Contacts of the strand formed by residues 21 - 30 (chain E) in PDB entry 4LML
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 ILE 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E GLY* 1.3 81.4 - - - +
22E TYR* 1.3 63.8 + - - +
23E LEU* 4.0 6.3 - - + -
40E ALA* 4.0 17.5 - - + -
41E PHE 3.3 8.3 - - - +
42E LEU* 4.0 9.6 - - + -
43E SER* 5.5 0.2 - - - -
77E PHE* 4.1 9.9 - - + -
105E PHE* 4.4 5.2 - - + -
127E ILE* 4.1 14.8 - - + -
129E LEU* 3.6 28.9 - - + -
146E GLU 3.0 14.0 + - - +
147E LYS* 3.8 6.4 - - - +
149E GLY 4.9 0.3 + - - -
164E PHE* 3.4 36.3 - - + -
185E TYR* 3.7 30.2 - - + -
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Residues in contact with TYR 22 (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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173D PHE* 5.9 1.4 - - - -
175D LEU* 3.2 46.3 - - + +
176D GLU* 3.4 33.6 + - + +
21E ILE* 1.3 73.6 - - - +
23E LEU* 1.3 78.5 + - - +
24E ILE* 3.3 14.0 + - + +
40E ALA* 3.0 4.5 - - - +
41E PHE* 2.9 48.8 + + + -
43E SER* 5.5 0.2 + - - -
146E GLU 4.3 1.3 - - - +
149E GLY* 2.8 43.5 + - - -
150E LYS* 3.5 2.2 - - - +
151E ASN* 3.6 21.8 + - + -
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Residues in contact with LEU 23 (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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21E ILE* 4.0 9.8 + - + -
22E TYR* 1.3 74.8 - - - +
24E ILE* 1.3 60.8 + - - +
26E CYS* 3.8 24.2 - - - -
38E VAL* 3.4 28.7 - - + -
39E ASN 4.3 0.4 - - - +
40E ALA* 3.7 2.9 - - + -
127E ILE* 5.1 3.4 - - + -
150E LYS* 3.1 40.7 - - + +
151E ASN 3.3 4.0 + - - -
154E VAL* 4.1 6.3 - - + +
161E ILE* 6.2 2.2 - - + -
164E PHE* 3.9 50.6 - - + -
187E LEU* 4.1 15.5 - - + -
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Residues in contact with ILE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 4.8 1.6 - - - +
78D VAL* 4.0 27.4 - - + +
130D ILE* 5.9 3.6 - - + -
175D LEU* 6.1 1.1 - - + -
22E TYR* 3.3 17.2 + - + +
23E LEU* 1.3 76.8 - - - +
25E GLU* 1.3 69.7 + - + +
39E ASN 2.9 9.4 + - - +
40E ALA 4.1 11.4 - - - -
41E PHE* 3.9 29.4 - - + -
104E ARG* 3.4 47.3 - - - +
151E ASN* 4.4 14.8 + - - +
154E VAL* 3.3 18.7 + - - +
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Residues in contact with GLU 25 (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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78D VAL* 3.6 23.2 - - - +
79D ASN* 3.1 31.5 + - - +
80D VAL 3.8 13.5 - - - +
110D LEU* 3.9 19.7 - - + +
24E ILE* 1.3 84.9 + - + +
26E CYS* 1.3 66.1 + - - +
27E TYR* 3.9 13.7 - - + -
38E VAL* 3.6 3.5 - - - +
39E ASN* 2.7 54.2 + - + +
154E VAL* 5.0 2.8 - - - -
155E PHE* 5.5 4.3 + - - +
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Residues in contact with CYS 26 (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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110D LEU* 4.7 1.2 - - - +
23E LEU* 3.8 30.1 - - - -
24E ILE 4.3 0.6 + - - -
25E GLU* 1.3 81.8 + - - +
27E TYR* 1.3 68.0 + - - +
36E PHE* 4.9 8.5 - - - -
37E LYS 3.4 11.4 - - - +
38E VAL* 4.1 12.6 - - - -
154E VAL* 4.7 14.6 - - + +
155E PHE* 4.4 6.3 + - - +
156E LEU* 3.6 35.3 + - + +
161E ILE* 5.2 2.9 - - + -
187E LEU* 4.3 12.1 - - + -
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Residues in contact with TYR 27 (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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81D GLU* 2.9 71.6 + - - +
82D ASN* 4.4 4.7 + - - -
110D LEU* 3.6 24.0 - - + -
25E GLU* 3.9 22.7 - - + -
26E CYS* 1.3 85.4 - - - +
28E SER* 1.3 70.8 + - - +
29E LEU 3.5 2.0 + - - -
36E PHE* 4.1 0.7 - - - +
37E LYS* 2.8 69.1 + - + +
38E VAL 4.6 3.6 + - - -
39E ASN* 4.4 7.5 - - + +
106E SER* 5.0 1.2 - - - -
107E ALA 5.6 0.2 + - - -
156E LEU* 3.7 15.5 - - - +
157E THR 5.6 0.4 - - - +
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Residues in contact with SER 28 (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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33D ALA* 6.0 2.4 - - - +
81D GLU* 4.4 6.1 + - - -
27E TYR* 1.3 94.0 - - - +
29E LEU* 1.3 63.0 + - - +
30E ASP* 3.5 4.4 + - - +
35E THR* 3.6 1.9 + - - +
36E PHE* 3.3 13.3 - - - -
37E LYS* 3.8 17.8 + - - +
108E ARG* 5.6 1.6 + - - -
156E LEU* 4.3 1.6 - - - +
157E THR* 5.3 6.8 + - - -
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Residues in contact with LEU 29 (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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27E TYR 3.5 1.4 - - - -
28E SER* 1.3 74.5 - - - +
30E ASP* 1.3 69.7 + - - +
31E ASP* 3.7 15.0 + - - +
35E THR 3.4 5.6 - - - +
36E PHE* 3.7 12.3 - - + -
113E LEU* 4.4 12.8 - - + -
125E LEU* 3.8 20.0 - - + -
156E LEU* 4.1 15.1 - - + +
159E TRP* 3.6 38.9 + - + +
189E ILE* 3.4 33.2 - - + -
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Residues in contact with ASP 30 (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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28E SER 3.5 3.3 + - - +
29E LEU* 1.3 73.8 - - - +
31E ASP* 1.3 60.6 + - - +
32E LYS* 3.1 22.0 + - - +
33E ALA* 3.1 26.8 + - + +
34E GLU* 2.8 28.8 + - - -
35E THR* 2.5 21.3 + - - +
108E ARG* 4.8 5.4 + - - +
113E LEU* 3.9 3.3 - - - +
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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