Contacts of the strand formed by residues 94 - 100 (chain D) 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 GLU 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ARG* 2.6 40.9 + - - -
25D GLU* 3.7 24.3 + - - +
92D HIS* 3.3 23.5 + - - -
93D ILE* 1.3 68.8 - - - +
95D LEU* 1.3 66.9 + - - +
515D GLU 3.9 7.0 - - - +
516D ALA* 4.1 8.8 - - - +
551D ASN* 3.2 13.2 + - - -
555D LYS* 5.2 6.6 + - - +
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Residues in contact with LEU 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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93D ILE* 2.9 32.3 + - + +
94D GLU* 1.3 78.1 - - - +
96D ALA* 1.3 67.8 + - - +
97D THR 4.2 16.2 - - - +
98D PRO* 5.5 0.3 - - - +
99D ALA* 4.9 3.8 - - + -
514D LEU* 4.3 11.4 - - + +
515D GLU* 3.2 29.3 + - - +
516D ALA 3.5 0.2 - - - +
517D VAL* 3.2 41.1 - - + +
547D LEU* 5.1 5.8 - - + -
551D ASN* 3.4 14.4 - - - +
574D LEU* 5.5 4.5 - - + -
578D VAL* 4.3 24.2 - - + -
144F ILE* 5.3 2.4 - - - +
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Residues in contact with ALA 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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94D GLU 3.9 0.6 + - - -
95D LEU* 1.3 75.6 - - - +
97D THR* 1.3 62.9 + - - +
98D PRO* 4.1 1.0 - - - +
551D ASN* 2.9 12.2 + - - +
554D LEU* 3.0 42.4 - - + -
555D LYS* 3.9 16.8 - - + +
558D LEU* 5.2 2.2 - - + -
144F ILE* 3.1 33.0 - - - +
145F PRO* 5.6 6.7 - - + +
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Residues in contact with THR 97 (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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95D LEU* 4.2 11.0 - - - +
96D ALA* 1.3 82.5 - - - +
98D PRO* 1.3 84.2 - - + +
99D ALA* 5.0 0.5 - - - +
456D MET 5.8 0.2 - - - +
457D GLY* 5.9 2.2 - - - -
458D ALA 5.6 1.1 - - - +
459D GLU* 4.5 21.5 - - + +
554D LEU* 4.6 5.2 - - - +
558D LEU* 5.5 2.4 - - - +
571D LYS* 3.4 44.8 - - + +
574D LEU* 4.2 12.5 - - - +
144F ILE* 4.9 2.1 - - - +
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Residues in contact with PRO 98 (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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95D LEU* 5.0 2.2 - - + +
96D ALA 4.1 4.5 - - - +
97D THR* 1.3 104.4 - - + +
99D ALA* 1.3 62.2 + - - +
458D ALA* 3.8 14.7 + - + +
459D GLU* 5.1 6.5 - - + -
462D GLN* 3.1 32.5 - - - +
513D ILE* 4.0 10.8 - - + -
514D LEU 3.2 19.3 - - - +
515D GLU* 4.2 17.0 - - + +
571D LYS* 5.6 1.2 - - - +
575D GLN* 4.2 3.8 + - - -
144F ILE* 4.7 14.8 - - + -
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Residues in contact with ALA 99 (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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95D LEU* 4.9 3.3 - - + +
97D THR 5.0 0.7 - - - +
98D PRO* 1.3 76.2 - - - +
100D ALA* 1.3 59.9 + - - +
458D ALA* 3.8 6.3 - - - -
514D LEU* 3.0 33.3 + - - +
574D LEU* 6.0 0.7 - - + -
575D GLN* 3.1 35.0 - - - +
578D VAL* 3.6 31.0 - - + -
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Residues in contact with ALA 100 (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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99D ALA* 1.3 74.5 - - - +
101D HIS* 1.3 60.7 + - - +
102D ILE* 2.9 12.3 + - - +
104D PHE* 6.1 0.4 - - + -
105D VAL* 4.3 8.9 - - + +
112D ILE* 5.3 4.3 - - + -
128D TYR* 3.8 31.2 - - + +
458D ALA* 4.0 4.7 - - + +
512D MET 3.7 14.8 - - - +
513D ILE* 4.3 12.8 - - + +
514D LEU* 4.8 2.0 - - - -
575D GLN* 4.1 13.3 + - - +
578D VAL* 4.9 1.7 - - - +
579D ASP* 4.9 1.4 - - - +
582D LEU* 4.5 4.5 - - - +
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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