Contacts of the strand formed by residues 91 - 99 (chain E) in PDB entry 3AB0
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 ALA 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.8 31.4 - - + +
39E GLN 3.2 24.0 - - - +
40E THR* 3.9 2.9 - - - +
41E PRO* 4.4 2.7 - - - -
89E ASP 3.3 1.6 + - - -
90E THR* 1.3 79.9 - - - +
92E MET* 1.3 61.1 + - - +
93E TYR* 3.3 12.3 - - + -
111E THR* 5.4 1.3 - - - -
112E VAL 2.8 30.5 + - - +
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Residues in contact with MET 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ARG* 3.6 0.7 - - - -
39E GLN* 2.9 36.6 + - + +
91E ALA* 1.3 71.8 - - - +
93E TYR* 1.3 61.1 + - - +
94E TYR* 3.6 28.2 + - + -
108E ALA 4.4 5.2 - - - +
109E GLY* 3.4 29.4 - - - +
110E THR 3.4 17.9 - - - +
111E THR* 3.9 24.0 - - + +
41F GLY 5.3 3.4 - - - +
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Residues in contact with TYR 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLU* 4.0 2.4 - - - +
20E LEU* 3.7 20.9 - - + -
36E TRP* 4.0 6.4 - + + -
37E VAL 3.6 3.6 - - - -
38E ARG* 2.8 32.9 + - + +
48E VAL* 4.0 23.8 - - + -
67E PHE* 3.8 24.1 - + - -
80E LEU* 3.9 17.3 - - + -
82E MET* 3.9 9.3 - - - -
89E ASP* 3.4 25.9 + - - +
91E ALA* 3.3 26.0 - - + -
92E MET* 1.3 71.2 - - - +
94E TYR* 1.3 63.4 + - - +
95E CYS 3.9 1.2 + - - -
109E GLY* 3.6 1.4 - - - -
110E THR* 2.8 37.9 + - - +
112E VAL* 3.7 18.4 - - + -
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Residues in contact with TYR 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLU* 3.6 0.9 - - - -
36E TRP* 3.5 7.8 - - - -
37E VAL* 2.6 41.5 + - - +
39E GLN* 3.4 33.3 + - + -
45E LEU* 4.7 1.8 - - + -
92E MET* 3.9 25.6 - - + -
93E TYR* 1.3 73.4 - - - +
95E CYS* 1.3 61.5 + - - +
96E ALA* 4.7 0.6 - - - +
106E TRP* 3.6 34.3 - + + -
107E GLY 3.1 23.8 - - - -
108E ALA 3.3 22.1 + - - -
109E GLY* 3.8 7.0 - - - -
41F GLY 3.1 24.8 + - - -
42F SER 3.6 7.1 + - - -
43F SER* 4.1 2.9 - - - -
44F PRO* 4.0 16.2 - - + -
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Residues in contact with CYS 95 (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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4E LEU* 3.4 13.7 - - + +
6E GLU* 2.9 23.9 + - + +
22E CYS* 2.0 53.4 - - + -
34E MET* 4.0 5.8 - - - -
35E SER 3.8 3.1 - - - -
36E TRP* 3.9 8.1 - - + -
78E LEU* 3.8 16.2 - - - -
94E TYR* 1.3 74.6 - - - +
96E ALA* 1.3 62.8 + - - +
106E TRP* 3.6 2.3 - - - +
107E GLY 2.8 25.8 + - - -
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Residues in contact with ALA 96 (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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4E LEU* 4.0 4.5 - - - -
34E MET* 3.4 9.5 - - - +
35E SER* 2.8 46.0 + - - +
37E VAL* 4.6 10.1 - - + -
94E TYR 4.7 0.7 - - - +
95E CYS* 1.3 78.4 - - - +
97E ARG* 1.3 60.2 + - - +
103E PHE* 3.7 34.5 - - + -
105E VAL 3.5 4.9 - - - +
106E TRP* 5.0 6.7 - - + -
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Residues in contact with ARG 97 (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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2E VAL* 4.2 12.1 - - - +
4E LEU* 4.0 3.5 - - + +
27E PHE* 3.6 47.0 - - + +
32E TYR* 3.6 45.6 + - - -
34E MET* 3.6 21.3 - - + -
96E ALA* 1.3 74.0 - - - +
98E ASN* 1.3 59.4 + - - +
99E ARG* 4.5 4.9 - - - +
103E PHE* 3.4 15.6 - - - -
104E ASP* 2.7 54.3 + - - +
105E VAL* 3.1 34.4 + - + +
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Residues in contact with ASN 98 (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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121D LEU* 4.8 1.9 - - - +
122D ASP* 4.2 6.0 - - - +
32E TYR* 3.4 27.4 - - - +
33E ALA* 2.8 38.8 + - + +
34E MET 3.5 0.2 - - - -
35E SER* 2.7 48.1 + - - +
50E SER* 4.4 0.9 + - - -
96E ALA 3.6 0.8 + - - -
97E ARG* 1.3 76.0 - - - +
99E ARG* 1.3 60.9 + - - +
100E GLY 3.0 21.5 - - - +
101E TRP* 4.0 8.3 - - - -
102E TYR 4.0 2.5 - - - -
103E PHE* 3.5 15.2 - - - -
104E ASP* 4.4 0.4 - - - -
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Residues in contact with ARG 99 (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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95D ILE* 4.6 18.2 - - - +
122D ASP* 3.8 2.5 - - - -
124D ASP* 5.3 16.1 + - - +
32E TYR* 3.4 35.7 + - + -
97E ARG* 3.9 3.8 + - - +
98E ASN* 1.3 77.4 - - - +
100E GLY* 1.3 58.4 + - - +
102E TYR* 2.9 48.2 + - + +
104E ASP* 3.5 28.1 + - - +
50F ARG* 5.0 5.1 + - - -
91F TYR* 4.6 1.9 + - - -
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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