Contacts of the helix formed by residues 48 - 58 (chain D) in PDB entry 1IVH
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 LEU 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D PHE* 3.4 40.7 + - + +
46D LYS 3.5 1.0 + - - -
47D ASN* 1.3 75.8 - - - +
49D ARG* 1.3 55.3 + - + +
51D PHE* 3.0 2.3 + - - +
52D TRP* 2.8 73.5 + - + +
93D VAL* 6.5 0.2 - - - -
96D SER* 5.1 7.0 - - - -
130D ILE* 3.7 25.6 - - + -
169D ASN* 5.3 6.3 - - - +
172D ASP* 3.9 25.6 - - + +
220D ASN* 4.5 9.2 - - - +
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN 3.1 0.6 + - - -
48D LEU* 1.3 80.5 - - + +
50D GLU* 1.3 60.5 + - - +
52D TRP* 3.5 7.7 + - - +
53D LYS* 3.3 35.8 + - - +
127D GLY 4.3 4.2 + - - +
128D GLU 3.0 20.2 + - - -
130D ILE* 3.5 24.5 - - + +
172D ASP* 2.6 36.0 + - - +
174D ASP* 2.8 32.5 + - - -
200D LYS* 4.6 4.9 - - - +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN* 2.8 35.5 + - + +
49D ARG* 1.3 73.4 - - - +
51D PHE* 1.3 64.9 + - - +
53D LYS* 3.2 16.4 + - + +
54D GLN* 3.3 27.7 + - + +
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.8 20.9 - + - -
28D LEU* 3.8 10.3 - - + -
31D HIS* 4.4 9.6 - - + -
32D LEU* 3.7 32.5 - - + -
45D PHE* 3.6 26.0 - + + -
47D ASN* 2.7 16.5 + - + +
48D LEU 3.3 7.9 - - - +
50D GLU* 1.3 72.5 - - - +
52D TRP* 1.3 84.6 + + - +
54D GLN* 2.9 22.4 + - - +
55D LEU* 2.9 48.6 + - + +
86D ILE* 5.1 1.6 - - + -
93D VAL* 3.6 21.1 - - + -
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Residues in contact with TRP 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 2.8 45.0 + - + +
49D ARG* 3.7 5.8 - - - +
50D GLU 3.3 0.2 - - - -
51D PHE* 1.3 97.7 - + - +
53D LYS* 1.3 56.0 + - - +
55D LEU* 3.2 11.5 + - + -
56D GLY 2.8 24.3 + - - -
61D LEU* 3.2 25.3 - - + +
93D VAL* 4.0 12.6 - - + -
96D SER* 3.8 22.0 - - - -
97D TYR* 3.8 38.6 - - + -
100D HIS* 3.0 42.8 + + + -
127D GLY* 3.6 15.5 - - - +
129D TYR 4.1 3.1 - - - -
130D ILE* 3.9 20.9 - - + +
169D ASN* 4.7 4.0 - - - -
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 3.3 22.7 + - - +
50D GLU* 3.2 10.4 + - - +
51D PHE 3.2 1.0 - - - -
52D TRP* 1.3 77.4 - - - +
54D GLN* 1.3 59.0 + - + +
56D GLY* 3.5 0.9 + - - -
57D ASN* 3.0 25.3 + - - +
126D SER 3.6 10.6 - - - +
127D GLY 3.9 12.2 + - - +
128D GLU* 3.4 40.7 + - + +
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.5 34.4 - - + -
31D HIS* 3.9 20.0 + - - +
47D ASN* 6.1 0.8 - - - +
50D GLU* 3.3 30.3 + - + +
51D PHE* 2.9 25.7 + - - +
53D LYS* 1.3 75.9 - - + +
55D LEU* 1.3 66.4 + - - +
56D GLY 3.1 0.2 - - - -
57D ASN* 3.1 15.0 + - - +
58D LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D MET* 5.6 2.7 - - - -
27D PHE* 4.5 11.2 - - + -
28D LEU* 5.4 1.8 - - + -
51D PHE* 2.9 49.9 + - + +
52D TRP* 3.4 33.9 - - + +
54D GLN* 1.3 75.8 - - - +
56D GLY* 1.3 61.9 + - - +
58D LEU* 3.2 7.2 + - + +
59D GLY 3.0 16.3 + - - -
60D VAL* 3.2 35.6 + - + +
61D LEU* 3.8 12.3 - - + -
86D ILE* 4.5 9.6 - - + -
97D TYR* 4.0 21.5 - - + -
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D TRP 2.8 10.7 + - - -
53D LYS 3.5 0.4 + - - -
55D LEU* 1.3 77.6 - - - +
57D ASN* 1.3 56.9 + - - +
59D GLY* 3.0 18.6 + - - -
61D LEU* 3.4 13.4 - - - +
125D ILE* 3.5 13.2 - - - +
126D SER* 3.4 24.6 - - - -
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 5.2 3.1 - - - -
53D LYS 3.0 15.0 + - - +
54D GLN* 3.1 21.3 + - - +
56D GLY* 1.3 78.5 - - - +
58D LEU* 1.3 70.1 + - - +
59D GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 6.1 0.3 - - - +
23D THR* 4.3 16.2 - - + -
24D MET* 3.3 36.8 - - + -
27D PHE* 3.7 42.4 - - + -
54D GLN 3.0 18.4 + - - +
55D LEU* 3.5 15.0 - - + +
56D GLY 3.2 0.2 - - - -
57D ASN* 1.3 86.1 - - - +
59D GLY* 1.3 59.6 + - - +
60D VAL* 3.4 7.2 - - + +
72D SER* 5.3 0.2 + - - -
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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