Contacts of the helix formed by residues 81 - 93 (chain D) in PDB entry 1S77
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 MET 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D LEU 3.4 2.2 + - - +
78D LEU 3.4 8.2 + - - +
79D PRO 2.9 1.2 + - - -
80D LYS* 1.3 74.4 - - - +
82D ILE* 1.3 55.7 + - - +
83D ALA 3.0 1.3 - - - -
84D ARG* 2.8 4.7 + - - +
85D ILE* 2.4 60.3 + - + +
112D GLU* 3.8 0.4 - - - -
114D VAL* 5.6 0.4 - - + -
115D ALA* 3.2 36.1 - - + -
118D THR* 3.9 16.8 - - + +
119D ILE* 4.2 14.6 - - + -
216D CYS* 4.3 8.1 - - - +
219D MET* 3.6 14.1 - - + +
220D LEU* 3.5 29.6 - - + -
223D SER* 3.4 20.4 - - - +
224D THR* 4.8 1.8 - - + -
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PRO* 2.8 26.2 - - + +
81D MET* 1.3 69.6 - - - +
83D ALA* 1.3 57.4 + - + +
84D ARG 2.5 18.2 + - - -
85D ILE* 4.0 0.7 - - - -
86D ASN* 3.0 50.5 + - + +
87D ASP* 3.2 6.6 + - - +
111D PRO* 5.8 1.6 - - + -
112D GLU* 2.9 37.0 + - + +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PRO 4.6 0.9 - - - +
80D LYS* 3.3 23.3 - - + +
81D MET 3.0 0.8 - - - -
82D ILE* 1.3 80.1 - - + +
84D ARG* 1.3 69.8 + - - +
87D ASP* 3.5 16.4 - - - +
223D SER* 5.3 0.5 - - - -
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D MET 3.3 5.8 - - - +
82D ILE 2.5 6.7 + - - -
83D ALA* 1.3 82.4 + - - +
85D ILE* 1.3 56.6 + - - +
86D ASN 3.3 0.7 - - - -
87D ASP* 2.6 47.9 + - - +
88D TRP* 2.6 54.1 + - - +
91D GLU* 5.4 2.6 - - - +
215D ARG* 4.4 0.4 - - - +
219D MET* 3.7 29.1 - - + +
222D GLU* 3.2 50.4 + - + -
223D SER* 3.7 17.3 - - - +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D MET* 2.4 44.4 + - + +
82D ILE* 4.0 0.2 - - - -
84D ARG* 1.3 71.2 - - - +
86D ASN* 1.3 72.2 + - - +
88D TRP* 2.9 22.2 - - - +
89D PHE* 3.1 35.2 + - + -
111D PRO* 3.7 23.6 - - + +
112D GLU* 4.2 2.5 - - - +
114D VAL* 4.3 10.1 - - + -
115D ALA* 3.7 32.5 - - + +
219D MET* 3.7 26.0 - - - -
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Residues in contact with ASN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE* 3.0 38.4 + - + +
85D ILE* 1.3 75.4 - - - +
87D ASP* 1.3 59.4 - - - +
88D TRP 2.8 10.9 + - - -
89D PHE* 3.0 14.6 + - + +
90D GLU* 3.0 35.9 + - + +
111D PRO* 3.2 38.3 - - - +
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Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE 3.2 2.8 + - - +
83D ALA* 3.5 10.3 - - - +
84D ARG* 2.6 56.7 + - - +
86D ASN* 1.3 77.4 - - - +
88D TRP* 1.3 55.9 + - - +
90D GLU* 4.5 4.9 - - - -
91D GLU* 3.3 19.3 + - - +
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Residues in contact with TRP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ARG* 2.6 26.7 + - - +
85D ILE 2.9 9.9 - - - +
86D ASN 2.8 0.8 - - - -
87D ASP* 1.3 78.8 - - - +
89D PHE* 1.3 89.5 + + - -
91D GLU* 2.8 12.3 + - + +
92D VAL* 2.7 56.0 + - + +
100D PRO* 4.1 17.6 - - + +
102D ALA* 4.0 5.8 - - + -
103D PHE* 3.5 35.4 - - + -
106D LEU* 5.1 4.9 - - + -
215D ARG* 2.9 59.6 - - + +
219D MET* 3.3 20.0 - - + -
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ILE* 3.4 34.8 - - + -
86D ASN* 3.0 19.4 + - + +
88D TRP* 1.3 104.1 - + - +
90D GLU* 1.3 57.0 + - + +
91D GLU 2.6 16.0 + - - -
92D VAL* 2.9 15.6 + - - +
93D LYS* 3.1 25.4 + - - +
103D PHE* 3.6 22.4 - + + -
106D LEU* 4.6 18.8 - - + -
107D GLN* 3.1 46.0 - - - +
111D PRO* 4.9 5.6 - - + -
219D MET* 6.3 0.4 - - - -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASN* 3.0 21.0 + - + +
87D ASP* 4.6 4.3 - - - -
89D PHE* 1.3 77.1 - - + +
91D GLU* 1.3 63.2 + - - +
93D LYS* 4.3 20.4 - - + +
94D ALA* 5.3 1.9 + - - +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ARG* 5.7 2.2 - - - +
87D ASP 3.3 17.7 - - - +
88D TRP* 3.0 15.7 - - + +
89D PHE 2.6 6.7 + - - -
90D GLU* 1.3 80.2 - - - +
92D VAL* 1.3 58.8 + - - +
93D LYS 3.0 4.7 - - - -
94D ALA* 3.1 30.6 + - - +
95D LYS* 4.1 5.9 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TRP* 2.7 61.0 + - + +
89D PHE 2.9 4.7 + - - +
91D GLU* 1.3 75.7 - - + +
93D LYS* 1.3 60.4 + - - +
94D ALA 3.1 3.5 + - - -
95D LYS* 3.3 30.1 + - + +
99D ARG* 4.2 14.9 + - + +
100D PRO* 4.0 24.5 - - + -
103D PHE* 3.7 24.5 - - + -
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Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.2 20.9 - - - +
90D GLU* 4.3 19.1 - - + -
91D GLU 3.0 0.4 - - - -
92D VAL* 1.3 78.3 - - - +
94D ALA* 1.3 55.4 + - - +
95D LYS 3.3 1.6 - - - -
96D ARG* 3.3 23.6 + - - -
99D ARG* 4.1 23.7 - - - +
103D PHE* 4.7 16.9 - - + -
107D GLN* 5.8 1.8 - - - +
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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