Contacts of the strand formed by residues 99 - 110 (chain E) in PDB entry 5J0Z
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 THR 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E SER* 4.4 8.7 - - - +
47E TRP* 3.4 14.6 - - - +
48E LYS* 4.1 15.7 - - + +
93E SER 4.0 0.2 - - - +
94E VAL* 3.5 1.4 - - - -
95E SER* 2.7 49.1 + - - +
97E ASP* 2.6 27.2 + - - -
98E GLY* 1.3 77.0 - - - +
100E VAL* 1.3 67.5 + - - +
101E GLN* 5.8 1.8 - - + -
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Residues in contact with VAL 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E SER* 3.0 29.7 + - - -
47E TRP* 2.7 58.0 + - + +
49E ASP* 4.3 0.7 - - + -
52E LEU* 3.9 24.5 - - + -
71E ILE* 3.6 22.2 - - + -
92E ILE* 3.7 17.5 - - + -
93E SER 3.5 5.4 - - - +
94E VAL* 4.2 6.1 - - + +
98E GLY 4.1 5.4 - - - +
99E THR* 1.3 76.6 - - - +
101E GLN* 1.3 66.3 + - - +
102E TYR 4.0 0.4 - - - -
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 5.6 1.4 - - - +
179A ARG* 6.3 0.7 - - - +
45E LEU 3.8 1.2 + - - -
46E SER* 3.0 28.8 + - - +
91E ASP* 3.5 3.1 - - - +
92E ILE* 3.3 4.7 - - - -
93E SER* 2.7 49.2 + - - +
95E SER* 5.1 9.4 - - - +
99E THR* 5.8 2.5 - - + -
100E VAL* 1.3 78.2 - - - +
102E TYR* 1.3 59.4 + - - +
103E LEU* 5.5 0.4 - - - +
145E ASP* 5.4 1.0 + - - -
148E LYS* 3.7 28.1 + - - +
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU 4.5 0.9 - - - -
44E SER* 3.4 5.0 - - - -
45E LEU* 2.8 66.1 + - + +
47E TRP* 3.6 24.0 - + + -
68E PRO* 5.7 0.4 - - + -
73E ILE* 4.0 34.1 - - + -
85E ARG* 5.2 1.8 + - - -
89E VAL* 3.9 30.1 - - + +
91E ASP 3.7 2.0 - - - -
92E ILE* 3.9 17.9 - - + +
100E VAL* 4.0 1.4 - - + -
101E GLN* 1.3 73.5 - - - +
103E LEU* 1.3 63.8 + - - +
104E GLU* 3.0 48.4 + - + +
148E LYS* 5.4 2.1 + - - -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ARG* 3.8 28.5 - - - +
177A GLU* 4.0 10.3 - - - +
42E PHE* 3.9 29.8 - - + -
43E LEU 3.6 7.0 - - - +
44E SER* 3.6 26.9 - - - -
89E VAL* 3.8 3.3 - - - +
90E VAL* 2.7 56.9 + - + +
91E ASP* 2.9 22.7 + - + +
101E GLN 5.5 0.2 - - - +
102E TYR* 1.3 79.6 - - - +
104E GLU* 1.3 57.1 + - - +
148E LYS* 5.5 2.2 - - - +
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PHE* 3.3 7.4 - - - +
43E LEU* 2.8 61.7 + - + +
85E ARG* 2.6 45.6 + - - -
87E ALA* 3.4 17.5 - - + +
88E ASP 3.2 17.9 - - - +
89E VAL* 4.3 0.8 - - - +
90E VAL* 3.7 3.8 - - - -
102E TYR* 3.0 33.5 + - + +
103E LEU* 1.3 75.0 - - - +
105E ARG* 1.3 59.1 + - - +
106E PHE* 3.9 2.0 - - - +
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 4.2 21.2 - - - +
78A PHE 2.6 23.4 + - - +
79A VAL 2.8 28.5 + - - -
81A VAL* 4.5 4.8 + - - +
407A ACT 3.7 17.0 - - - +
25E ILE* 3.4 21.8 - - + +
40E ASN* 3.1 34.6 + - - +
41E ALA 3.5 11.7 - - - +
42E PHE* 3.6 24.9 - - + -
86E ASP 4.2 0.2 - - - +
87E ALA* 3.4 2.1 - - - -
88E ASP* 3.0 41.8 + - - +
90E VAL* 3.4 9.3 - - + +
104E GLU* 1.3 74.3 - - - +
106E PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 4.2 9.4 - - + -
39E VAL* 3.9 26.0 - - + -
40E ASN* 3.3 7.0 - - - +
41E ALA* 2.8 79.1 + - + +
42E PHE 4.1 2.0 - - - -
43E LEU* 3.9 24.2 - - + -
78E PHE* 3.2 44.2 - + - -
85E ARG* 3.7 20.6 - - + -
86E ASP 3.3 10.1 - - - +
87E ALA* 4.1 1.6 - - + -
104E GLU* 3.9 4.9 - - - +
105E ARG* 1.3 74.9 - - - +
107E SER* 1.3 67.2 + - - +
108E ALA* 4.0 7.6 - - + -
128E ILE* 5.3 2.7 - - + -
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU 3.8 15.2 + - - -
84A ALA* 5.4 5.0 + - - +
28E TYR* 4.5 4.3 - - - -
39E VAL 3.1 16.4 - - - -
40E ASN* 3.9 20.4 - - - -
83E ASN* 5.9 0.3 - - - +
86E ASP* 3.0 39.0 + - - +
106E PHE* 1.3 78.8 - - - +
108E ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LYS* 3.5 4.8 - - - +
39E VAL* 3.0 36.3 + - + +
78E PHE* 5.1 1.1 - - + -
81E VAL* 4.2 16.6 - - + -
83E ASN* 3.9 19.3 - - - +
85E ARG* 4.1 14.8 - - + -
106E PHE* 4.0 13.4 - - + -
107E SER* 1.3 75.5 - - - +
109E ARG* 1.3 61.6 + - - +
110E VAL* 3.7 1.4 + - + -
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Residues in contact with ARG 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ASP* 4.3 5.5 + - - +
34E ALA* 3.7 7.1 - - - +
36E THR* 3.4 39.8 + - - +
37E PHE 3.8 5.8 - - - +
38E LYS* 3.7 39.5 - - + +
81E VAL* 3.3 5.9 - - - +
82E GLU* 3.2 52.8 + - + +
83E ASN* 3.7 30.7 + - + +
108E ALA* 1.3 72.1 - - - +
110E VAL* 1.3 61.2 - - - +
402E SO4 3.1 36.5 + - - -
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Residues in contact with VAL 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E THR* 3.2 8.8 - - - -
37E PHE* 2.9 63.7 + - + +
39E VAL* 4.0 24.9 - - + -
80E ASN* 3.4 16.8 - - - +
81E VAL* 4.1 11.7 - - + -
82E GLU* 5.6 0.4 - - - -
106E PHE* 6.1 0.2 - - + -
108E ALA* 4.2 2.0 - - + +
109E ARG* 1.3 75.2 - - - +
111E LEU* 1.3 63.5 + - - +
112E SER 3.7 1.7 + - - +
127E HIS 3.3 26.9 - - - +
128E ILE* 4.4 12.1 - - + -
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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