Contacts of the helix formed by residues 98 - 112 (chain D) in PDB entry 1S89
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 ASN 98 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 3.7 28.2 - - - +
19D HIS* 4.3 2.0 + - - -
66D GLY 4.8 0.2 - - - +
67D PRO* 3.8 21.5 - - + +
71D ASP* 3.0 25.1 + - - -
96D VAL* 3.4 21.3 - - - +
97D PRO* 1.3 77.2 - - - +
99D ASP* 1.3 61.8 + - - +
100D PRO* 3.3 3.8 - - - -
101D ASP* 3.0 13.3 + - - +
102D VAL* 2.9 24.1 + - - +
204D PGA 3.3 21.5 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA* 6.0 1.6 - - + -
96D VAL* 3.0 31.6 + - + +
97D PRO 3.1 0.4 - - - +
98D ASN* 1.3 77.0 - - - +
100D PRO* 1.3 73.8 - - + +
102D VAL* 3.0 5.7 + - - +
103D LYS* 2.6 58.6 + - - +
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Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PRO* 3.6 28.2 - - + +
103C LYS* 3.9 18.2 - - + +
104C ALA* 4.0 10.3 - - - +
107C ARG* 4.4 9.9 - - + -
97D PRO 3.7 8.1 - - - +
98D ASN 3.3 1.1 - - - -
99D ASP* 1.3 98.3 - - + +
101D ASP* 1.3 70.8 + - - +
103D LYS* 3.3 2.2 + - + -
104D ALA* 2.9 31.2 + - - +
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLN* 5.2 1.4 - - - +
104C ALA* 3.4 18.1 - - - +
107C ARG* 2.7 47.2 + - - -
108C LEU* 4.3 1.0 - - - +
66D GLY 4.5 2.8 - - - +
69D GLY* 5.3 0.7 - - - -
71D ASP* 3.7 24.5 - - + +
72D GLN* 3.1 23.4 + - + +
98D ASN* 3.1 10.5 - - + +
100D PRO* 1.3 83.7 - - - +
102D VAL* 1.3 61.7 + - - +
104D ALA* 3.4 2.9 + - - +
105D LEU* 3.0 25.1 + - - +
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D HIS* 3.5 31.2 - - + +
71D ASP* 4.0 7.6 - - - +
88D PHE* 3.7 25.9 - - + -
90D TRP* 4.4 18.8 - - + -
96D VAL* 4.1 8.3 - - + -
98D ASN* 2.9 19.0 + - - +
99D ASP* 3.0 10.3 + - - +
101D ASP* 1.3 77.7 - - - +
103D LYS* 1.3 76.7 + - + +
105D LEU* 3.3 3.3 + - - +
106D LEU* 3.2 28.0 + - + +
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PRO* 3.9 16.8 - - + -
90D TRP* 4.5 23.6 - - - -
99D ASP* 2.6 48.5 + - - +
100D PRO* 3.8 4.5 - - + +
102D VAL* 1.3 88.1 - - + +
104D ALA* 1.3 58.6 + - - +
106D LEU* 3.3 12.0 + - + +
107D ARG* 2.8 30.2 + - - +
90E TRP* 5.3 1.4 - - - -
103E LYS* 4.4 35.9 - - + +
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Residues in contact with ALA 104 (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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72C GLN* 3.0 27.1 + - - +
100C PRO* 3.9 3.7 - - - +
101C ASP* 3.7 36.2 - - - +
104C ALA* 4.7 2.5 - - + -
72D GLN* 5.9 0.2 - - + -
100D PRO 2.9 18.2 + - - +
101D ASP* 3.6 7.4 - - - +
103D LYS* 1.3 76.2 - - - +
105D LEU* 1.3 63.7 + - - +
107D ARG* 3.2 4.6 + - - +
108D LEU* 3.0 19.9 + - - +
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Residues in contact with LEU 105 (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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72C GLN* 3.9 7.9 + - - +
17D VAL* 4.9 4.9 - - + -
71D ASP* 3.9 28.3 - - - +
74D VAL* 4.0 11.9 - - + -
75D GLY* 3.7 31.6 - - - +
78D ILE* 3.9 17.3 - - + -
86D LEU* 4.1 15.3 - - + -
88D PHE* 3.7 29.2 - - + -
101D ASP 3.0 17.0 + - - +
102D VAL 3.6 4.9 - - - +
104D ALA* 1.3 76.9 - - - +
106D LEU* 1.3 62.6 + - - +
108D LEU* 3.3 2.3 + - - +
109D ALA* 3.0 21.1 + - - +
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Residues in contact with LEU 106 (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 LEU* 4.7 3.6 - - + -
88D PHE* 4.0 22.0 - - + -
