Contacts of the helix formed by residues 75 - 89 (chain I) 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 GLU 75 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.9 22.0 - - + -
40I HIS* 2.9 25.8 + - - -
41I VAL* 3.9 2.0 - - - -
66I TYR* 5.2 0.2 + - - -
72I ARG* 3.9 19.3 - - - +
73I ALA 3.9 5.2 - - - +
74I ILE* 1.3 76.2 - - - +
76I PRO* 1.4 76.9 - - + +
77I GLU* 4.0 9.6 - - + +
78I THR* 3.2 14.5 + - - +
79I PHE* 3.0 20.8 + - - +
105I ASN* 2.4 52.5 + - - +
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Residues in contact with PRO 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I HIS* 4.2 1.6 - - - +
41I VAL* 3.7 23.7 - - + -
75I GLU* 1.4 98.4 - - + +
77I GLU* 1.3 65.7 + - - +
79I PHE* 3.3 1.0 + - - +
80I THR* 2.9 35.2 + - - -
101I VAL* 4.1 5.3 - - + +
103I GLY* 3.9 31.0 - - - +
104I ILE 4.0 2.0 - - - +
105I ASN* 4.0 12.1 - - - +
109I PHE* 3.6 26.0 - - + -
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 5.3 2.2 - - - +
75I GLU* 4.0 3.4 - - + +
76I PRO* 1.3 83.2 - - - +
78I THR* 1.3 63.1 + - - +
80I THR* 3.4 5.5 - - - -
81I GLN* 3.3 25.6 + - - +
105I ASN* 3.0 38.3 + - - +
107I LYS* 4.3 12.7 + - - +
109I PHE* 3.9 39.6 - - + +
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Residues in contact with THR 78 (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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100A TYR* 5.6 0.2 - - - +
103A TYR* 3.7 34.1 - - + -
105A GLU* 3.1 27.5 + - - +
66I TYR* 3.8 14.5 + - - +
72I ARG* 5.3 1.7 + - - -
74I ILE* 3.8 17.5 - - + -
75I GLU* 3.2 18.5 + - - +
77I GLU* 1.3 74.5 - - - +
79I PHE* 1.3 61.6 + - - +
81I GLN* 3.1 9.8 + - - +
82I LEU* 3.0 24.1 + - - +
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Residues in contact with PHE 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I TYR* 3.6 23.6 - + - -
41I VAL* 3.5 28.5 - - + -
43I LEU* 3.9 17.5 - - + -
59I PHE* 3.9 25.4 - + + -
63I THR* 3.8 30.1 - - + -
74I ILE* 4.2 13.9 - - + -
75I GLU 3.0 16.1 + - - +
76I PRO 3.7 3.8 - - - +
77I GLU 3.3 0.2 - - - -
78I THR* 1.3 74.8 - - - +
80I THR* 1.3 65.2 + - - +
82I LEU* 2.8 21.4 + - + +
83I VAL* 2.8 35.6 + - + +
101I VAL* 3.7 21.1 - - + -
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Residues in contact with THR 80 (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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76I PRO 2.9 15.1 + - - -
77I GLU 3.4 12.1 - - - +
79I PHE* 1.3 76.5 - - - +
81I GLN* 1.3 62.8 + - - +
83I VAL* 3.4 1.2 + - - -
84I SER* 3.0 20.3 + - - -
101I VAL* 3.6 10.4 - - - +
109I PHE* 3.1 24.4 - - + -
111I ALA* 4.0 9.1 - - + +
113I PHE* 3.3 30.9 - - + -
119I ILE* 4.0 26.5 - - + -
121I GLU* 5.9 0.4 - - + -
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Residues in contact with GLN 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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102A ILE 3.3 3.3 + - - +
103A TYR 3.4 30.1 - - - +
104A GLY* 3.9 18.3 - - - +
105A GLU* 5.7 0.2 - - - +
57H GLN* 4.5 15.6 + - - +
77I GLU 3.3 14.3 + - - +
78I THR* 3.1 6.0 + - - +
79I PHE 3.1 0.8 - - - -
80I THR* 1.3 78.4 - - - +
82I LEU* 1.3 59.0 + - - +
84I SER* 3.5 5.4 + - - -
85I SER* 3.0 30.8 + - - -
119I ILE* 3.5 23.7 - - - +
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Residues in contact with LEU 82 (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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102A ILE* 3.6 31.6 - - - +
103A TYR* 3.9 16.6 - - + +
