Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 2JYW
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 ASP 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU 4.1 0.9 - - - +
29A ARG* 4.6 0.5 - - - -
30A MET* 3.1 63.0 + - + +
72A TRP* 4.7 0.2 - - - -
74A LEU* 4.2 3.5 - - - +
77A ASP 5.1 0.9 - - - +
78A GLN* 1.3 76.3 - - - +
80A TYR* 1.3 93.8 + - - +
81A ARG 3.5 0.2 + - - -
107A HIS* 3.1 30.4 - - + +
108A VAL 3.7 0.9 + - - -
109A SER* 3.8 10.9 + - - -
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Residues in contact with TYR 80 (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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66A LEU* 6.3 2.0 - - + -
69A ILE* 3.0 35.8 - - + +
72A TRP* 3.5 7.9 - + + -
74A LEU* 3.3 37.2 - - + +
79A ASP* 1.3 79.8 + - - +
81A ARG* 1.3 58.0 + - - +
82A VAL* 3.3 12.6 + - + +
101A PHE* 5.2 9.6 - + + -
102A ILE* 5.8 0.7 - - + -
107A HIS* 3.2 39.8 + + - -
108A VAL* 3.5 31.4 - - + -
109A SER 3.0 29.5 + - - +
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Residues in contact with ARG 81 (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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26A GLU 3.9 0.5 - - - +
27A VAL* 3.1 3.4 - - - -
28A GLU* 2.6 61.5 + - + +
30A MET* 3.6 31.1 - - + +
35A TRP* 3.7 42.3 - - - -
79A ASP* 3.5 2.5 + - - -
80A TYR* 1.3 69.4 - - - +
82A VAL* 1.3 60.5 + - - +
109A SER* 3.8 10.9 - - - +
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Residues in contact with VAL 82 (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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25A TYR* 4.1 3.4 - - + -
26A GLU 3.6 1.1 - - - -
27A VAL* 3.2 27.6 - - + -
65A PHE* 3.0 47.8 - - + -
69A ILE* 4.0 3.4 - - + -
80A TYR* 3.7 19.1 - - + -
81A ARG* 1.3 76.0 - - - +
83A THR* 1.3 62.7 + - - +
108A VAL* 4.3 0.7 - - + -
109A SER 3.2 5.6 + - - +
110A LEU* 2.9 57.4 - - + +
111A CYS 3.2 1.0 + - - -
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Residues in contact with THR 83 (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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25A TYR* 3.2 4.3 - - - +
26A GLU* 2.6 53.9 + - + +
82A VAL* 1.3 76.6 + - - +
84A CYS* 1.3 59.9 + - - +
85A PHE* 2.9 38.4 - - + -
111A CYS* 3.4 27.5 - - - +
113A LYS* 5.9 0.2 - - - +
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Residues in contact with CYS 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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23A LEU* 4.5 1.8 - - - -
24A CYS 3.6 9.9 - - - -
25A TYR* 4.1 6.3 - - + +
61A ALA* 3.8 23.6 - - - -
62A GLU* 5.1 0.7 - - - -
65A PHE* 4.7 9.2 - - + -
83A THR* 1.3 74.3 - - - +
85A PHE* 1.3 70.0 + - - +
86A THR* 2.9 29.8 - - - -
110A LEU* 6.0 0.6 - - + +
111A CYS 3.0 9.9 + - - +
112A ILE* 3.6 29.3 - - + +
113A LYS* 2.9 29.6 + - - +
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Residues in contact with PHE 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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9A PHE* 5.3 4.4 - - - -
22A TYR 5.0 0.2 - - - +
23A LEU* 3.9 1.6 - - - -
24A CYS* 2.6 60.9 + - + +
25A TYR* 3.5 24.2 - - - -
26A GLU* 3.5 25.1 - - + -
43A GLY* 4.6 2.2 - - - -
83A THR* 2.9 31.2 - - + -
84A CYS* 1.3 74.5 - - - +
86A THR* 1.3 59.9 + - - +
113A LYS* 3.4 52.0 - - + +
141A MET* 4.6 8.1 - - - -
149A CYS* 4.7 8.7 - - - -
152A THR* 4.1 19.1 - - + -
153A PHE* 5.5 2.9 - - + -
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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