Contacts of the strand formed by residues 83 - 92 (chain D) in PDB entry 3ZJX
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 VAL 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D GLU 4.5 1.8 - - - +
82D ASP* 1.3 71.3 - - - +
84D TYR* 1.3 70.8 + - - +
85D VAL* 3.4 8.6 + - + +
108D LYS 5.6 5.4 - - - +
109D ASN* 5.0 3.1 - - - +
182D TYR* 3.1 6.8 - - - -
183D LEU* 2.8 51.6 + - + +
185D LYS* 3.4 36.8 - - + +
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Residues in contact with TYR 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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82D ASP 3.6 4.4 + - - +
83D VAL* 1.3 77.3 - - - +
85D VAL* 1.3 61.5 + - - +
86D GLY* 3.7 18.6 - - - -
87D LYS* 3.1 35.9 + - + +
180D ILE* 3.9 33.0 - - + -
181D ALA 4.4 0.4 - - - -
182D TYR* 4.2 7.0 - - + -
1296D BOG 4.4 4.0 + - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 3.8 17.5 - - + +
84D TYR* 1.3 78.0 - - - +
86D GLY* 1.3 59.9 + - - +
105D PHE* 4.0 23.8 - - + -
107D CYS* 3.8 34.5 - - + -
181D ALA* 3.0 16.1 + - + +
182D TYR* 4.1 9.6 - - - -
183D LEU* 4.2 9.9 - - + +
252D LEU* 4.8 3.8 - - + -
1296D BOG 2.9 47.9 + - - +
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Residues in contact with GLY 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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84D TYR* 3.4 18.5 - - - -
85D VAL* 1.3 83.1 - - - +
87D LYS* 1.3 57.8 + - - -
180D ILE* 3.4 6.2 - - - +
181D ALA 2.8 29.0 + - - +
1296D BOG 3.3 19.7 - - - +
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Residues in contact with LYS 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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84D TYR* 3.1 19.7 + - - +
86D GLY* 1.3 72.3 - - - -
88D ALA* 1.3 66.9 + - - +
89D LEU* 6.3 1.8 - - + -
103D GLN* 4.6 4.2 + - - -
178D GLU* 3.2 32.5 + - + +
179D VAL 3.3 4.9 - - - +
180D ILE* 4.1 19.7 - - + -
1296D BOG 3.4 8.0 - - - +
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Residues in contact with ALA 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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87D LYS* 1.3 77.1 - - - +
89D LEU* 1.3 69.5 + - - +
90D LEU* 5.8 2.5 - - + -
102D SER* 5.7 1.8 - - - -
103D GLN* 3.8 24.2 - - - +
178D GLU* 3.4 6.5 - - - +
179D VAL* 2.7 41.8 + - + +
1296D BOG 3.7 20.2 - - + -
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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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87D LYS* 6.3 1.8 - - + -
88D ALA* 1.3 78.0 - - - +
90D LEU* 1.3 75.5 + - - +
91D THR* 4.3 3.4 - - - +
176D THR* 4.1 19.7 - - + -
177D VAL 3.3 13.5 - - - +
178D GLU* 3.7 26.7 - - + +
259D LEU* 4.1 8.3 - - + -
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Residues in contact with LEU 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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88D ALA* 5.6 2.7 - - + -
89D LEU* 1.3 82.1 - - - +
91D THR* 1.3 62.0 + - - +
92D ASN 4.1 0.2 + - - -
100D LEU* 3.9 31.9 - - + +
101D LYS 3.5 24.0 - - - +
102D SER* 4.2 13.0 - - - +
103D GLN* 5.9 0.9 - - - +
169D ILE* 3.4 43.5 - - + -
171D VAL* 4.5 5.9 - - + +
175D THR 4.0 1.7 - - - +
176D THR* 3.4 1.6 - - - -
177D VAL* 2.9 36.3 + - + +
179D VAL* 4.5 7.6 - - + -
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Residues in contact with THR 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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89D LEU* 5.0 4.0 - - - +
90D LEU* 1.3 72.0 + - - +
92D ASN* 1.3 61.7 + - - +
93D ASP* 3.4 35.4 + - - +
100D LEU* 3.6 19.6 - - - +
176D THR* 2.8 32.7 + - - +
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Residues in contact with ASN 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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91D THR* 1.3 72.5 - - - +
93D ASP* 1.3 58.0 + - - +
94D THR* 2.9 29.7 + - - +
96D GLN 3.1 18.1 + - - -
98D GLN* 3.3 19.1 - - - +
100D LEU* 3.8 8.0 - - + +
171D VAL* 2.9 33.2 + - + -
172D PRO 3.0 12.1 + - - +
173D ALA* 4.1 1.3 - - - -
174D ASN* 3.0 19.4 + - - -
175D THR 2.8 25.2 + - - +
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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