Contacts of the helix formed by residues 75 - 90 (chain Y) in PDB entry 3SDI
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 SER 75 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103Q LEU 4.6 4.0 + - - -
41Y LEU* 5.7 0.4 - - - -
66Y HIS* 5.2 0.8 + - - -
73Y ARG 3.8 1.0 + - - -
74Y ILE* 1.3 78.5 - - - +
76Y VAL* 1.3 60.4 + - - +
77Y ALA* 3.8 4.3 + - - +
78Y ALA* 3.1 24.8 + - - +
79Y ALA* 2.8 29.4 + - - +
105Y LYS* 3.8 30.6 - - - -
106Y GLU* 3.3 21.8 - - - -
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Residues in contact with VAL 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y LEU* 3.9 13.2 - - + -
74Y ILE 3.9 0.8 + - - -
75Y SER* 1.3 70.9 - - - +
77Y ALA* 1.3 63.5 + - - +
79Y ALA* 4.6 1.6 - - - -
80Y SER* 2.9 28.2 + - - -
101Y ILE* 3.7 32.5 - - + +
103Y GLY* 3.6 35.4 - - - +
104Y TYR 4.4 1.6 - - - +
105Y THR* 4.4 7.6 - - + +
106Y GLU* 2.9 15.0 + - - +
109Y THR* 3.8 18.2 - - - +
111Y TYR* 3.7 16.8 - - + -
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Residues in contact with ALA 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q LEU 5.1 1.3 - - - +
104Q GLU* 3.8 23.1 - - + +
75Y SER* 3.2 5.4 - - - +
76Y VAL* 1.3 76.5 - - - +
78Y ALA* 1.3 56.8 + - - +
80Y SER* 2.9 17.2 + - - -
81Y LYS* 3.2 8.8 + - - +
106Y GLU* 3.0 20.9 + - - +
111Y TYR* 3.6 28.4 - - - +
119Y ARG* 2.9 11.1 + - - +
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Residues in contact with ALA 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q THR 4.5 4.5 - - - +
103Q LEU* 3.7 40.8 - - + +
66Y HIS* 5.6 0.2 - - + -
74Y ILE* 3.8 13.7 - - + -
75Y SER* 3.1 18.1 + - - +
77Y ALA* 1.3 78.7 - - - +
79Y ALA* 1.3 65.7 + - - +
81Y LYS* 3.3 6.0 + - - +
82Y ILE* 3.1 26.7 + - - +
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Residues in contact with ALA 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y LEU* 3.7 28.3 - - + -
59Y LEU* 3.4 16.7 - - + +
63Y CYS* 3.8 17.9 - - - -
74Y ILE* 3.8 11.1 - - + +
75Y SER 2.8 21.1 + - - +
76Y VAL 4.0 2.5 - - - +
78Y ALA* 1.3 68.7 - - - +
80Y SER* 1.3 66.9 + - - +
82Y ILE* 3.0 13.5 + - - +
83Y LEU 3.4 8.0 + - - -
101Y ILE* 4.5 5.2 - - + -
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Residues in contact with SER 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Y VAL 2.9 15.3 + - - -
77Y ALA 2.9 10.6 + - - -
79Y ALA* 1.3 78.1 - - - +
81Y LYS* 1.3 55.6 + - - +
83Y LEU* 3.4 4.8 + - - +
84Y SER* 2.9 26.7 + - - -
101Y ILE* 3.8 23.4 - - - +
111Y TYR* 3.5 27.4 - - - -
113Y VAL* 3.9 6.8 - - - +
119Y ARG* 2.6 32.1 + - - -
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Residues in contact with LYS 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q ARG 5.2 0.2 + - - -
101Q LEU* 3.2 23.3 + - - +
102Q THR 3.9 15.9 - - - +
104Q GLU* 3.0 33.9 + - + +
53X VAL* 6.2 0.7 - - - -
54X GLN* 5.7 1.3 - - - -
57X GLU* 2.8 32.4 + - - -
77Y ALA 3.2 13.3 + - - +
78Y ALA* 3.8 4.5 - - - +
79Y ALA 3.1 1.0 - - - -
80Y SER* 1.3 77.7 + - - +
82Y ILE* 1.3 60.2 + - - +
83Y LEU 3.3 0.2 - - - -
84Y SER* 3.9 3.8 - - - -
85Y ASN* 2.9 48.6 + - - +
119Y ARG* 3.5 28.0 - - - +
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Residues in contact with ILE 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q THR 5.6 3.1 - - - +
103Q LEU* 5.9 4.5 - - + -
58Y TRP* 3.6 29.6 - - + -
59Y LEU* 3.9 9.6 - - + -
62Y GLN* 4.2 25.4 - - + +
63Y CYS* 5.4 0.2 - - - -
66Y HIS* 6.0 0.7 - - + +
74Y ILE* 3.7 30.3 - - + -
78Y ALA* 3.1 12.3 + - + +
79Y ALA* 3.0 9.2 + - - +
