Contacts of the helix formed by residues 47 - 57 (chain B) in PDB entry 1V0O
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 THR 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.0 24.0 - - + +
36B LEU* 6.1 0.2 - - - +
48B ILE* 1.3 63.7 + - - +
49B ARG* 3.1 9.7 - - - +
50B GLU* 3.4 14.8 + - + +
51B ILE* 3.0 53.7 + - + +
75B LEU* 4.0 24.0 - - + +
77B LEU* 4.3 15.9 - - + -
154B VAL* 5.3 5.6 + - - +
155B ARG* 4.6 23.4 + - - +
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Residues in contact with ILE 48 (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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47B THR* 1.3 78.2 - - - +
49B ARG* 1.3 60.3 + - + +
51B ILE* 3.7 13.3 - - + +
52B SER* 2.5 40.3 + - - +
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Residues in contact with ARG 49 (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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47B THR 3.1 4.4 - - - +
48B ILE* 1.3 87.6 - - + +
50B GLU* 1.3 64.0 + - - +
51B ILE 3.3 0.2 - - - -
52B SER* 3.3 9.8 + - - -
53B ILE* 3.2 27.7 + - - +
152B ILE* 3.3 39.8 + - - +
153B PRO* 2.8 38.8 + - - +
154B VAL* 3.9 26.2 - - + +
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Residues in contact with GLU 50 (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 LYS* 3.2 32.6 + - - -
34B ILE* 5.7 2.0 - - - +
47B THR* 3.4 16.0 + - + +
49B ARG* 1.3 74.3 - - - +
51B ILE* 1.3 66.3 + - + +
53B ILE* 3.3 7.3 + - - +
54B LEU* 3.1 46.2 + - + +
77B LEU* 4.1 9.4 - - - +
79B PHE* 4.1 6.6 - - - -
144B PHE* 4.0 20.5 + - + +
145B GLY* 3.6 21.0 - - - -
154B VAL* 3.9 21.1 - - + +
155B ARG* 4.5 8.8 + - - -
2638B INR 4.6 0.7 + - - -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.0 39.5 + - + +
48B ILE* 3.7 13.7 - - + +
50B GLU* 1.3 76.9 - - - +
52B SER* 1.3 62.0 + - - +
54B LEU* 3.3 9.2 + - - +
55B LYS* 3.0 44.7 + - - +
65B LEU* 4.2 15.3 - - + +
68B VAL* 3.9 32.1 - - + -
77B LEU* 4.1 21.3 - - + -
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Residues in contact with SER 52 (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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48B ILE* 2.5 30.6 + - - +
49B ARG* 3.4 13.0 - - - -
50B GLU 3.2 0.2 - - - -
51B ILE* 1.3 78.0 - - - +
53B ILE* 1.3 62.5 + - - +
55B LYS* 3.3 7.4 + - - +
56B GLU* 3.0 37.9 + - - +
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Residues in contact with ILE 53 (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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49B ARG 3.2 8.8 + - - +
50B GLU* 3.6 7.2 - - - +
51B ILE 3.3 0.2 - - - -
52B SER* 1.3 78.4 - - - +
54B LEU* 1.3 58.3 + - - +
56B GLU* 3.2 6.9 + - - +
57B LEU* 3.0 50.8 + - + +
121B VAL* 4.1 11.0 - - + -
144B PHE* 3.8 23.3 - - + +
147B ALA* 4.0 15.5 - - + -
149B ALA* 3.8 30.7 - - + -
154B VAL* 3.3 34.5 - - + -
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Residues in contact with LEU 54 (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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50B GLU* 3.1 41.4 + - + +
51B ILE* 3.3 4.2 + - - +
53B ILE* 1.3 75.9 - - + +
55B LYS* 1.3 61.5 + - - +
57B LEU* 3.2 20.3 - - + +
58B LYS* 4.5 4.3 - - - -
62B ILE* 5.2 2.7 - - + -
63B VAL* 4.2 17.0 - - + +
64B LYS* 5.9 0.9 - - - -
65B LEU* 4.1 31.0 + - + +
77B LEU* 5.1 2.0 - - + -
79B PHE* 3.7 33.7 - - + -
142B ALA* 6.2 0.9 - - - -
143B ASP 6.0 0.7 - - - +
144B PHE* 3.9 31.6 - - + +
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Residues in contact with LYS 55 (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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51B ILE* 3.0 34.2 + - + +
52B SER* 3.5 13.0 - - - +
54B LEU* 1.3 78.0 - - - +
56B GLU* 1.3 71.8 + - - +
58B LYS* 3.9 19.5 + - - +
65B LEU* 5.4 4.5 - - + +
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Residues in contact with GLU 56 (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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52B SER* 3.0 27.1 - - - +
53B ILE* 3.2 6.1 + - - +
55B LYS* 1.3 90.5 - - - +
57B LEU* 1.3 69.9 + - + +
58B LYS* 3.5 8.7 + - - +
115B TYR* 3.6 8.5 + - - -
119B ARG* 5.3 4.9 + - + +
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Residues in contact with LEU 57 (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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53B ILE* 3.0 39.7 + - + +
54B LEU* 3.2 17.6 - - + +
56B GLU* 1.3 80.1 - - + +
58B LYS* 1.3 65.5 + - - +
59B HIS 4.0 1.1 + - - -
62B ILE* 4.1 18.7 - - + +
63B VAL 5.5 1.6 - - - +
64B LYS* 5.9 0.9 - - - +
115B TYR* 3.6 23.1 - - + -
116B CYS* 4.0 17.0 - - - -
119B ARG* 3.8 24.0 - - + -
121B VAL* 4.1 14.1 - - + -
144B PHE* 3.7 25.6 - - + -
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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