Contacts of the strand formed by residues 75 - 79 (chain F) in PDB entry 3EXG
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 ARG 75 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F ASP* 3.4 25.9 + - - -
22F LYS* 3.0 18.3 + - + +
23F VAL* 3.5 39.4 - - + +
24F PHE* 3.7 1.7 + - - -
73F GLY 4.5 2.7 - - - +
74F LEU* 1.3 81.5 - - - +
76F PRO* 1.3 66.0 - - - +
77F ILE* 4.5 0.7 - - - +
111F PRO* 3.5 22.2 - - + +
161F ILE* 3.1 19.4 + - + +
162F ARG* 3.0 17.8 + - - +
163F ASP 2.9 27.9 + - - -
164F ASN* 2.9 21.8 + - - -
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Residues in contact with PRO 76 (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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24F PHE* 3.4 39.7 - - + +
26F LEU* 4.6 0.7 - - + -
66F ALA* 3.3 35.9 - - + +
70F ALA* 4.0 9.6 - - + +
74F LEU* 3.5 7.0 - - + +
75F ARG* 1.3 95.1 - - - +
77F ILE* 1.3 63.7 + - - +
78F CYS 3.8 0.2 - - - -
111F PRO 3.8 5.6 - - - +
112F ILE* 3.8 13.8 - - + +
113F VAL* 3.1 24.3 + - - +
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Residues in contact with ILE 77 (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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13F MET* 4.3 21.1 - - + +
17F LEU* 5.7 3.1 - - + -
23F VAL* 4.4 14.1 - - + -
24F PHE 2.8 22.1 + - - +
25F LEU* 3.5 22.1 - - + +
26F LEU* 3.1 25.2 + - - -
75F ARG 4.5 0.7 - - - +
76F PRO* 1.3 76.2 - - - +
78F CYS* 1.3 58.8 + - - +
113F VAL* 3.5 11.4 - - + +
115F ARG* 3.7 32.5 - - + -
157F ILE* 5.5 0.9 - - + -
161F ILE* 3.5 35.4 - - + -
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Residues in contact with CYS 78 (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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26F LEU* 3.5 6.5 - - + -
62F PHE* 3.8 32.8 - - - -
63F ALA* 4.0 12.1 - - - -
66F ALA* 3.8 20.9 - - + -
76F PRO 3.8 0.8 - - - -
77F ILE* 1.3 72.5 - - - +
79F GLU* 1.3 58.1 + - - +
80F PHE* 3.7 9.0 + - - -
112F ILE* 4.5 1.6 - - + -
113F VAL 2.6 14.5 + - - +
114F PHE* 3.4 30.0 - - + +
115F ARG 3.1 24.0 + - - +
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Residues in contact with GLU 79 (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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25F LEU* 4.3 9.6 - - + +
26F LEU 3.0 12.0 + - - +
27F GLY* 3.6 17.0 - - - -
28F GLU 4.4 9.4 + - - +
30F VAL* 3.9 23.2 - - + +
35F GLY* 5.4 2.6 - - - -
36F ALA* 4.8 9.9 + - - +
37F TYR* 5.3 4.5 - - - -
39F VAL* 5.0 4.1 - - - +
40F SER* 4.6 10.2 + - - -
62F PHE* 3.7 12.3 - - - -
77F ILE 3.6 2.2 + - - -
78F CYS* 1.3 74.1 - - - +
80F PHE* 1.3 72.6 + - - +
81F MET* 4.3 11.8 + - - +
115F ARG* 2.9 54.1 + - - +
116F GLY* 4.4 0.9 - - - -
117F PRO* 5.4 1.4 - - - +
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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