Contacts of the helix formed by residues 75 - 89 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O PHE* 4.1 25.8 - - + -
40W HIS* 3.0 21.2 + - - -
41W VAL* 3.9 3.1 - - - -
72W ARG* 4.2 10.3 - - - +
73W ALA* 3.6 7.1 + - - +
74W ILE* 1.3 75.4 - - - +
76W PRO* 1.4 66.1 - - + +
77W GLU* 4.0 9.0 - - + +
78W THR* 3.2 15.4 + - - +
79W PHE* 2.9 28.9 + - - +
105W ASN* 2.7 67.4 + - - +
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Residues in contact with PRO 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W HIS* 4.2 0.4 - - - +
41W VAL* 3.7 22.8 - - + -
75W GLU* 1.4 99.5 - - + +
77W GLU* 1.3 64.7 + - - +
79W PHE* 3.2 1.6 + - - +
80W THR* 2.9 36.6 + - - -
101W VAL* 4.2 7.7 - - + +
103W GLY* 3.9 31.4 - - - +
104W ILE 4.0 10.5 - - - +
105W ASN* 4.2 2.2 - - - +
109W PHE* 3.7 24.7 - - + -
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Residues in contact with GLU 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75W GLU* 3.4 2.7 + - + +
76W PRO* 1.3 84.6 - - - +
78W THR* 1.3 62.3 + - - +
80W THR* 3.6 4.6 - - - +
81W GLN* 3.4 24.8 + - - +
105W ASN* 3.1 37.9 + - - +
107W LYS* 4.7 8.8 + - - +
109W PHE* 3.9 41.8 - - + +
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Residues in contact with THR 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O TYR* 4.0 30.4 - - + -
105O GLU* 3.2 34.5 + - - +
66W TYR* 3.9 16.7 + - + +
72W ARG* 5.7 1.4 + - - -
74W ILE* 3.9 10.8 - - + -
75W GLU* 3.2 17.8 + - - +
76W PRO 3.1 0.2 - - - -
77W GLU* 1.3 76.6 - - - +
79W PHE* 1.3 69.1 + - - +
80W THR 3.1 1.6 - - - -
81W GLN* 3.3 4.6 + - - +
82W LEU* 3.0 20.1 + - - +
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Residues in contact with PHE 79 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W TYR* 3.6 24.7 - + - -
41W VAL* 3.6 26.5 - - + -
43W LEU* 4.0 22.7 - - + -
59W PHE* 3.8 30.7 - + + -
63W THR* 3.6 33.4 - - + -
74W ILE* 4.2 13.0 - - + -
75W GLU 2.9 16.8 + - - +
76W PRO 3.7 3.4 - - - +
78W THR* 1.3 76.3 - - - +
80W THR* 1.3 51.6 + - - +
82W LEU* 2.9 13.8 + - + +
83W VAL* 2.7 51.2 + - + +
101W VAL* 3.9 11.7 - - + -
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Residues in contact with THR 80 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76W PRO 2.9 21.9 + - - -
77W GLU 3.6 8.3 - - - +
79W PHE* 1.3 76.6 - - - +
81W GLN* 1.3 58.0 + - - +
83W VAL* 3.2 5.9 + - - +
84W SER* 2.9 25.8 + - - -
101W VAL* 3.6 13.6 - - - +
109W PHE* 3.2 22.7 - - + -
111W ALA* 4.1 13.0 - - + -
113W PHE* 3.5 27.3 - - + -
119W ILE* 3.9 20.2 - - + -
121W GLU* 6.1 0.2 - - - +
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Residues in contact with GLN 81 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ILE 3.3 9.4 - - - +
103O TYR 3.4 29.6 - - - +
104O GLY* 4.2 16.2 - - - +
57V GLN* 4.8 15.2 + - - +
77W GLU 3.4 17.4 + - - +
78W THR 3.3 4.6 + - - +
80W THR* 1.3 76.0 - - - +
82W LEU* 1.3 63.3 + - - +
84W SER* 3.5 7.7 + - - -
85W SER* 3.1 20.3 + - - -
119W ILE* 3.8 22.1 - - - +
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Residues in contact with LEU 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ILE* 3.7 31.5 + - - +
103O TYR* 4.0 16.8 - - + +
59W PHE* 4.2 6.1 - - + -
62W LYS* 3.9 37.7 - - + +
63W THR* 4.5 3.4 - - + -
