Contacts of the strand formed by residues 41 - 48 (chain E) in PDB entry 1OP8
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 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.6 14.4 - - + -
33E LEU 3.1 15.7 - - - +
34E SER* 4.5 10.3 - - - +
35E LEU* 4.0 3.8 - - - +
37E ASP 4.8 5.2 - - - +
40E THR* 1.3 81.5 - - - +
42E CYS* 1.3 71.3 + - - +
73E ILE* 5.4 7.4 - - + -
141E TRP* 4.6 11.7 - - + +
151E TRP* 3.7 50.0 - - + +
192E ASN* 4.7 6.5 + - - +
193E GLY* 3.1 42.1 + - - +
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Residues in contact with CYS 42 (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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32E LEU* 4.0 7.1 - - - +
33E LEU* 2.8 42.9 + - + +
35E LEU* 3.7 13.2 - - + +
41E ILE* 1.3 79.5 - - - +
43E ALA* 1.3 61.0 + - - +
57E HIS* 5.1 1.3 - - - -
58E CYS* 2.0 54.7 - - + -
141E TRP* 5.1 1.0 - - - -
193E GLY 3.3 13.0 - - - +
195E SER* 3.4 11.0 - - - +
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Residues in contact with ALA 43 (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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30E MET* 4.1 11.2 - - + -
31E VAL 3.3 10.5 - - - +
33E LEU* 3.6 5.2 - - - +
42E CYS* 1.3 75.3 - - - +
44E GLY* 1.3 55.1 + - - +
54E THR* 2.7 27.0 + - - -
139E ALA 4.7 1.6 - - - +
140E GLY* 5.0 0.9 - - - -
141E TRP* 4.8 7.0 - - + -
193E GLY 3.5 6.0 + - - +
194E ASP* 3.9 5.2 - - - +
195E SER 2.8 6.9 + - - -
196E GLY* 3.0 10.5 - - - -
197E SER* 3.5 29.6 - - - +
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Residues in contact with GLY 44 (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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30E MET* 3.9 4.3 - - - +
31E VAL* 2.9 35.8 + - - -
33E LEU* 4.8 0.9 - - - -
43E ALA* 1.3 76.8 - - - +
45E ALA* 1.3 60.5 + - - -
52E VAL* 4.3 5.4 - - - -
53E LEU 3.3 12.8 - - - -
54E THR* 4.3 1.8 - - - -
196E GLY 3.5 4.7 + - - -
197E SER 4.2 0.2 - - - +
198E PRO* 3.5 14.8 - - - +
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Residues in contact with ALA 45 (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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29E TYR* 3.6 6.7 - - + +
31E VAL* 3.6 4.9 - - - +
44E GLY* 1.3 75.4 - - - +
46E LEU* 1.3 59.5 + - - +
47E ILE* 3.3 7.6 + - + +
52E VAL* 3.3 2.7 - - - +
53E LEU 2.8 34.0 + - - +
121E LEU* 4.0 14.8 - - + -
196E GLY 5.4 0.2 - - - +
198E PRO* 3.7 29.4 - - + -
209E PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 46 (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 PRO 5.4 0.7 - - - +
29E TYR* 3.1 14.1 + - - +
31E VAL* 3.5 7.2 - - + +
45E ALA* 1.3 70.0 - - - +
47E ILE* 1.3 51.7 + - - +
48E ALA 3.0 23.8 - - - +
49E LYS 4.0 8.7 - - - +
51E TRP 3.5 9.9 - - - +
52E VAL* 3.9 15.9 - - + +
68E LEU* 4.4 15.0 - - + -
108E LEU* 4.7 1.6 - - + -
112E ALA* 4.4 5.4 - - + -
114E ILE* 4.2 5.4 - - + -
118E VAL* 3.7 26.7 - - + -
119E THR 3.5 18.1 - - - +
120E ILE* 3.3 22.7 - - + -
121E LEU* 2.6 33.5 + - - +
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Residues in contact with ILE 47 (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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45E ALA* 3.3 10.5 + - + +
46E LEU* 1.3 74.1 - - - +
48E ALA* 1.3 63.5 + - + +
51E TRP* 3.0 20.1 + - + +
53E LEU* 4.0 9.9 - - + +
105E LEU* 3.5 30.3 - - + -
120E ILE* 3.2 15.4 - - - +
121E LEU 3.5 18.9 - - - +
122E HIS* 5.9 0.2 - - - -
123E LEU* 3.8 24.5 - - + +
209E PHE* 3.9 17.5 - - + -
238E ILE* 3.9 12.8 - - + -
242E ILE* 3.7 20.6 - - + +
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Residues in contact with ALA 48 (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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46E LEU* 3.0 21.3 - - - +
47E ILE* 1.3 82.1 - - + +
49E LYS* 1.3 67.8 + - - +
50E ASP* 3.1 2.5 + - - +
51E TRP* 3.2 37.0 + - + -
120E ILE* 3.3 13.4 - - - +
242E ILE* 5.2 6.3 - - + -
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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