Contacts of the strand formed by residues 33 - 40 (chain F) in PDB entry 3VI4
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 33 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ARG* 3.0 53.7 - - + +
79B SER 4.2 1.6 - - - -
81B GLY* 3.5 19.2 + - - -
82B THR* 3.6 23.2 + - - +
119B GLU* 4.6 4.4 + - - -
32F TYR* 1.3 74.3 - - - +
34F ILE* 1.3 61.6 + - - +
35F GLU* 3.7 17.3 - - - +
50F GLU* 4.0 11.2 - - - -
51F ILE* 3.3 20.4 - - - -
52F LEU* 3.2 45.2 - - + +
57F TYR* 3.6 31.4 - - + -
59F HIS* 4.2 11.0 - + - -
98F ARG* 3.4 5.4 - - - +
99F ALA 2.8 44.3 + - - +
100F LEU* 4.5 2.5 - - - -
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Residues in contact with ILE 34 (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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4F LEU* 4.9 5.4 - - + -
22F CYS* 4.7 12.8 - - - +
24F ALA* 5.0 0.2 - - + -
27F TYR* 4.4 11.7 - - - +
29F PHE* 3.3 35.9 - - + -
32F TYR 3.6 2.1 + - - +
33F TRP* 1.3 75.8 - - - +
35F GLU* 1.3 64.3 + - - +
36F TRP* 3.5 31.8 - - + +
50F GLU* 3.1 25.6 - - - +
51F ILE* 3.0 21.5 + - + +
53F PRO* 4.6 4.7 - - + +
79F ALA* 3.4 25.4 - - + +
96F CYS* 4.5 3.6 - - + -
97F SER 3.3 11.9 - - - +
98F ARG* 5.2 0.4 - - - -
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Residues in contact with GLU 35 (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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96E HIS* 5.6 0.2 - - - -
101E PHE* 4.0 5.6 - - - -
33F TRP* 3.7 6.8 - - - +
34F ILE* 1.3 73.7 - - - +
36F TRP* 1.3 63.4 + - - +
37F VAL* 4.1 2.0 - - + +
47F TRP* 2.7 33.2 + - + +
49F GLY 3.7 2.0 - - - -
50F GLU* 2.4 34.4 - - - +
95F TYR 3.5 0.5 - - - +
96F CYS* 3.1 10.4 - - - +
97F SER* 2.8 50.3 + - - +
98F ARG 4.1 3.1 - - - -
99F ALA* 3.4 32.1 - - + +
105F MET* 3.7 18.6 - - + +
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Residues in contact with TRP 36 (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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6F GLN* 4.4 9.0 - - - -
20F ILE* 4.3 18.2 - - + -
21F SER 4.5 2.5 - - - -
22F CYS* 3.7 22.7 - - + -
34F ILE* 3.5 19.7 - - + +
35F GLU* 1.3 75.9 - - - +
37F VAL* 1.3 65.7 + - - +
47F TRP* 3.9 1.6 - - - -
48F LEU* 2.9 34.4 + - + -
49F GLY 2.9 17.5 + - - +
51F ILE* 4.5 6.4 - - + +
70F PHE* 3.1 42.3 - + + -
79F ALA* 4.1 19.0 - - + +
80F TYR 4.0 13.5 + - - -
81F MET* 3.8 37.2 - - + -
94F TYR* 5.2 4.9 - + + -
95F TYR 3.4 19.1 - - - -
96F CYS* 3.6 15.3 - - + -
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Residues in contact with VAL 37 (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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103E PHE* 4.2 18.2 - - + -
35F GLU* 5.0 2.5 - - + -
36F TRP* 1.3 81.9 - - - +
38F LYS* 1.3 65.6 + - - +
45F LEU* 4.0 18.8 - - + -
46F GLU 3.2 27.1 - - - +
47F TRP* 4.3 16.2 - - + -
48F LEU* 4.3 3.8 - - - -
93F VAL 4.0 0.3 - - - +
94F TYR* 3.5 5.4 - - - -
95F TYR* 2.8 47.0 + - + +
97F SER* 5.5 1.3 - - - +
105F MET* 4.5 12.8 - - + -
108F TRP* 4.6 16.8 - - + -
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Residues in contact with LYS 38 (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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37F VAL* 1.3 73.9 - - - +
39F GLN* 1.3 64.0 + - - +
40F ARG* 3.6 27.5 + - + +
44F GLY 3.8 0.9 - - - +
45F LEU 3.4 1.7 - - - -
46F GLU* 2.7 51.1 + - + +
48F LEU* 3.7 16.1 - - + +
64F PHE* 3.8 33.4 - - + -
89F GLU* 2.8 34.9 + - - +
90F ASP* 4.2 4.4 + - - +
92F ALA* 4.0 6.1 - - + -
93F VAL 3.9 2.5 - - - -
94F TYR* 3.4 35.8 + - + +
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Residues in contact with GLN 39 (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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43E GLN* 2.8 42.2 + - - +
90E ILE* 6.0 1.4 - - - +
92E PHE* 5.3 2.0 - - + -
38F LYS* 1.3 73.3 - - - +
40F ARG* 1.3 67.4 + - - +
41F PRO* 4.0 4.9 - - - +
44F GLY* 3.1 17.9 - - - +
45F LEU* 3.5 18.6 - - + +
92F ALA* 3.3 5.1 - - - +
93F VAL* 3.0 48.1 + - + +
95F TYR* 4.4 14.5 + - + -
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Residues in contact with ARG 40 (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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38F LYS* 3.6 28.3 + - + +
39F GLN* 1.3 77.4 - - - +
41F PRO* 1.3 73.9 - - + +
42F GLY 2.9 2.3 + - - +
43F HIS* 3.0 70.5 + - + +
44F GLY* 3.5 12.1 + - - +
46F GLU* 5.2 5.4 + - - +
88F SER 4.4 4.2 + - - -
89F GLU* 3.4 51.1 + - - +
91F SER 3.4 17.0 - - - +
92F ALA* 4.1 0.7 - - + -
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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