Contacts of the strand formed by residues 81 - 89 (chain R) in PDB entry 4N3E
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 81 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R PHE* 3.4 5.9 - - - -
74R GLU* 2.5 43.1 + - + -
75R ILE* 3.7 1.0 - - - -
76R ASP* 3.1 50.9 + - + +
79R ASN* 4.6 4.0 - - + +
80R PHE* 1.3 76.5 - - - +
82R CYS* 1.3 63.0 + - - +
83R LYS* 3.9 17.8 - - + +
102R GLU* 3.8 31.2 + - + -
103R VAL 3.2 15.3 - - - -
104R LYS* 3.7 28.0 - - + -
115R LYS* 4.9 0.9 - - - -
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Residues in contact with CYS 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R PHE* 4.0 6.4 - - + -
24R VAL* 3.4 37.7 - - + -
72R PHE* 4.4 2.7 - - - -
74R GLU 3.3 3.8 - - - -
75R ILE* 3.6 28.3 - - - -
81R TYR* 1.3 79.6 - - - +
83R LYS* 1.3 65.9 + - - +
84R TYR* 3.8 22.4 - - + -
101R TYR 4.5 0.4 - - - -
102R GLU* 3.3 4.2 - - - +
103R VAL* 2.7 40.3 + - + +
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Residues in contact with LYS 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q LYS* 3.1 29.9 - - - +
72R PHE* 4.0 0.7 - - - -
73R ASP* 3.0 34.6 + - + +
74R GLU* 2.8 43.3 + - + +
81R TYR* 3.9 11.0 - - - +
82R CYS* 1.3 72.7 - - - +
84R TYR* 1.3 61.1 + - - +
100R VAL* 4.7 17.3 - - + -
101R TYR 3.3 10.5 - - - +
102R GLU* 3.7 29.8 - - + -
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Residues in contact with TYR 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R LEU 5.0 0.2 - - - -
24R VAL* 4.7 10.3 - - + -
27R ARG* 4.0 24.7 + - - -
70R HIS* 3.8 29.2 - + + -
71R LYS 3.3 13.9 - - - +
72R PHE* 3.7 23.1 - + + -
73R ASP* 3.4 1.3 - - - -
82R CYS* 3.8 20.9 - - + -
83R LYS* 1.3 73.5 - - - +
85R THR* 1.3 62.1 + - - +
100R VAL* 3.5 2.3 - - - +
101R TYR* 2.6 74.1 + + + +
103R VAL* 4.2 15.9 - - + -
201R 2AN 3.2 29.5 - + - -
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Residues in contact with THR 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R HIS* 3.3 8.2 - - - -
71R LYS* 2.9 35.6 + - - -
73R ASP* 2.9 21.9 + - - -
83R LYS* 6.0 0.3 - - - +
84R TYR* 1.3 76.4 + - - +
86R LEU* 1.3 72.8 + - - +
87R PHE* 3.3 13.4 + - + +
98R LYS* 3.8 21.9 + - + +
99R VAL 3.4 11.9 - - - +
100R VAL* 3.2 26.1 - - + +
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Residues in contact with LEU 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R MET* 3.8 31.2 - - + -
69R LEU 3.9 8.1 - - - +
70R HIS* 3.6 26.6 - - + +
85R THR* 1.3 69.1 - - - +
87R PHE* 1.3 58.9 + - - +
88R GLU 4.1 7.0 - - - +
91R VAL* 4.0 17.5 - - + -
92R LEU* 3.6 23.1 - - + +
98R LYS* 3.2 10.9 - - - +
99R VAL* 2.8 46.3 + - + +
101R TYR* 4.2 16.1 - - + +
202R 2AN 4.2 13.9 - - + -
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Residues in contact with PHE 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R VAL* 4.0 14.6 - - + -
69R LEU* 3.5 26.6 + - + -
70R HIS 3.6 23.6 - - - -
71R LYS* 3.6 27.1 - - + -
85R THR* 3.3 22.5 + - + +
86R LEU* 1.3 76.0 - - - +
88R GLU* 1.3 78.1 + - + +
92R LEU* 3.9 13.2 - - - +
97R GLU 4.2 4.7 - - - +
98R LYS* 4.5 8.5 - - + -
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Residues in contact with GLU 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R TYR* 3.0 27.9 + - + +
68R MET* 3.3 4.0 - - - +
69R LEU* 2.9 55.4 + - + +
86R LEU* 3.8 3.6 - - - +
87R PHE* 1.3 99.2 - - + +
89R GLY* 1.3 63.0 - - - +
92R LEU* 4.2 8.7 - - - +
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Residues in contact with GLY 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R TYR* 3.3 27.4 - - - -
68R MET* 4.1 1.8 - - - -
88R GLU* 1.3 83.9 - - - +
90R ASP* 1.3 62.0 + - - -
91R VAL* 3.1 8.6 + - - -
92R LEU* 3.2 24.6 + - - +
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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