Contacts of the helix formed by residues 83 - 97 (chain D) in PDB entry 1SZU
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 TYR 83 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 3.5 8.2 - - - -
27C ALA* 3.7 18.4 - - + +
69D GLN* 6.2 0.7 - - - +
73D LEU* 5.1 7.6 - - + -
76D THR* 3.2 31.0 - - + -
77D CYS* 4.3 3.6 + - - -
78D PHE* 3.6 39.6 + + - +
81D LEU 3.5 4.9 - - - -
82D ALA* 1.3 75.5 - - - +
84D GLU* 1.3 66.5 + - - +
85D PRO* 3.5 10.9 - - + -
86D TYR* 3.5 30.4 + - + -
87D LEU 3.6 2.1 + - - -
299D ALA 3.3 12.3 + - - -
300D GLY 2.4 31.2 + - - -
302D PRO* 3.7 36.7 - - + +
305D CYS* 4.6 0.2 - - - -
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Residues in contact with GLU 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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2C ASN* 5.2 7.2 + - - -
7C LEU* 4.0 33.2 - - + +
10C ARG* 4.7 8.2 + - - +
26C PHE* 4.3 3.4 - - + -
27C ALA 4.7 2.5 + - - +
28C ASP* 5.0 5.2 - - - +
38C VAL* 3.6 24.2 - - + +
72D LYS* 6.0 0.2 + - - -
83D TYR* 1.3 70.9 - - - +
85D PRO* 1.3 63.3 - - + +
87D LEU* 3.0 8.7 + - + +
88D GLU* 2.6 44.3 + - + +
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Residues in contact with PRO 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLN* 4.0 15.5 - - - +
83D TYR* 3.4 18.6 - - + -
84D GLU* 1.3 93.9 - - + +
86D TYR* 1.3 62.0 + - - +
88D GLU* 3.9 2.7 - - + +
89D LEU* 3.0 24.9 + - - +
302D PRO* 4.4 2.9 - - + +
305D CYS* 3.7 23.4 - - + +
306D VAL* 3.9 25.6 - - + +
309D LEU* 4.0 13.4 - - + +
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Residues in contact with TYR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 3.7 15.4 - - + +
19C VAL* 4.4 10.2 - - - +
78D PHE* 3.4 50.1 - + + -
83D TYR* 3.5 19.5 + - + +
84D GLU 3.2 0.4 - - - -
85D PRO* 1.3 79.5 - - - +
87D LEU* 1.3 65.2 + - - +
89D LEU* 3.2 3.8 + - - +
90D CYS* 3.0 40.7 + - - -
105D THR 4.9 0.2 - - - -
106D LEU* 3.9 11.1 - - - +
107D LEU* 3.3 41.0 + - + +
299D ALA* 3.8 14.6 - - + +
300D GLY* 3.7 21.1 - - - -
305D CYS* 3.8 10.9 - - - -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.7 37.2 - - + +
10C ARG* 3.7 26.5 - - + +
11C ARG* 3.7 28.9 - - - +
14C ALA* 4.1 4.3 - - + -
15C ILE* 4.0 18.6 - - + -
26C PHE* 4.0 20.4 - - + -
78D PHE* 4.4 0.8 - - + -
83D TYR 3.6 1.4 + - - -
84D GLU* 3.0 8.4 + - + +
86D TYR* 1.3 79.2 - - - +
88D GLU* 1.3 63.6 + - - +
90D CYS* 3.4 1.9 + - - +
91D GLU* 3.1 41.1 + - - +
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Residues in contact with GLU 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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10C ARG* 4.6 9.2 - - - +
84D GLU* 2.6 26.6 + - + +
85D PRO* 3.9 5.7 - - - +
87D LEU* 1.3 76.6 - - - +
89D LEU* 1.3 60.4 + - - +
91D GLU* 3.6 14.4 + - - +
92D ILE* 3.2 34.0 + - + +
309D LEU* 3.9 28.6 - - + +
313D LYS* 5.8 4.5 - - - -
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Residues in contact with LEU 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 PRO 3.0 18.4 + - - +
86D TYR 3.2 3.8 + - - +
88D GLU* 1.3 73.6 - - - +
90D CYS* 1.3 67.8 + - - +
92D ILE* 3.2 1.9 + - + -
93D MET* 2.9 46.0 + - + +
107D LEU* 3.6 33.7 - - + -
266D PHE* 5.0 3.6 - - + -
270D ILE* 5.4 1.3 - - + -
276D LEU* 3.6 24.2 - - + -
305D CYS* 4.4 6.7 - - + +
308D ALA* 3.9 15.7 - - + -
309D LEU* 3.7 17.4 - - + +
312D LEU* 4.0 24.0 - - + -
