Contacts of the helix formed by residues 59 - 69 (chain C) in PDB entry 2V5Q
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 HIS 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ALA 3.2 24.0 - - - -
23C ARG 3.2 16.7 + - - -
24C ALA 3.8 3.5 - - - -
25C GLY* 3.3 22.6 + - - -
54C ALA* 2.9 15.1 + - + +
57C SER* 3.4 32.9 + - - -
58C GLY* 1.3 76.8 + - - +
60C LEU* 1.3 62.7 + - - +
61C GLU* 3.4 6.9 + - - +
62C ILE* 3.4 17.8 + - + +
63C VAL* 3.1 26.0 + - - +
95C ILE* 4.3 0.2 - - - -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLY 3.0 10.2 + - - +
59C HIS* 1.3 71.9 - - - +
61C GLU* 1.3 82.7 + - + +
63C VAL* 3.2 5.1 + - - +
64C GLU* 3.1 28.1 + - - +
94C GLU* 3.5 55.0 - - + +
95C ILE* 3.8 20.4 - - + -
98C VAL* 4.0 12.6 - - + -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 3.5 22.1 - - - +
31C ARG* 5.3 7.2 - - - +
58C GLY 5.3 0.3 - - - +
59C HIS* 3.4 3.3 - - - +
60C LEU* 1.3 96.1 + - + +
62C ILE* 1.3 58.3 + - - +
64C GLU* 3.5 7.3 + - - +
65C VAL* 3.0 33.9 + - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA 4.2 2.0 - - - +
22C ALA* 4.1 6.3 - - + +
25C GLY* 3.4 40.4 - - - +
26C GLN 3.7 6.5 - - - +
27C ASP* 3.4 25.5 + - - +
30C VAL* 3.9 27.6 - - + -
54C ALA* 3.5 22.0 - - + -
59C HIS* 3.4 14.6 + - + +
60C LEU 3.3 0.2 - - - -
61C GLU* 1.3 73.7 - - - +
63C VAL* 1.3 65.4 + - - +
65C VAL* 3.4 7.8 + - + +
66C LEU* 2.9 36.7 + - + +
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.7 22.8 - - + +
54C ALA* 3.7 5.6 - - + +
55C ALA* 3.6 33.2 - - - +
59C HIS 3.1 19.8 + - - +
60C LEU* 3.3 9.2 - - - +
62C ILE* 1.3 76.5 - - - +
64C GLU* 1.3 58.6 + - - +
66C LEU* 3.1 7.0 + - - +
67C LEU* 2.9 33.8 + - + +
95C ILE* 4.1 14.8 - - + -
98C VAL* 3.5 27.8 - - + -
99C LEU* 4.5 3.4 - - + -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 3.1 22.0 + - + +
61C GLU* 4.0 6.6 - - - +
62C ILE 3.3 0.2 - - - -
63C VAL* 1.3 78.2 - - - +
65C VAL* 1.3 63.3 + - - +
67C LEU* 3.3 7.6 + - - +
68C LYS* 3.0 53.3 + - - +
98C VAL* 3.7 28.6 - - + +
102C TYR* 4.3 12.2 + - + +
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 5.8 0.4 - - - +
30C VAL* 4.2 11.7 - - + -
31C ARG* 4.0 40.2 - - + +
34C ILE* 3.9 22.4 - - + -
61C GLU 3.0 22.4 + - - +
62C ILE* 3.6 8.3 - - + +
64C GLU* 1.3 75.2 - - + +
66C LEU* 1.3 62.1 + - - +
68C LYS* 3.5 7.8 + - + +
69C HIS* 2.9 41.8 + - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 4.5 9.4 - - + -
22C ALA* 4.6 0.2 - - + -
30C VAL* 4.7 3.4 - - + -
34C ILE* 4.1 19.7 - - + -
40C VAL* 4.3 18.2 - - + +
50C PRO* 3.6 50.3 - - + +
51C LEU* 3.8 11.0 - - + +
54C ALA* 4.4 1.8 - - + -
62C ILE* 2.9 37.0 + - + +
63C VAL 3.1 5.4 + - - +
65C VAL* 1.3 73.2 - - - +
67C LEU* 1.3 66.8 + - - +
69C HIS* 3.2 11.9 + - - +
70C GLY 3.4 0.3 + - - -
71C ALA* 3.1 32.7 + - + +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.7 26.2 - - + -
63C VAL* 2.9 35.9 + - + +
64C GLU 3.3 8.0 + - - +
66C LEU* 1.3 75.5 - - - +
68C LYS* 1.3 56.9 + - - +
70C GLY* 3.1 18.9 + - - -
71C ALA 4.0 9.4 + - - +
73C VAL* 3.9 16.6 - - + -
98C VAL* 3.7 34.1 - - + +
99C LEU* 4.2 5.4 - - + -
102C TYR* 3.6 41.3 - - + -
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLU* 3.0 39.7 + - - +
65C VAL* 3.9 8.7 - - + +
66C LEU 3.3 0.2 - - - -
67C LEU* 1.3 74.2 - - - +
69C HIS* 1.3 65.2 + - + +
70C GLY 3.2 3.4 + - - -
102C TYR* 3.4 29.8 - - + +
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Residues in contact with HIS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ARG* 6.5 0.2 - - + -
34C ILE* 3.5 28.6 - - + +
40C VAL* 3.5 28.0 - - + +
65C VAL* 2.9 36.3 + - + +
66C LEU 3.2 5.3 + - - +
68C LYS* 1.3 83.4 - - + +
70C GLY* 1.3 59.0 + - - +
71C ALA 3.5 2.2 - - - -
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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