81Y LYS* 1.3 78.2 - - - +
83Y LEU* 1.3 62.7 + - - +
85Y ASN* 3.8 3.9 - - - +
86Y LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Y TRP* 4.1 28.0 - - + +
56Y GLU* 4.2 15.3 - - + -
58Y TRP* 4.8 5.8 - - + -
59Y LEU* 3.8 18.8 - - + +
79Y ALA 3.4 3.2 + - - -
80Y SER* 3.6 8.3 - - - +
82Y ILE* 1.3 78.2 - - - +
84Y SER* 1.3 63.8 + - - +
86Y LEU* 3.1 7.2 + - + +
87Y VAL* 3.0 31.9 + - + +
97Y MET* 4.1 20.4 - - + -
99Y THR* 3.5 29.2 - - + +
101Y ILE* 4.1 16.8 - - + -
113Y VAL* 4.4 10.1 - - + -
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Residues in contact with SER 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X GLN* 4.7 3.5 + - - -
80Y SER 2.9 17.7 + - - -
81Y LYS* 3.7 6.1 - - - +
83Y LEU* 1.3 77.0 - - - +
85Y ASN* 1.3 63.0 + - - +
87Y VAL* 3.8 6.1 + - - +
88Y TYR* 3.1 26.7 + - - +
113Y VAL* 3.8 18.5 - - - +
117Y GLY* 4.0 12.9 + - - -
119Y ARG* 3.7 32.0 - - - +
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Residues in contact with ASN 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q LEU 4.9 0.5 - - - +
102Q THR* 4.0 23.2 - - - +
54X GLN* 2.9 28.8 + - - +
81Y LYS* 2.9 45.4 + - - +
82Y ILE* 3.9 3.8 - - - +
84Y SER* 1.3 73.2 + - - +
86Y LEU* 1.3 68.7 + - - +
88Y TYR* 3.3 6.6 + - - +
89Y GLN* 3.3 22.2 + - - +
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Residues in contact with LEU 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Y TRP* 3.5 57.0 - - + +
58Y TRP* 3.8 26.0 - - + -
82Y ILE 3.0 13.7 + - - +
83Y LEU* 3.4 8.7 - - + +
85Y ASN* 1.3 74.9 - - - +
87Y VAL* 1.3 64.5 + - + +
89Y GLN* 2.8 39.5 + - + +
90Y TYR* 3.5 24.0 + - + -
95Y LEU* 5.1 0.4 - - + -
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Residues in contact with VAL 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Y TRP* 5.6 0.4 - - + -
83Y LEU* 3.0 18.8 + - + +
84Y SER* 4.0 8.1 - - - +
86Y LEU* 1.3 87.4 - - + +
88Y TYR* 1.3 63.1 + - - +
90Y TYR* 3.2 13.3 + - - +
91Y LYS* 3.3 10.7 + - - +
95Y LEU* 4.2 15.2 - - + +
97Y MET* 3.9 37.9 - - + -
113Y VAL* 5.2 2.0 - - + -
114Y ASP 3.4 11.4 - - - +
115Y SER* 3.4 33.4 - - - +
117Y GLY* 4.2 5.4 - - - +
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Residues in contact with TYR 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X GLY 4.0 3.6 - - - -
51X ASP* 3.2 34.8 + - - -
54X GLN* 3.6 44.8 - - + +
93X ARG* 3.0 26.1 + - - -
95X TYR* 3.4 27.0 - + - -
84Y SER 3.1 19.0 + - - +
85Y ASN 3.6 6.7 - - - +
86Y LEU 3.1 0.6 + - - -
87Y VAL* 1.3 75.1 - - - +
89Y GLN* 1.3 74.0 + - - +
91Y LYS* 3.3 28.5 + - + +
117Y GLY* 4.6 11.4 - - - -
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Residues in contact with GLN 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ARG* 5.4 5.4 + - - -
85Y ASN 3.3 14.1 + - - +
86Y LEU* 2.8 18.2 + - + +
88Y TYR* 1.3 87.1 - - - +
90Y TYR* 1.3 67.1 + - + +
91Y LYS 3.6 2.4 + - - +
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Residues in contact with TYR 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Y TRP* 3.6 37.7 - + - -
86Y LEU* 3.5 31.1 + - + -
87Y VAL 3.2 5.7 + - - +
88Y TYR 3.1 0.8 - - - -
89Y GLN* 1.3 83.8 - - + +
91Y LYS* 1.3 66.1 + - - +
92Y GLY 3.2 0.2 + - - -
93Y ALA* 2.9 28.1 + - + +
94Y GLY 4.5 0.7 + - - -
95Y LEU* 3.7 31.0 + - + +
88Z TYR* 6.5 0.2 - + - -
92Z PHE* 3.9 35.9 - + - -
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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
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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