Contacts of the strand formed by residues 90 - 100 (chain N) in PDB entry 1ZYR
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 90 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090M LYS* 3.0 43.7 - - - +
1093M GLN* 3.5 26.0 - - - +
1094M ALA* 3.3 25.8 - - + +
21N TRP* 3.3 23.1 + - + +
22N SER* 2.9 25.6 - - - -
23N TYR* 3.4 4.8 + - - -
49N ILE* 5.3 0.7 - - - -
50N PHE* 4.5 0.7 - - - -
88N TYR 3.2 14.1 - - - +
89N ARG* 1.3 73.7 - - - +
91N GLY* 1.3 62.3 + - - +
518N PRO* 5.3 3.4 - - + -
519N VAL 2.9 26.7 - - - +
520N LEU* 4.1 6.7 - - + -
521N PRO* 4.2 5.8 - - + -
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Residues in contact with GLY 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N ILE 5.3 0.3 - - - +
22N SER* 2.9 17.2 + - - -
23N TYR 3.7 10.3 - - - -
24N GLY 4.0 0.9 - - - -
26N VAL* 4.7 2.0 - - - -
49N ILE* 4.1 10.3 - - - -
50N PHE* 3.7 12.8 - - - -
90N MET* 1.3 78.3 - - - +
92N HIS* 1.3 62.9 + - - +
518N PRO* 3.9 2.6 - - - +
519N VAL* 3.1 25.9 + - - +
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Residues in contact with HIS 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N ILE* 4.5 9.0 - - + -
19N ARG* 4.1 27.0 - - + +
22N SER* 3.1 17.5 + - - +
24N GLY 3.1 18.6 + - - -
25N GLU* 3.1 45.8 + - + +
26N VAL* 3.4 8.7 + - - +
91N GLY* 1.3 76.7 - - - +
93N ILE* 1.3 58.9 + - - +
94N GLU* 3.1 30.7 + - - +
516N ALA* 4.7 3.8 - - + -
517N VAL 3.2 15.5 - - - +
519N VAL* 3.6 10.2 - - - +
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Residues in contact with ILE 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLU* 4.3 4.3 - - - +
26N VAL* 4.0 14.4 - - + +
92N HIS* 1.3 76.5 - - - +
94N GLU* 1.3 75.3 + - - +
95N LEU* 3.9 4.9 + - + +
516N ALA* 3.6 1.9 - - - -
517N VAL* 2.8 36.5 + - + +
519N VAL* 3.9 14.6 - - + -
544N TYR* 4.1 17.0 - - + +
547N LEU* 3.8 25.8 - - + -
548N ILE* 3.2 37.0 - - + -
551N ASN* 3.3 23.3 - - + +
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Residues in contact with GLU 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N ARG* 2.7 41.6 + - - -
25N GLU* 3.3 27.5 + - - +
92N HIS* 3.1 23.4 - - - -
93N ILE* 1.3 83.6 - - - +
95N LEU* 1.3 68.7 + - - +
515N GLU 4.3 2.2 - - - +
516N ALA* 3.8 6.2 - - - +
551N ASN* 2.8 19.3 + - - +
555N LYS* 4.0 14.4 + - - +
147P LEU* 5.8 8.7 - - + -
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Residues in contact with LEU 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N ILE* 4.8 2.5 - - + +
94N GLU* 1.3 81.0 - - - +
96N ALA* 1.3 66.3 + - - +
97N THR 4.7 3.1 - - - +
98N PRO 4.9 2.9 - - - -
99N ALA* 4.5 11.0 - - + +
514N LEU* 3.2 32.1 - - + +
515N GLU* 3.0 34.8 + - + +
517N VAL* 3.8 31.2 - - + +
547N LEU* 4.7 10.1 - - + -
551N ASN* 3.3 9.6 - - - +
555N LYS* 5.7 0.2 - - - -
574N LEU* 3.8 27.4 - - + -
578N VAL* 4.8 5.2 - - + -
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Residues in contact with ALA 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 1.3 76.0 - - - +
97N THR* 1.3 62.7 + - - +
98N PRO* 4.0 3.4 - - - +
551N ASN* 3.0 16.2 - - - +
554N LEU* 3.2 42.0 - - + -
555N LYS* 4.9 6.1 - - + +
558N LEU* 4.2 7.2 - - + -
574N LEU* 3.9 2.8 - - + +
144P ILE* 3.2 26.5 - - - +
145P PRO* 4.9 6.1 - - - -
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Residues in contact with THR 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 4.9 1.8 - - - +
96N ALA* 1.3 82.6 - - - +
98N PRO* 1.3 78.4 - - + +
99N ALA* 4.4 2.8 - - - +
459N GLU* 3.2 39.7 - - + +
554N LEU* 4.7 5.2 - - - +
558N LEU* 5.2 3.6 - - - +
571N LYS* 3.0 51.7 + - + +
574N LEU* 4.0 13.1 - - - +
144P ILE* 3.9 8.1 - - + +
145P PRO* 5.2 3.3 - - - +
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Residues in contact with PRO 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 4.7 2.4 - - + -
96N ALA 4.0 4.0 - - - +
97N THR* 1.3 107.4 - - + +
99N ALA* 1.3 59.4 + - - +
458N ALA* 3.3 21.5 + - - +
459N GLU* 4.1 4.2 + - + -
462N GLN* 4.3 15.5 - - + +
513N ILE* 4.0 15.5 - - + -
514N LEU 3.3 13.5 - - - +
515N GLU* 3.7 35.4 - - + +
571N LYS* 5.4 1.0 - - - +
575N GLN* 4.3 0.7 + - - -
144P ILE* 3.9 15.9 - - + -
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Residues in contact with ALA 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N LEU* 4.5 4.7 - - + +
97N THR 4.4 2.9 - - - +
98N PRO* 1.3 75.1 - - - +
100N ALA* 1.3 62.0 + - - +
458N ALA* 3.4 3.1 - - - -
513N ILE* 4.1 2.0 - - - -
514N LEU* 3.0 30.7 + - - +
574N LEU* 4.4 3.1 - - + +
575N GLN* 2.9 37.7 - - + +
578N VAL* 3.7 26.2 - - + +
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Residues in contact with ALA 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N ALA* 1.3 72.9 - - - +
101N HIS* 1.3 69.1 + - - +
102N ILE* 3.0 6.1 + - - -
105N VAL* 4.4 7.3 - - + +
112N ILE* 5.2 2.5 - - + -
128N TYR* 3.1 34.3 - - + +
458N ALA* 3.7 3.2 - - - +
512N MET 3.7 13.2 - - - +
513N ILE* 4.0 7.0 - - + -
514N LEU* 4.1 6.1 - - - +
575N GLN* 3.4 21.2 - - - +
578N VAL* 5.2 4.3 - - - +
579N ASP* 4.5 2.8 - - - +
582N LEU* 4.9 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