Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 3NUS
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 PHE 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LYS* 4.0 13.9 - - + -
78A ARG 3.4 21.3 - - - -
79A PRO* 3.0 16.5 + - + +
80A GLU* 3.1 4.7 - - - +
81A ASP* 1.3 86.1 - - + +
83A LYS* 1.3 60.1 + - - +
84A PHE* 3.8 19.8 + + + -
99A ALA* 4.2 9.4 - - + -
100A ARG 3.5 2.9 - - - +
101A GLU* 3.6 40.6 - - + -
102A LEU* 4.4 6.5 - - - +
108A TYR* 4.1 7.6 - + - -
110A ILE* 4.0 18.4 - - + -
147A PHE* 3.4 32.1 - + - -
149A PHE* 3.7 24.0 - + - -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PHE* 1.3 70.7 - - - +
84A PHE* 1.3 69.5 + - - +
85A GLY 3.8 0.2 + - - -
99A ALA* 3.4 1.5 - - - -
100A ARG* 2.9 59.6 + - + +
102A LEU* 4.1 18.0 - - + +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO* 3.6 33.9 - - + -
82A PHE* 3.8 19.0 + + + -
83A LYS* 1.3 83.6 - - - +
85A GLY* 1.3 59.9 + - - +
97A VAL* 4.0 21.1 - - + -
98A LEU 3.8 1.3 - - - -
99A ALA* 3.7 19.7 - - + -
110A ILE* 3.9 19.1 - - + -
112A ILE* 4.2 18.2 - - + -
149A PHE* 5.3 0.2 - + - -
156A TYR* 4.4 17.9 - + - -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 3.8 1.0 + - - -
84A PHE* 1.3 75.3 - - - +
86A LYS* 1.3 66.8 + - - -
87A ILE* 3.7 1.7 + - - +
97A VAL* 3.2 11.4 - - - +
98A LEU* 2.8 17.6 + - - -
99A ALA* 4.5 0.2 - - - +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY* 1.3 72.8 - - - +
87A ILE* 1.3 65.0 + - - +
88A LEU* 4.0 21.9 - - + +
97A VAL* 3.5 0.7 - - - +
98A LEU* 2.9 53.1 + - + +
161A TYR* 4.3 10.0 + - - -
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY 5.1 1.3 - - - +
86A LYS* 1.3 82.3 - - - +
88A LEU* 1.3 62.6 + - - +
89A GLY* 3.7 8.3 - - - +
90A GLU* 3.7 38.8 - - + +
95A THR* 3.9 20.0 - - + -
96A VAL 3.5 7.6 - - - +
97A VAL* 4.3 10.8 - - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 4.0 24.2 - - + +
87A ILE* 1.3 73.5 - - - +
89A GLY* 1.3 55.0 + - - +
96A VAL* 2.6 20.8 + - + +
98A LEU* 3.6 37.7 - - + +
109A ALA* 3.5 32.1 - - + -
161A TYR* 3.9 21.3 - - + -
374A JNZ 3.9 31.2 + - + +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.6 3.1 - - - +
88A LEU* 1.3 82.5 - - - +
90A GLU* 1.3 62.8 + - - -
95A THR* 3.4 6.1 - - - +
96A VAL* 2.7 40.8 + - - +
374A JNZ 5.2 4.5 - - - -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.7 30.5 - - + +
89A GLY* 1.3 79.3 - - - +
91A GLY* 1.3 62.8 + - - +
94A SER 3.8 4.3 - - - +
95A THR* 4.1 10.5 + - + +
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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