* 3.0 45.6 + - + +
118E PHE* 4.3 19.5 - - + -
122E LEU* 4.6 13.9 - - + -
158E PHE* 4.9 4.0 + - - +
161E MET* 5.9 1.8 - - + -
162E LEU* 3.6 28.5 - - + +
165E LEU* 4.8 1.8 - - + -
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Residues in contact with TYR 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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60E TRP* 3.1 67.6 - + + +
63E MET* 5.1 6.2 - - - -
88E LEU 3.2 9.7 + - - +
89E PRO* 2.9 14.6 + - + +
91E THR* 1.3 77.0 - - - +
93E GLN* 1.3 79.4 + - - +
95E LEU* 2.4 35.4 + - - +
96E ARG* 3.1 43.1 + - + -
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Residues in contact with GLN 93 (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 PRO* 2.8 25.6 + - + +
90E ASP* 3.7 13.9 - - - +
92E TYR* 1.3 93.4 - - - +
94E HIS* 1.3 58.8 + - + +
95E LEU 2.9 5.5 + - - -
96E ARG* 3.1 29.6 + - - +
97E THR* 3.3 16.4 + - - -
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Residues in contact with HIS 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ASP 3.1 14.9 + - - +
91E THR 3.8 4.7 - - - +
92E TYR 2.9 1.2 + - - -
93E GLN* 1.3 78.2 - - - +
95E LEU* 1.3 58.0 + - - +
97E THR* 4.2 12.9 + - + +
98E ILE* 2.8 22.0 + - + +
162E LEU* 4.5 4.3 - - + -
165E LEU* 3.7 21.3 - - + -
166E LYS* 3.7 41.8 - - + +
169E PHE* 2.7 32.2 + - - +
170E PRO* 4.9 0.2 - - + -
171E SER* 4.1 9.0 - - - -
172E GLY 4.0 12.2 + - - -
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Residues in contact with LEU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E VAL* 5.1 3.1 - - + -
60E TRP* 4.5 20.2 - - + +
63E MET* 4.6 4.5 - - + -
91E THR* 3.0 34.3 - - + +
92E TYR* 2.4 28.4 + - - +
94E HIS* 1.3 68.8 - - - +
96E ARG* 1.3 62.3 + - - +
98E ILE* 3.9 7.7 - - + +
99E LEU* 3.0 30.2 + - - +
115E PHE* 3.9 29.3 - - + -
118E PHE* 4.4 3.8 - - + -
119E MET* 3.9 22.9 - - + -
122E LEU* 4.6 9.9 - - + -
165E LEU* 3.7 21.5 - - + -
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Residues in contact with ARG 96 (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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60E TRP* 4.6 10.7 - - + -
92E TYR* 3.1 46.6 + - + +
93E GLN* 3.3 26.5 + - - +
95E LEU* 1.3 74.8 - - - +
97E THR* 1.3 57.8 + - - +
99E LEU* 2.4 36.3 + - - +
100E SER* 2.9 14.2 + - - +
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Residues in contact with THR 97 (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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93E GLN 3.3 13.8 + - - -
94E HIS* 4.2 15.7 + - + +
96E ARG* 1.3 78.1 - - - +
98E ILE* 1.3 65.4 + - - +
100E SER* 3.0 20.4 + - - -
101E ARG* 3.1 21.4 + - + +
171E SER* 3.6 29.2 - - - +
172E GLY* 3.6 7.9 - - - +
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Residues in contact with ILE 98 (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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94E HIS* 2.8 30.5 - - + +
95E LEU* 4.1 13.5 - - + +
96E ARG 2.9 2.0 + - - -
97E THR* 1.3 74.1 - - - +
99E LEU* 1.3 61.5 + - + +
101E ARG 3.6 0.2 + - - -
102E TYR* 3.3 23.9 + - - +
109E LEU* 3.8 17.8 - - + +
115E PHE* 4.3 9.6 - - + -
165E LEU* 4.0 17.0 - - + -
169E PHE* 3.3 52.0 - - + -
172E GLY* 3.8 21.8 - - - +
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Residues in contact with LEU 99 (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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53E LYS* 4.4 20.4 - - + +
56E VAL* 3.9 29.2 - - + -
60E TRP* 4.0 14.8 - - + -
95E LEU 3.0 19.7 + - - +
96E ARG* 2.4 22.9 + - - +
98E ILE* 1.3 72.0 - - + +
100E SER* 1.3 65.5 + - - +
102E TYR 3.4 1.6 + - - -
103E GLU* 3.1 21.7 + - - +
106E MET* 4.1 19.1 - - + +
109E LEU* 3.6 28.5 - - + -
115E PHE* 5.1 8.1 - - + -
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Residues in contact with SER 100 (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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96E ARG* 2.9 12.5 + - - +
97E THR* 3.0 13.0 + - - -
99E LEU* 1.3 72.8 - - - +
101E ARG* 1.3 62.7 + - - +
102E TYR 2.8 5.5 + - - -
103E GLU* 2.7 45.1 - - - +
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Residues in contact with ARG 101 (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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360A HIS* 3.1 35.2 + - - -
362A LYS* 3.9 23.4 - - - +
97E THR* 3.1 18.8 + - + +
98E ILE 3.7 0.2 - - - +
100E SER* 1.3 81.3 - - - +
102E TYR* 1.3 74.4 + - + +
105E LYS* 3.5 20.4 + - - -
171E SER* 3.2 28.8 + - - +
172E GLY 3.7 9.9 - - - +
173E LEU* 4.0 23.8 - - + +
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE 3.3 17.3 - - - +
99E LEU 3.4 4.2 + - - -
100E SER 2.8 2.0 + - - -
101E ARG* 1.3 78.9 - - + +
103E GLU* 1.3 56.0 + - - +
104E GLY 3.2 3.4 - - - -
105E LYS* 2.7 54.0 + - + +
106E MET* 2.8 20.5 + - - +
108E THR* 4.3 7.0 - - - -
109E LEU* 4.0 49.1 - - + -
169E PHE* 4.5 2.0 - + - -
172E GLY 3.3 21.5 - - - -
173E LEU* 3.9 16.7 - - + +
174E PHE* 2.9 37.8 + - + +
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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