Contacts of the strand formed by residues 97 - 109 (chain E) in PDB entry 3DOY
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 LYS 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E ILE 6.1 0.2 - - - +
22E PRO* 3.2 15.4 - - + +
83E PHE* 4.0 16.2 - - + -
87E TRP* 3.6 33.1 - - + -
93E ILE* 3.4 32.8 - - - +
94E ALA* 2.9 11.4 + - - +
96E THR* 1.3 79.5 - - - +
98E ILE* 1.3 65.1 + - - +
99E VAL* 6.2 0.9 - - + -
131E MET* 5.8 1.2 - - - -
155E ILE* 4.3 11.2 - - + -
156E ALA 3.2 16.4 - - - +
157E GLU* 2.6 34.8 + - - +
158E ARG* 3.1 14.6 + - - -
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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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22E PRO* 3.9 6.3 - - + -
97E LYS* 1.3 79.6 - - - +
99E VAL* 1.3 68.9 + - - +
100E TYR* 3.2 43.3 - - + +
155E ILE* 3.8 1.0 - - - -
156E ALA 2.7 39.6 + - - +
157E GLU 5.2 1.1 - - - +
158E ARG* 3.7 39.5 - - + +
59F PHE* 4.0 30.1 - - + -
62F LYS* 3.7 23.6 - - + -
64F ILE* 5.5 0.7 - - + -
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Residues in contact with VAL 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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21E LEU* 5.2 6.5 - - + -
22E PRO* 4.3 19.3 - - + +
23E HIS* 4.4 16.4 + - + -
75E ALA* 5.9 2.2 - - + +
79E GLY* 5.2 12.6 - - - -
97E LYS* 5.7 0.9 - - + -
98E ILE* 1.3 80.8 - - - +
100E TYR* 1.3 66.0 + - - +
101E PHE 4.2 0.7 + - - -
153E ALA* 4.0 22.7 - - + -
154E MET 3.4 12.1 - - - +
155E ILE* 4.4 17.7 - - + -
58F HIS* 5.1 2.4 + - - -
59F PHE* 3.5 24.9 - - - -
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Residues in contact with TYR 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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98E ILE* 3.2 36.8 - - + +
99E VAL* 1.3 80.4 - - - +
101E PHE* 1.3 66.5 + - - +
102E MET* 5.5 1.3 - - + -
153E ALA* 3.3 3.1 - - - +
154E MET* 2.7 54.0 + - + +
156E ALA* 4.0 23.8 - - + -
59F PHE* 6.0 1.6 - + - -
62F LYS* 3.5 17.7 + - - -
64F ILE* 4.7 21.0 - - + +
112F PRO* 4.5 25.8 - - + +
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Residues in contact with PHE 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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71E VAL* 3.9 20.2 - - + -
72E GLU* 3.6 24.2 - - - -
75E ALA* 3.5 31.4 - - + -
99E VAL 4.2 0.2 + - - -
100E TYR* 1.3 76.9 - - - +
102E MET* 1.3 62.8 + - - +
103E THR 3.8 8.3 - - - -
104E ILE* 3.3 29.6 - - + -
151E LEU* 3.7 22.4 - - + -
152E LYS 4.2 3.8 - - - -
153E ALA* 4.4 3.8 - - + +
68F VAL* 3.7 14.8 - - + -
109F PHE* 3.7 31.4 - + + +
1006F CL 3.7 25.8 - - + +
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Residues in contact with MET 102 (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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100E TYR* 4.3 2.0 - - + +
101E PHE* 1.3 77.6 - - - +
103E THR* 1.3 68.9 + - + +
132E ILE* 3.8 31.4 - - + -
152E LYS* 2.8 41.8 + - - +
153E ALA 4.2 1.3 - - - -
154E MET* 3.6 55.6 - - + +
108F LYS* 4.2 0.3 - - - +
109F PHE* 3.0 31.4 + - - +
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Residues in contact with THR 103 (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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101E PHE* 3.8 2.2 - - - -
102E MET* 1.3 87.5 - - + +
