Contacts of the helix formed by residues 27 - 38 (chain B) in PDB entry 3F8F
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 TYR 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 1.3 88.7 + - - +
28B VAL* 1.3 65.1 + - - +
29B TYR* 3.7 20.3 - + + +
30B GLY* 3.1 26.0 + - - -
31B ILE* 2.9 25.1 + - - +
33B LYS* 6.1 0.3 - - - +
76B ARG* 3.3 57.2 + - + -
77B LYS 3.3 22.2 - - - +
78B TYR* 3.7 21.8 - + + -
79B TYR* 4.7 2.2 - - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 1.3 74.4 - - - +
29B TYR* 1.3 66.9 + - + +
31B ILE* 3.5 9.0 + - - +
32B ILE* 3.1 32.4 + - + +
47B GLU* 4.2 3.8 - - + -
50B LEU* 3.7 22.7 - - + -
51B TYR* 3.5 44.0 - - + +
54B PHE* 3.9 7.6 - - + -
77B LYS* 4.5 2.4 + - + +
79B TYR* 3.8 25.4 - - + +
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.3 19.8 - + + -
28B VAL* 1.3 80.4 - - + +
30B GLY* 1.3 62.2 + - - +
32B ILE* 3.4 9.5 + - + +
33B LYS* 2.9 30.4 + - - +
47B GLU* 3.6 28.4 + - - -
51B TYR* 4.6 4.5 - - - -
76B ARG* 5.4 6.1 - - - -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASN* 3.7 18.7 + - - -
27B TYR* 3.1 25.8 + - - -
29B TYR* 1.3 75.7 - - - +
31B ILE* 1.3 60.4 + - - +
33B LYS* 3.7 7.9 - - - +
34B GLN* 2.9 32.4 + - - +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 4.0 22.9 - - + -
20B VAL* 4.2 22.7 - - + -
21B LEU* 4.3 12.8 - - + -
26B ASN* 3.6 28.3 - - + +
27B TYR 2.9 26.2 + - - +
28B VAL* 3.6 7.9 - - - +
30B GLY* 1.3 73.8 - - - +
32B ILE* 1.3 60.8 + - - +
34B GLN* 3.7 2.7 - - - +
35B VAL* 2.9 36.0 + - + +
45B LEU* 4.6 2.0 - - + -
50B LEU* 4.6 6.7 - - + -
54B PHE* 3.6 33.0 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.1 19.5 + - + +
29B TYR* 3.8 9.9 - - + +
31B ILE* 1.3 80.1 - - - +
33B LYS* 1.3 63.9 + - - +
35B VAL* 3.9 4.8 - - - +
36B LYS* 3.0 26.1 + - + +
43B MET 4.9 0.9 - - - +
44B GLU* 5.3 4.7 - - + -
45B LEU* 3.9 35.3 + - + +
47B GLU* 4.0 27.1 - - + -
50B LEU* 3.4 27.6 - - + -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 6.1 0.9 - - - +
29B TYR 2.9 18.6 + - - +
30B GLY* 3.7 7.4 - - - +
32B ILE* 1.3 78.0 - - - +
34B GLN* 1.3 57.4 + - - +
36B LYS* 3.2 7.5 + - - +
37B GLU* 2.9 61.7 + - + +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.7 23.0 + - + +
109A ASN* 5.6 1.8 + - - +
20B VAL* 3.8 20.5 + - + +
23B GLN* 4.6 17.6 - - - +
26B ASN* 3.2 20.8 + - - +
30B GLY 2.9 20.6 + - - +
31B ILE* 3.7 4.7 - - - +
33B LYS* 1.3 73.1 - - - +
35B VAL* 1.3 57.7 + - - +
37B GLU* 3.3 14.2 + - - +
38B ALA* 2.9 28.2 + - - +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.4 6.8 - - + +
106A LEU* 4.7 3.6 - - + -
16B ILE* 3.5 31.2 - - + -
20B VAL* 3.7 17.7 - - + -
31B ILE* 2.9 21.9 + - + +
32B ILE 3.9 3.6 - - - +
34B GLN* 1.3 74.6 - - - +
36B LYS* 1.3 64.8 + - - +
38B ALA* 3.3 7.2 + - - +
39B SER* 3.0 22.5 + - - -
43B MET* 3.9 31.0 - - + +
45B LEU* 3.9 24.5 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.0 20.6 + - + +
33B LYS* 3.2 7.2 + - - +
35B VAL* 1.3 75.9 - - - +
37B GLU* 1.3 61.1 + - + +
39B SER* 3.0 6.6 + - - -
40B ASN 3.2 0.3 + - - -
41B GLY* 2.7 55.5 + - - +
43B MET 3.3 15.7 + - - +
44B GLU* 3.3 40.3 + - + -
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Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 4.9 7.1 + - - +
33B LYS* 2.9 57.1 + - + +
34B GLN* 3.6 11.8 - - - +
35B VAL 3.2 0.2 - - - -
36B LYS* 1.3 79.1 - - + +
38B ALA* 1.3 60.5 + - - +
39B SER 3.1 0.9 + - - -
40B ASN* 3.4 14.9 + - - +
41B GLY 4.9 0.4 - - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.8 26.3 - - + +
105A ASN* 3.1 34.1 - - + +
106A LEU* 3.8 23.8 - - + +
109A ASN* 4.4 10.3 - - - +
34B GLN 2.9 17.0 + - - +
35B VAL 3.9 4.7 - - - +
36B LYS 3.3 0.4 - - - -
37B GLU* 1.3 76.0 - - - +
39B SER* 1.3 57.4 + - - +
40B ASN* 3.6 3.0 + - - -
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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