Contacts of the strand formed by residues 85 - 92 (chain F) in PDB entry 3A13
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 TRP 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F PHE 3.3 1.0 - - - +
30F ARG* 3.2 2.8 - - - -
31F VAL* 2.7 37.0 + - - +
33F PRO* 3.9 17.0 - - + -
39F ILE* 3.6 56.5 - - + +
77F PHE* 4.5 8.7 - - + +
78F HIS 3.4 11.4 - - - -
79F ASP* 3.3 47.9 - - - +
80F MET* 4.2 1.1 - - - -
83F GLY* 3.6 23.1 - - - -
84F SER* 1.3 79.9 - - - +
86F ILE* 1.3 64.1 + - - +
87F VAL* 3.5 6.7 + - + -
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Residues in contact with ILE 86 (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 VAL* 3.5 26.0 - - + -
29F PHE 3.2 2.7 - - - +
30F ARG* 4.0 23.6 - - + -
76F ASP* 3.3 6.2 - - - +
77F PHE* 3.5 0.9 - - - -
78F HIS* 2.9 48.8 + - + +
80F MET* 3.6 22.9 - - - +
85F TRP* 1.3 71.2 - - - +
87F VAL* 1.3 58.5 + - - +
88F ARG* 5.0 8.0 - - + +
124F GLU* 4.7 1.1 - - + -
349F VAL* 3.2 26.9 - - + +
350F PHE* 3.5 33.2 - - + -
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ALA 3.7 1.6 - - - +
28F VAL* 3.7 1.1 - - - -
29F PHE* 2.8 39.8 + - + +
31F VAL* 3.8 25.4 - - + -
39F ILE* 3.9 17.0 - - + -
43F ALA* 3.8 20.6 - - + -
74F ALA* 4.1 5.8 - - + -
76F ASP 3.2 6.5 - - - +
77F PHE* 3.9 25.8 - - + -
85F TRP* 4.1 4.0 - - + -
86F ILE* 1.3 77.2 - - - +
88F ARG* 1.3 73.5 + - - +
89F ILE* 4.0 13.5 - - + -
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Residues in contact with ARG 88 (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 ILE* 4.0 3.8 - - + -
27F ALA 3.7 3.6 - - - -
28F VAL* 4.3 18.2 - - + +
74F ALA* 3.4 4.2 - - - -
75F TYR* 3.0 59.0 + - + +
76F ASP* 2.8 45.5 + - + +
78F HIS* 6.3 0.8 - - - +
86F ILE* 5.0 8.4 - - + +
87F VAL* 1.3 73.5 - - - +
89F ILE* 1.3 62.2 + - - +
348F ASP 5.3 2.6 + - - -
349F VAL* 4.9 15.2 + - - +
351F HIS 5.8 0.6 + - - -
352F LEU* 3.9 29.3 - - - +
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Residues in contact with ILE 89 (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 ILE* 3.2 5.5 - - - -
27F ALA 2.9 37.2 + - - +
29F PHE* 3.8 25.8 - - + -
31F VAL* 6.2 0.7 - - + -
43F ALA* 4.3 6.3 - - - +
46F VAL* 3.9 17.9 - - + -
47F ALA* 3.9 24.9 - - + +
72F ALA* 3.9 4.3 - - + -
73F LYS 3.3 16.6 - - - +
74F ALA* 4.0 3.6 - - + -
75F TYR* 4.1 2.5 - - - -
87F VAL* 4.0 16.4 - - + -
88F ARG* 1.3 81.9 - - - +
90F ALA* 1.3 63.3 + - - +
91F TYR* 3.5 28.3 - - + +
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Residues in contact with ALA 90 (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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17F TYR* 3.8 29.4 - - + -
19F PRO* 4.5 3.1 - - + -
24F ASP* 4.2 12.1 - - + +
25F ILE 3.3 6.5 - - - +
26F ILE* 4.5 1.1 - - + -
71F SER 4.5 0.3 - - - +
72F ALA* 3.1 7.1 - - - -
73F LYS* 2.8 36.3 + - + +
75F TYR* 3.9 15.0 - - + -
89F ILE* 1.3 72.5 - - - +
91F TYR* 1.3 62.6 + - - +
92F PRO* 4.4 1.4 - - - +
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Residues in contact with TYR 91 (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 ASP* 3.3 5.4 - - - -
25F ILE* 2.7 55.2 + - + +
27F ALA* 3.8 9.9 - - + -
29F PHE* 4.0 10.2 - - - -
50F SER* 2.7 46.9 + - - -
51F SER* 4.4 4.7 - - - -
70F LEU 5.9 0.4 - - - -
72F ALA* 3.4 20.9 - - + -
89F ILE* 3.5 37.1 - - + +
90F ALA* 1.3 75.8 - - - +
92F PRO* 1.3 70.7 - - + +
95F ALA* 5.5 1.3 - - + -
96F PHE* 3.7 32.5 - + + -
108F ILE* 3.5 23.7 - - + +
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Residues in contact with PRO 92 (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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23F ARG* 3.8 2.0 - - + +
24F ASP* 3.7 13.6 - - - +
69F ASP 3.7 20.9 - - - +
70F LEU* 4.0 23.3 - - - +
71F SER 4.1 11.2 - - - +
90F ALA 4.4 1.1 - - - +
91F TYR* 1.3 85.4 - - + +
93F PHE* 1.3 66.1 + - - +
94F HIS* 3.7 21.8 - - + +
95F ALA* 3.1 21.5 + - + +
96F PHE* 3.8 4.5 - - - -
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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