104E ILE* 1.3 70.5 + - - +
105E ASP* 4.0 14.2 + - - +
134E GLN* 4.9 2.8 + - - -
151E LEU* 3.5 3.7 - - - +
152E LYS* 3.1 58.8 + - - +
107F VAL* 3.2 18.2 - - - +
108F LYS* 4.1 17.0 - - + -
109F PHE* 4.4 0.6 - - - -
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Residues in contact with ILE 104 (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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71E VAL* 4.3 17.9 - - + -
101E PHE* 3.3 31.6 - - + -
103E THR* 1.3 81.0 - - - +
105E ASP* 1.3 68.2 + - - +
107E VAL* 3.4 26.5 - - + -
149E ALA* 5.6 0.4 - - + -
150E GLU 3.5 9.4 - - - +
151E LEU* 4.6 0.9 - - + -
68F VAL* 4.3 9.9 - - + -
71F VAL* 4.9 6.1 - - + -
104F ILE* 4.6 6.7 - - + -
107F VAL* 2.9 59.0 + - + +
109F PHE* 3.9 14.6 - - + -
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Residues in contact with ASP 105 (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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103E THR* 4.0 17.8 + - - -
104E ILE* 1.3 78.4 - - - +
106E LYS* 1.3 83.1 + - + +
107E VAL* 3.0 7.5 + - - +
134E GLN* 5.3 4.2 + - - -
150E GLU* 2.8 46.9 + - + +
151E LEU* 5.9 0.3 - - - -
104F ILE 4.1 0.2 - - - -
105F ASP* 3.5 8.8 - - - +
106F LYS* 3.1 32.8 + - - +
107F VAL 4.7 0.6 - - - +
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Residues in contact with LYS 106 (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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105E ASP* 1.3 78.9 - - + +
107E VAL* 1.3 62.4 + - - +
108E LYS* 3.9 0.9 + - - +
148E GLU* 3.8 14.4 - - - +
149E ALA* 4.0 5.7 - - - -
150E GLU* 2.9 41.6 + - + +
104F ILE 3.7 1.5 + - - -
105F ASP* 2.6 28.5 + - - +
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Residues in contact with VAL 107 (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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71E VAL* 4.6 7.0 - - + -
104E ILE* 3.4 28.7 - - + -
105E ASP 3.3 14.1 - - - +
106E LYS* 1.3 75.3 - - - +
108E LYS* 1.3 60.1 + - - +
109E PHE* 3.8 14.8 - - + -
148E GLU 3.0 12.6 - - - +
149E ALA* 3.8 14.4 - - + -
103F THR* 3.3 9.4 - - - +
104F ILE* 3.0 60.8 + - + +
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Residues in contact with LYS 108 (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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106E LYS 3.9 1.1 + - - +
107E VAL* 1.3 75.9 - - - +
109E PHE* 1.3 69.3 + - - +
110E ARG* 3.3 53.0 + - + +
147E ALA* 3.2 4.9 - - - +
148E GLU* 2.9 47.8 + - - +
102F MET 3.4 9.6 - - - +
103F THR* 4.3 11.9 - - + -
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Residues in contact with PHE 109 (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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67E GLY* 3.1 45.3 - - - -
68E VAL 4.2 0.2 - - - -
70E ILE* 4.6 10.8 - - + -
71E VAL* 4.3 9.4 - - + -
107E VAL* 3.8 15.3 - - + -
108E LYS* 1.3 77.7 - - - +
110E ARG* 1.3 61.9 + - - +
111E ILE 3.8 3.1 - - - +
146E VAL 3.7 4.7 - - - +
147E ALA* 4.1 16.4 - - + -
148E GLU 6.0 0.4 - - - -
101F PHE* 3.4 45.4 - - + +
102F MET* 2.9 22.9 + - - +
104F ILE* 3.7 30.3 - - + -
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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
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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