59I PHE* 4.4 4.9 - - + -
62I LYS* 4.0 38.4 - - + +
63I THR* 4.6 3.6 - - + -
74I ILE* 4.3 12.8 - - + -
78I THR 3.0 11.4 + - - +
79I PHE* 2.8 36.5 + - + +
81I GLN* 1.3 70.4 - - - +
83I VAL* 1.3 59.1 + - - +
85I SER* 3.5 2.0 + - - +
86I SER* 2.5 48.0 + - - +
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Residues in contact with VAL 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 4.7 1.8 - - + -
59I PHE* 3.8 27.5 - - + -
79I PHE* 2.8 52.4 + - + +
80I THR 3.7 6.1 - - - +
82I LEU* 1.3 73.0 - - - +
84I SER* 1.3 59.1 + - - +
86I SER* 3.2 2.4 + - - -
87I LEU* 2.9 50.1 + - + +
99I PRO* 4.3 9.9 - - + -
101I VAL* 4.5 2.5 - - + -
113I PHE* 3.7 26.2 - - + -
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Residues in contact with SER 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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80I THR 3.0 17.8 + - - -
81I GLN* 3.5 8.0 + - - -
83I VAL* 1.3 75.5 - - - +
85I SER* 1.3 59.5 + - - +
87I LEU* 3.0 5.4 + - - +
88I TYR* 2.9 28.9 + - - +
113I PHE* 3.8 3.7 - - - -
117I GLY* 2.5 33.5 + - - -
119I ILE* 3.6 21.6 - - - +
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Residues in contact with SER 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 2.8 51.7 + - - +
81I GLN 3.0 6.9 + - - -
82I LEU* 3.5 4.3 + - - -
84I SER* 1.3 79.0 - - - +
86I SER* 1.3 62.7 + - - +
88I TYR* 4.0 6.1 - - - +
89I GLU* 3.1 26.2 + - - +
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Residues in contact with SER 86 (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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55I LEU* 6.0 0.4 - - - -
58I MET* 4.6 7.9 - - - +
59I PHE* 3.8 22.1 - - - -
62I LYS* 3.4 24.1 + - - +
82I LEU* 2.5 31.0 + - - +
83I VAL 3.4 4.5 - - - -
85I SER* 1.3 77.0 + - - +
87I LEU* 1.3 65.0 + - - +
89I GLU* 3.6 21.4 - - - +
90I ARG* 4.2 7.4 + - - +
95I TYR* 4.9 6.3 - - - -
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Residues in contact with LEU 87 (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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55I LEU* 4.1 27.8 - - + -
59I PHE* 5.5 2.2 - - + -
83I VAL* 2.9 31.9 + - + +
84I SER 3.6 2.9 - - - +
86I SER* 1.3 74.5 - - - +
88I TYR* 1.3 59.9 + - - +
89I GLU 3.1 1.8 - - - -
90I ARG* 2.9 29.3 + - - +
94I PRO* 5.4 0.7 - - - +
95I TYR* 4.4 13.9 - - + -
97I VAL* 4.2 8.3 - - + -
99I PRO* 4.1 8.3 - - + -
113I PHE* 3.9 14.4 - - + -
114I ASP 3.7 13.0 - - - +
115I LEU 3.9 13.7 - - - +
116I ILE* 3.7 7.4 - - - +
117I GLY* 3.6 29.8 - - - +
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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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50H ALA* 3.8 15.9 - - + -
51H ASP* 3.0 31.9 + - - -
54H ALA* 3.5 30.9 - - + +
55H VAL* 5.3 0.5 + - - +
95H ILE* 4.1 20.1 - - + +
84I SER* 2.9 15.4 + - - +
85I SER* 4.2 7.2 - - - +
87I LEU* 1.3 75.9 - - - +
89I GLU* 1.3 63.0 + - - +
91I ARG* 3.0 39.8 + - + +
116I ILE 3.4 20.8 + - - +
117I GLY* 5.1 1.1 - - - -
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Residues in contact with GLU 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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62I LYS* 4.6 14.0 + - - -
85I SER 3.1 18.2 + - - +
86I SER* 3.6 13.1 - - - +
87I LEU 3.1 0.8 - - - -
88I TYR* 1.3 77.5 - - - +
90I ARG* 1.3 88.4 + - + +
91I ARG 3.3 2.1 + - - -
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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