90D TRP* 4.1 28.0 - - + +
102D VAL* 3.2 22.9 + - + +
103D LYS* 3.7 15.5 - - + +
105D LEU* 1.3 78.8 - - - +
107D ARG* 1.3 61.9 + - - +
109D ALA* 3.4 4.6 + - - +
110D THR* 2.9 28.4 + - - -
116D VAL* 4.4 16.8 - - + -
118D THR* 4.1 20.2 - - + -
90E TRP* 4.6 7.4 - - + -
106E LEU* 6.4 2.7 - - + -
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY 4.1 2.0 + - - -
67C PRO* 3.1 35.8 + - - +
97C PRO* 3.7 17.9 - - - +
98C ASN* 3.8 13.2 - - - +
100C PRO* 4.4 7.6 - - + -
101C ASP* 2.8 43.5 + - - -
103D LYS 2.8 18.5 + - - +
104D ALA* 3.4 4.0 - - - +
106D LEU* 1.3 76.8 - - - +
108D LEU* 1.3 70.1 + - - +
110D THR* 3.0 5.5 + - - -
111D VAL* 3.0 39.6 + - - +
90E TRP* 3.8 21.5 - - + -
92E PRO* 3.1 37.2 + - + +
93E LEU* 4.0 4.4 - - - +
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Residues in contact with LEU 108 (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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67C PRO 4.1 3.1 - - - +
68C MET 3.7 29.2 - - - +
69C GLY* 3.7 17.9 - - - +
72C GLN* 3.0 35.2 - - + +
75D GLY* 3.3 29.8 - - - +
78D ILE* 4.6 3.8 - - + -
79D SER* 4.3 2.2 - - - -
104D ALA 3.0 10.7 + - - +
105D LEU* 3.7 4.5 - - + +
107D ARG* 1.3 90.5 - - - +
109D ALA* 1.3 61.2 + - - +
111D VAL* 3.2 4.4 + - + -
112D TRP* 2.9 47.6 + - + +
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Residues in contact with ALA 109 (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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78D ILE* 4.4 9.1 - - + +
86D LEU* 3.9 18.6 - - + -
105D LEU 3.0 15.9 + - - +
106D LEU* 3.7 7.4 - - - +
107D ARG 3.3 0.2 - - - -
108D LEU* 1.3 76.8 - - - +
110D THR* 1.3 60.0 + - - +
113D ASN 3.5 1.9 + - - -
114D ILE* 3.4 27.9 + - + +
116D VAL* 3.7 24.9 - - + -
119E ASN* 3.3 15.2 + - - -
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Residues in contact with THR 110 (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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106D LEU 2.9 13.7 + - - -
107D ARG 3.0 9.1 + - - -
108D LEU 3.0 0.2 - - - -
109D ALA* 1.3 77.2 - - - +
111D VAL* 1.3 66.1 + - - +
113D ASN* 3.1 14.4 + - - +
116D VAL* 5.9 0.3 - - - +
90E TRP* 3.5 27.5 - - - +
92E PRO* 3.9 21.7 - - + +
118E THR* 3.6 35.4 + - - +
119E ASN* 3.9 13.0 - - + +
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Residues in contact with VAL 111 (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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67C PRO 4.6 3.6 - - - +
68C MET* 4.3 31.4 - - + -
107D ARG* 3.0 37.0 + - - +
108D LEU* 3.2 9.6 + - + +
110D THR* 1.3 77.3 - - - +
112D TRP* 1.3 67.1 + - + +
113D ASN* 3.2 6.2 + - - +
141D PRO* 3.6 19.3 - - + +
92E PRO* 3.5 29.2 - - + +
93E LEU* 4.2 12.1 - - + -
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Residues in contact with TRP 112 (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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64C LEU* 4.7 5.8 - - + -
68C MET* 3.0 58.2 + - + -
6D ARG* 5.7 1.7 + - - -
78D ILE* 4.0 19.7 - - + +
79D SER* 3.4 39.8 - - - +
81D GLY* 6.2 0.7 - - - -
108D LEU* 2.9 37.7 + - + +
109D ALA 4.1 0.4 - - - +
111D VAL* 1.3 76.4 - - + +
113D ASN* 1.3 69.8 + - - +
114D ILE* 3.3 12.3 + - + +
138D ILE* 4.0 0.9 - - - +
140D ILE* 3.6 35.3 - - + +
141D PRO* 3.8 29.6 - - + -
143D TYR* 4.5 16.6 - + + -
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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