66W TYR* 6.3 0.4 - - + -
74W ILE* 4.5 11.4 - - + -
78W THR 3.0 13.2 + - - +
79W PHE* 2.9 35.2 + - + +
81W GLN* 1.3 75.3 - - - +
83W VAL* 1.3 60.4 + - - +
85W SER* 3.4 2.0 + - - +
86W SER* 2.5 44.0 + - - +
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Residues in contact with VAL 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43W LEU* 4.6 3.4 - - + -
59W PHE* 3.8 23.1 - - + -
79W PHE* 2.7 53.6 + - + +
80W THR 3.4 6.3 - - - +
82W LEU* 1.3 71.4 - - - +
84W SER* 1.3 64.5 + - - +
86W SER* 3.2 3.5 + - - -
87W LEU* 3.0 39.0 + - + +
99W PRO* 4.4 8.1 - - + -
101W VAL* 4.3 2.5 - - + -
113W PHE* 3.6 36.1 - - + -
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Residues in contact with SER 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80W THR 2.9 16.8 + - - -
81W GLN* 3.5 10.6 + - - -
83W VAL* 1.3 76.3 - - - +
85W SER* 1.3 57.4 + - - +
87W LEU 3.4 0.2 + - - -
88W TYR* 2.9 28.8 + - - +
113W PHE* 4.0 2.7 - - - -
117W GLY* 2.7 35.9 + - - -
119W ILE* 3.7 22.2 - - - +
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Residues in contact with SER 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG* 3.2 47.6 + - - +
81W GLN 3.1 8.0 + - - -
82W LEU* 3.4 7.1 + - - +
84W SER* 1.3 77.2 - - - +
86W SER* 1.3 69.9 + - - +
88W TYR* 4.0 6.5 - - - +
89W GLU* 3.1 23.6 + - - +
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Residues in contact with SER 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55W LEU* 6.2 0.7 - - - -
58W MET* 4.3 9.9 - - - +
59W PHE* 3.7 20.4 - - - -
62W LYS* 3.2 30.5 + - - +
82W LEU* 2.5 30.9 + - - +
83W VAL 3.7 3.1 - - - -
85W SER* 1.3 78.5 + - - +
87W LEU* 1.3 63.6 + - - +
89W GLU* 3.5 19.9 - - - +
90W ARG* 4.1 8.7 + - - +
95W TYR* 5.0 6.3 - - - -
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Residues in contact with LEU 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55W LEU* 4.0 27.4 - - + -
59W PHE* 5.3 2.7 - - + -
83W VAL* 3.0 36.5 + - + +
84W SER 3.7 1.3 - - - +
86W SER* 1.3 74.2 - - - +
88W TYR* 1.3 66.4 + - - +
89W GLU 3.1 2.0 - - - -
90W ARG* 3.0 23.0 + - - +
91W ARG 3.8 0.2 + - - -
94W PRO* 5.5 0.7 - - - +
95W TYR* 4.3 16.2 - - + +
97W VAL* 4.1 7.4 - - + -
99W PRO* 3.9 15.9 - - + -
113W PHE* 4.2 2.5 - - + -
114W ASP 3.9 19.7 - - - +
115W LEU 4.0 14.9 - - - +
116W ILE* 3.9 7.9 - - - +
117W GLY* 3.7 18.4 - - - +
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Residues in contact with TYR 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V ALA* 3.6 23.3 - - + -
51V ASP* 2.8 32.2 + - - -
54V ALA* 3.4 25.7 - - + +
55V VAL* 5.9 0.3 - - - +
95V ILE* 4.4 14.5 - - + +
84W SER* 2.9 17.8 + - - +
85W SER* 4.2 6.5 - - - +
86W SER 3.6 0.2 - - - -
87W LEU* 1.3 76.5 - - - +
89W GLU* 1.3 62.4 + - - +
91W ARG* 3.1 38.9 + - + +
116W ILE* 3.3 22.1 + - - +
117W GLY 5.7 0.4 - - - -
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Residues in contact with GLU 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62W LYS* 4.5 14.4 + - - -
85W SER 3.1 16.9 + - - +
86W SER* 3.5 13.9 - - - +
87W LEU 3.1 0.4 - - - -
88W TYR* 1.3 76.4 - - - +
90W ARG* 1.3 93.4 + - + +
91W ARG* 3.3 3.2 + - - +
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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