Contacts of the helix formed by residues 34 - 46 (chain V) in PDB entry 6L49
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 34 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25U PHE* 3.9 15.7 - + + -
26U PRO* 3.8 24.9 - - + -
29U ARG* 4.6 9.8 - - + +
30U VAL* 3.7 23.3 - - + +
33U LEU* 4.8 13.0 - - + +
55U LEU* 5.1 4.0 - - + +
33V SER* 1.3 80.6 + - - +
35V SER* 1.3 64.2 + - - +
36V ILE 3.7 0.9 - - - -
37V TYR* 3.5 30.7 - + + -
38V VAL* 3.3 31.4 + - + +
56V MET* 3.6 4.4 - - - +
60V ASN* 2.6 28.0 + - - +
63V VAL* 3.7 27.6 - - + -
64V ASN* 4.1 15.5 - - - -
67V PHE* 5.8 4.6 - + + -
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Residues in contact with SER 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-121J C 3.6 21.7 + - - +
33V SER* 3.2 11.9 + - - -
34V TYR* 1.3 77.5 - - - +
36V ILE* 1.3 76.1 + - - +
39V TYR* 2.9 29.8 + - - +
56V MET* 3.3 28.3 - - - +
60V ASN* 5.5 0.6 - - - +
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Residues in contact with ILE 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I C 5.6 5.2 - - - +
-123J A 5.4 0.4 - - + -
-122J G 3.4 50.9 - - + +
-121J C 3.3 38.1 - - + +
35V SER* 1.3 88.3 + - - +
37V TYR* 1.3 61.9 + - + +
39V TYR* 3.7 13.0 - - + +
40V LYS* 2.8 52.1 + - - +
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Residues in contact with TYR 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-122J G 2.3 47.3 + - - -
-121J C 4.4 10.5 - - - -
18U SER* 5.2 2.7 + - - -
24U GLN* 3.3 29.3 - - + +
25U PHE* 3.6 17.9 - - + -
26U PRO* 3.4 37.2 - - + +
29U ARG* 3.6 17.2 + - + -
33V SER 3.8 15.7 - - - -
34V TYR* 3.5 26.9 - + + -
35V SER 3.2 0.4 - - - -
36V ILE* 1.3 78.3 - - + +
38V VAL* 1.3 59.2 + - - +
40V LYS* 3.2 10.0 + - + +
41V VAL* 3.0 30.3 + - - +
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Residues in contact with VAL 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U PHE* 3.6 24.2 - - + -
59U THR* 3.3 22.2 - - + +
63U LEU* 3.7 12.1 - - + -
34V TYR* 3.3 28.3 + - + +
37V TYR* 1.3 72.2 - - - +
39V TYR* 1.3 60.2 + - - +
41V VAL* 3.7 6.2 - - - +
42V LEU* 2.8 28.1 + - - +
51V ILE* 5.5 1.1 - - + -
56V MET* 3.7 8.3 - - + -
59V MET* 3.7 27.4 - - + +
63V VAL* 3.9 11.9 - - + -
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Residues in contact with TYR 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I G 3.3 31.5 - - + -
118I G 2.6 36.4 + - - -
35V SER 2.9 21.9 + - - +
36V ILE* 3.7 15.7 - - + +
37V TYR 3.2 0.2 - - - -
38V VAL* 1.3 77.7 - - - +
40V LYS* 1.3 65.0 + - + +
42V LEU* 3.3 17.5 + - + +
43V LYS* 2.9 64.7 + - + +
49V THR 5.4 0.2 - - - -
51V ILE* 4.7 10.8 - - + -
56V MET* 4.1 9.1 - - - +
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Residues in contact with LYS 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-123J A 4.7 7.7 - - - +
-122J G 3.4 24.4 + - - +
24U GLN* 4.4 21.3 - - + +
36V ILE* 2.8 38.9 + - + +
37V TYR* 3.2 8.5 + - + +
39V TYR* 1.3 81.7 - - + +
41V VAL* 1.3 61.6 + - - +
43V LYS* 3.7 7.4 - - + +
44V GLN* 2.9 34.0 + - + +
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Residues in contact with VAL 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U GLN* 3.8 22.7 - - + -
25U PHE* 4.2 14.8 - - + -
56U GLU* 4.2 25.6 - - + +
59U THR* 3.7 22.7 - - + -
60U ALA* 4.5 11.4 - - + -
63U LEU* 4.4 6.3 - - + -
37V TYR 3.0 20.5 + - - +
38V VAL* 3.7 8.1 - - - +
40V LYS* 1.3 76.6 - - - +
42V LEU* 1.3 56.1 + - - +
44V GLN* 3.2 9.4 + - - +
45V VAL* 2.9 31.5 + - + +
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Residues in contact with LEU 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63U LEU* 3.7 32.3 - - + +
78U ILE* 3.8 13.5 - - + -
38V VAL 2.8 17.9 + - - +
39V TYR* 3.6 16.8 - - + +
40V LYS 3.3 0.2 - - - -
41V VAL* 1.3 77.0 - - - +
43V LYS* 1.3 52.5 + - + +
45V VAL* 3.2 7.7 + - + +
46V HIS* 2.6 45.4 + - + +
49V THR* 3.8 32.1 - - + +
50V GLY 4.0 2.9 - - - +
51V ILE* 3.8 37.7 - - + -
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Residues in contact with LYS 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I G 5.8 3.7 - - - -
118I G 4.8 6.2 + - - -
39V TYR* 2.9 60.9 + - + +
40V LYS* 3.8 7.9 - - + +
41V VAL 3.3 0.2 - - - -
42V LEU* 1.3 75.8 - - - +
44V GLN* 1.3 61.1 + - - +
46V HIS 3.4 13.8 - - - +
47V PRO* 2.7 41.9 + - + +
48V ASP* 4.7 0.4 - - - +
49V THR 3.1 25.9 + - - +
50V GLY* 4.6 2.0 - - - +
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Residues in contact with GLN 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U GLN* 3.2 45.4 - - - +
56U GLU* 3.9 8.8 - - - +
40V LYS* 2.9 20.0 + - + +
41V VAL* 3.2 9.8 + - + +
43V LYS* 1.3 79.1 - - - +
45V VAL* 1.3 62.5 + - + +
47V PRO* 5.3 2.1 - - - +
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Residues in contact with VAL 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60U ALA* 4.1 30.3 - - + +
63U LEU* 4.2 17.5 - - + -
64U GLU* 4.2 13.4 - - - +
41V VAL* 2.9 19.0 + - + +
42V LEU* 3.4 15.5 - - + +
44V GLN* 1.3 82.4 - - + +
46V HIS* 1.3 87.8 + - + +
47V PRO* 4.3 3.4 - - - +
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Residues in contact with HIS 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63U LEU 4.1 5.8 + - - -
64U GLU* 3.4 49.4 + - - -
67U GLY* 4.2 9.4 - - - -
68U ASN* 4.1 7.9 + - - -
71U ARG* 3.3 43.4 + - - +
42V LEU* 2.6 30.9 + - + +
43V LYS* 3.4 11.2 - - - +
44V GLN 3.5 0.6 - - - -
45V VAL* 1.3 95.2 + - - +
47V PRO* 1.3 71.8 - - - +
48V ASP 3.6 0.4 - - - -
49V THR* 3.5 30.2 + - - +
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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