Contacts of the strand formed by residues 41 - 48 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F LEU* 4.6 14.4 - - + -
33F LEU 3.1 14.8 - - - +
34F SER* 4.4 10.5 - - - +
35F LEU* 4.0 3.0 - - - +
37F ASP 4.8 4.7 - - - +
40F THR* 1.3 81.4 - - - +
42F CYS* 1.3 70.9 + - - +
73F ILE* 5.3 6.7 - - + -
141F TRP* 4.4 11.7 - - + +
142F GLY* 5.0 0.4 - - - -
143F ARG* 5.9 1.3 - - - +
151F TRP* 3.6 53.8 - - + +
192F ASN 5.1 0.2 - - - +
193F GLY* 3.2 34.1 - - - +
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Residues in contact with CYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 4.2 7.3 - - - +
33F LEU* 2.8 41.9 + - + +
35F LEU* 3.8 13.9 - - + +
41F ILE* 1.3 78.5 - - - +
43F ALA* 1.3 60.6 + - - +
57F HIS* 5.1 1.3 - - - -
58F CYS* 2.0 54.1 - - + -
141F TRP* 5.3 1.0 - - - -
193F GLY* 3.3 12.3 - - - -
195F SER* 3.6 11.2 - - - +
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F MET* 4.1 10.5 - - + -
31F VAL 3.3 10.3 - - - +
33F LEU* 3.6 5.5 - - - +
42F CYS* 1.3 74.6 - - - +
44F GLY* 1.3 54.5 + - - +
54F THR* 2.7 28.1 + - - -
140F GLY* 4.8 6.3 - - - -
141F TRP* 5.1 3.8 - - + +
193F GLY 3.7 2.9 + - - +
194F ASP* 3.9 7.0 - - - +
195F SER 2.7 13.4 + - - +
196F GLY* 3.2 5.1 - - - -
197F SER* 3.5 30.3 - - - +
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Residues in contact with GLY 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F MET* 3.9 4.0 - - - +
31F VAL* 3.0 36.8 + - - +
33F LEU* 4.8 0.4 - - - -
43F ALA* 1.3 78.0 - - - +
45F ALA* 1.3 60.2 + - - -
52F VAL* 4.3 5.2 - - - -
53F LEU 3.3 12.8 - - - -
54F THR* 4.3 2.0 - - - -
196F GLY 3.5 4.7 - - - -
198F PRO* 3.5 15.2 - - - +
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR 3.6 6.7 - - - +
31F VAL* 3.6 5.5 - - - +
44F GLY* 1.3 75.2 - - - +
46F LEU* 1.3 59.3 + - - +
47F ILE* 3.2 7.0 + - + +
52F VAL* 3.3 3.0 - - - +
53F LEU* 2.9 34.4 + - + +
121F LEU* 3.9 15.9 - - + -
196F GLY 5.4 0.2 - - - +
198F PRO* 3.7 28.7 - - + -
209F PHE* 4.3 12.3 - - + -
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PRO 5.4 1.1 - - - +
29F TYR* 3.1 14.5 + - - +
31F VAL* 3.5 7.0 - - + +
45F ALA* 1.3 70.7 - - - +
47F ILE* 1.3 51.6 + - - +
48F ALA 3.1 26.5 - - - +
49F LYS 4.0 9.0 - - - +
51F TRP 3.5 8.5 - - - +
52F VAL* 3.9 16.4 - - + +
68F LEU* 4.3 17.3 - - + -
108F LEU* 4.4 1.8 - - + -
112F ALA* 4.1 10.8 - - + -
114F ILE* 4.4 7.9 - - + -
118F VAL* 4.1 23.6 - - + -
119F THR 3.7 25.1 - - - +
120F ILE* 3.2 4.5 - - + -
121F LEU* 2.7 33.0 + - - -
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Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA* 3.2 10.2 + - + +
46F LEU* 1.3 73.3 - - - +
48F ALA* 1.3 60.9 + - - +
51F TRP* 3.0 19.4 + - + +
53F LEU* 4.0 11.0 - - + +
105F LEU* 3.6 30.7 - - + -
120F ILE* 3.3 14.8 - - - +
121F LEU 3.6 18.8 - - - +
122F HIS* 5.6 0.5 + - - -
123F LEU* 4.2 13.4 - - + +
209F PHE* 3.9 24.9 - - + -
238F ILE* 3.9 11.7 - - + -
242F ILE* 3.7 23.3 - - + +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 3.1 21.8 - - - +
47F ILE* 1.3 81.9 - - + +
49F LYS* 1.3 66.8 + - - +
50F ASP* 3.1 2.4 + - - +
51F TRP* 3.2 36.8 + - + -
120F ILE* 3.6 14.3 - - - +
242F ILE* 4.9 8.1 - - + -
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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