Contacts of the strand formed by residues 97 - 109 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C PHE* 3.8 24.7 - - + -
87C TRP* 3.6 38.5 - - + -
93C ILE* 3.4 22.2 - - - +
94C ALA 3.2 6.3 + - - +
96C THR* 1.3 95.1 - - - +
98C ILE* 1.3 72.5 + - - +
99C VAL* 6.1 0.9 - - + -
131C MET* 6.3 1.0 - - - +
155C ILE* 4.9 5.6 - - + -
156C ALA 3.4 13.4 - - - +
157C GLU* 2.8 24.2 + - - +
158C ARG* 3.1 23.0 + - - -
3002C 2BE 4.3 7.0 - - + +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS* 1.3 82.4 - - - +
99C VAL* 1.3 62.4 + - - +
100C TYR* 3.1 51.4 - - + +
154C MET 3.7 0.5 - - - +
155C ILE* 3.6 3.5 - - - +
156C ALA* 3.0 37.8 + - + +
157C GLU 4.0 10.8 - - - +
158C ARG* 3.3 35.4 - - + +
3002C 2BE 3.5 35.0 - - + -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLY* 4.5 16.2 - - - +
82C ALA* 5.7 2.2 - - + -
83C PHE* 5.5 3.8 - - + -
97C LYS* 6.1 1.3 - - + -
98C ILE* 1.3 74.8 - - - +
100C TYR* 1.3 60.5 + - - +
101C PHE* 3.7 17.2 + - + -
153C ALA* 3.5 29.8 - - + -
154C MET 3.3 6.1 - - - +
155C ILE* 4.1 21.1 - - + -
3002C 2BE 2.9 68.1 + - + +
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ILE* 3.1 36.3 - - + +
99C VAL* 1.3 71.2 - - - +
101C PHE* 1.3 64.2 + - - +
102C MET* 3.6 5.2 + - + -
153C ALA* 3.0 4.5 - - - +
154C MET* 2.7 65.0 + - + +
156C ALA* 4.2 13.2 - - + -
157C GLU 5.3 0.5 + - - -
3002C 2BE 3.8 23.6 - + - -
112D PRO* 6.5 2.0 - - + -
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ALA* 3.0 48.0 - - + -
78C GLY* 4.9 2.9 - - - -
79C GLY* 4.3 6.7 - - - -
99C VAL* 3.7 14.3 + - + -
100C TYR* 1.3 74.1 - - - +
102C MET* 1.3 59.9 + - - +
103C THR 4.8 4.0 - - - +
104C ILE* 5.7 2.9 - - + -
135C VAL* 4.8 4.3 - - + -
151C LEU* 3.8 30.1 - - + -
152C LYS 3.6 13.7 - - - -
153C ALA* 3.6 16.4 - - + -
3002C 2BE 3.4 27.6 - - + -
109D PHE* 3.3 32.9 - - + +
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Residues in contact with MET 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C TYR* 4.3 11.2 - - + +
101C PHE* 1.3 73.9 - - - +
103C THR* 1.3 69.9 + - + +
132C ILE* 3.7 27.1 - - + -
152C LYS* 2.8 34.1 + - - +
153C ALA 4.3 2.9 - - - -
154C MET* 3.8 34.8 - - + -
108D LYS* 3.5 0.2 - - - -
109D PHE* 2.9 38.4 + - - +
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Residues in contact with THR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 4.8 2.1 - - - -
102C MET* 1.3 89.0 - - + +
104C ILE* 1.3 71.5 + - - +
105C ASP* 4.4 10.0 + - - -
151C LEU* 3.4 3.7 - - - +
152C LYS* 3.0 56.4 + - - +
107D VAL* 3.1 16.4 - - - +
108D LYS* 3.8 29.4 - - + +
109D PHE* 5.0 0.4 - - - -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C VAL* 4.0 21.3 - - + -
75C ALA* 6.2 1.3 - - + -
101C PHE* 5.7 4.7 - - + -
103C THR* 1.3 82.4 - - - +
105C ASP* 1.3 67.7 + - - +
107C VAL* 3.5 26.9 - - + -
150C GLU 3.4 4.9 - - - +
151C LEU* 3.4 22.7 - - + -
68D VAL* 4.5 11.7 - - + -
71D VAL* 5.8 1.8 - - + -
104D ILE* 5.3 2.7 - - + -
106D LYS 3.8 0.3 + - - -
107D VAL* 3.1 50.4 + - + +
109D PHE* 3.7 28.9 - - + -
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C THR* 4.4 10.2 + - - -
104C ILE* 1.3 86.0 + - - +
106C LYS* 1.3 79.3 + - + +
107C VAL* 3.1 8.3 + - - +
150C GLU* 2.9 42.1 + - + +
104D ILE 4.2 0.4 - - - -
105D ASP* 3.5 12.4 - - - +
106D LYS* 3.1 38.2 + - - +
107D VAL 4.5 0.2 + - - -
108D LYS* 5.1 5.0 + - - -
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASP* 1.3 81.7 - - + +
107C VAL* 1.3 62.4 + - - +
108C LYS* 3.6 19.5 + - - +
148C GLU* 3.4 20.9 - - - +
149C ALA* 3.8 3.6 - - - -
150C GLU* 3.8 33.8 + - + +
105D ASP* 3.5 30.3 + - - +
106D LYS* 6.0 3.1 - - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C VAL* 4.0 13.0 - - + -
104C ILE* 3.5 27.1 - - + -
105C ASP 3.6 2.9 - - - +
106C LYS* 1.3 73.8 - - - +
108C LYS* 1.3 65.4 + - - +
109C PHE* 3.4 38.1 - - + -
147C ALA* 5.8 0.4 - - + -
148C GLU 3.1 9.2 - - - +
149C ALA* 3.4 21.8 - - + -
103D THR* 3.0 10.6 - - - -
104D ILE* 2.9 48.5 + - + +
105D ASP* 4.5 0.9 - - - +
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS* 3.6 24.8 + - - +
107C VAL* 1.3 79.6 - - - +
109C PHE* 1.3 62.5 + - - +
110C ARG* 3.6 33.2 + - - +
147C ALA* 3.1 6.9 - - - +
148C GLU* 3.0 49.4 + - + +
102D MET 3.5 6.7 - - - +
103D THR* 4.0 15.0 - - + +
105D ASP* 5.2 3.2 + - - -
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C GLY* 3.2 43.7 - - - -
70C ILE* 4.4 9.2 - - + -
71C VAL* 4.1 9.0 - - + -
107C VAL* 3.4 27.6 - - + -
108C LYS* 1.3 74.2 - - - +
110C ARG* 1.3 62.9 + - - +
111C ILE 5.2 3.4 - - - +
146C VAL 3.7 4.5 - - - +
147C ALA* 3.8 19.7 - - + -
101D PHE* 3.6 44.1 - + + +
102D MET* 3.0 22.2 + - - +
104D ILE* 4.0 19.3 - - + -
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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