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Residues in contact with CYS 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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14C ALA* 3.9 6.3 - - + +
15C ILE* 3.7 15.7 - - + -
86D TYR* 3.0 41.9 + - - -
87D LEU 3.7 6.5 - - - +
89D LEU* 1.3 77.2 - - - +
91D GLU* 1.3 57.7 + - - +
93D MET 3.1 1.0 + - - -
94D ASN* 2.8 36.9 + - - -
105D THR* 3.3 39.5 + - - -
107D LEU* 3.8 13.9 - - - -
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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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10C ARG* 2.8 61.2 + - - +
14C ALA* 3.6 16.8 - - + -
87D LEU* 3.1 18.6 + - + +
88D GLU* 3.8 9.3 - - - +
89D LEU 3.3 0.2 - - - -
90D CYS* 1.3 79.3 - - - +
92D ILE* 1.3 63.7 + - + +
94D ASN* 3.4 11.2 + - - +
95D GLN* 3.4 24.9 + - - +
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Residues in contact with ILE 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 GLU* 3.2 24.2 + - + +
89D LEU 3.2 4.2 + - - +
91D GLU* 1.3 77.4 - - + +
93D MET* 1.3 57.4 + - - +
95D GLN* 3.2 18.4 - - + +
96D LYS* 2.9 45.2 + - + +
309D LEU* 3.4 30.1 - - + +
312D LEU* 3.8 28.3 - - + -
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 2.9 38.7 + - + +
92D ILE* 1.3 73.2 - - - +
94D ASN* 1.3 66.8 + - - +
95D GLN 3.0 2.2 - - - -
96D LYS* 4.3 3.1 - - - +
97D VAL* 2.9 33.2 + - + +
105D THR* 3.7 8.7 - - + +
251D LEU* 5.3 3.6 - - + -
252D PHE* 3.5 37.5 - - + -
266D PHE* 3.7 30.7 - - + -
270D ILE* 3.8 26.9 - - + -
280D THR* 3.5 15.3 - - - +
312D LEU* 4.2 12.3 - - - -
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Residues in contact with ASN 94 (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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13C GLN 4.5 0.6 + - - -
14C ALA* 3.0 41.8 + - - +
90D CYS 2.8 23.0 + - - +
91D GLU* 3.6 6.8 - - - +
92D ILE 3.3 0.2 - - - -
93D MET* 1.3 72.8 - - - +
95D GLN* 1.3 57.1 + - + +
103D LYS* 2.7 53.4 + - + +
104D LYS* 2.9 19.2 + - - +
105D THR* 2.8 19.6 + - - -
280D THR* 3.8 5.1 - - - +
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Residues in contact with GLN 95 (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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91D GLU* 3.4 14.8 + - - +
92D ILE* 3.2 27.9 + - - +
93D MET 3.0 0.6 - - - -
94D ASN* 1.3 82.1 - - - +
96D LYS* 1.3 72.8 + - + +
97D VAL 4.0 4.0 - - - +
103D LYS* 4.3 3.5 + - - +
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Residues in contact with LYS 96 (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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92D ILE* 2.9 35.1 + - + +
93D MET* 4.4 4.5 - - - +
95D GLN* 1.3 87.9 - - + +
97D VAL* 1.3 63.4 + - - +
98D PRO* 3.5 5.9 - - - +
251D LEU* 3.8 29.5 - - + +
252D PHE* 4.4 4.2 - - + -
255D GLU* 4.2 10.7 - - - +
312D LEU* 4.5 24.6 + - + +
315D PHE* 6.2 0.6 - - - +
316D GLU* 4.1 29.3 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D MET* 2.9 27.0 + - + +
95D GLN 3.5 2.3 - - - +
96D LYS* 1.3 77.8 - - - +
98D PRO* 1.3 78.6 - - + +
99D GLY 3.5 0.3 + - - -
103D LYS* 2.9 29.8 + - + -
252D PHE* 3.7 28.5 - - + -
261D PRO* 5.5 0.2 - - + -
264D THR* 3.8 26.9 - - + +
266D PHE* 5.1 0.7 - - + -
280D THR* 3.7 34.5 - - + +
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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