Contacts of the helix formed by residues 30 - 38 (chain T) in PDB entry 1I84
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 GLN 30 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18T PHE* 3.1 39.9 + - + +
19T ASP* 5.0 0.9 - - - +
20T ARG* 5.2 10.0 + - - +
25T LYS 4.4 2.1 - - - +
26T ILE* 3.4 19.2 - - + -
27T LEU* 2.9 29.3 + - + +
29T SER* 1.3 86.0 + - - +
31T CYS* 1.3 67.1 + - - +
32T GLY 2.8 1.8 + - - -
33T ASP* 2.9 24.0 + - + +
34T VAL* 3.0 16.7 + - + +
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Residues in contact with CYS 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T ILE* 3.5 12.8 - - - +
27T LEU 3.6 0.6 + - - -
28T TYR 3.7 15.5 - - - +
29T SER 2.9 1.2 + - - -
30T GLN* 1.3 76.0 - - - +
32T GLY* 1.3 59.0 + - - +
34T VAL* 3.2 4.8 + - - +
35T MET* 2.7 55.2 + - - +
47T VAL* 4.5 9.4 - - + -
51T LEU* 4.4 15.0 - - + -
64T LEU* 4.3 17.7 - - + -
69T PHE* 4.1 18.8 - - - -
72T MET* 4.6 8.7 - - - -
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Residues in contact with GLY 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T SER 3.3 7.8 + - - -
30T GLN 2.8 4.4 + - - -
31T CYS* 1.3 76.5 - - - +
33T ASP* 1.3 55.7 + - - -
35T MET* 3.1 8.5 + - - +
36T ARG* 2.9 48.9 + - - -
42T PRO* 5.0 0.6 - - - +
47T VAL* 4.0 21.0 - - - +
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Residues in contact with ASP 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804S ARG 5.3 0.2 - - - +
808S ALA* 4.2 16.5 - - + +
812S PHE* 6.4 1.3 - - + -
18T PHE* 4.2 16.1 - - + -
29T SER 4.9 1.1 + - - -
30T GLN* 2.9 17.6 + - - +
32T GLY* 1.3 71.7 - - - -
34T VAL* 1.3 52.4 + - - +
36T ARG* 3.3 19.2 + - - +
37T ALA* 2.6 37.6 + - - +
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Residues in contact with VAL 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ALA 5.0 0.2 - - - -
15T PHE* 4.2 19.7 - - + +
18T PHE* 3.5 48.2 - - + -
26T ILE* 4.1 14.8 - - + -
30T GLN* 3.0 17.8 + - + +
31T CYS 3.6 7.0 - - - +
33T ASP* 1.3 72.3 - - - +
35T MET* 1.3 66.1 + - - +
37T ALA* 3.6 0.9 + - - +
38T LEU* 3.1 28.4 + - + +
69T PHE* 3.7 25.6 - - + -
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Residues in contact with MET 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T CYS* 2.7 47.1 + - - +
32T GLY* 3.4 5.8 - - - +
34T VAL* 1.3 75.8 - - - +
36T ARG* 1.3 59.2 + - - +
38T LEU* 3.1 11.8 + - - +
40T GLN* 2.8 29.3 + - + +
42T PRO* 3.9 14.6 - - + -
47T VAL* 4.5 6.1 - - - -
69T PHE* 4.2 6.1 - - + -
72T MET* 4.1 2.5 - - - -
73T MET* 3.4 44.9 - - + +
76T ILE* 3.2 48.7 - - + -
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Residues in contact with ARG 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801S ALA* 5.0 2.4 + - - +
804S ARG* 4.0 34.4 - - - +
805S GLY* 3.3 22.7 - - - +
808S ALA* 4.0 9.2 - - + -
809S ARG* 3.0 19.2 - - - -
32T GLY* 2.9 33.0 + - - -
33T ASP* 3.3 22.4 + - - +
35T MET* 1.3 73.2 - - - +
37T ALA* 1.3 56.0 + - - +
38T LEU 2.9 1.6 - - - -
39T GLY 2.4 26.9 + - - -
40T GLN 2.9 23.5 + - - +
41T ASN* 4.8 0.8 - - - -
42T PRO* 2.7 33.8 + - + +
43T THR 4.2 5.5 + - - -
44T ASN* 4.1 19.0 + - - -
47T VAL* 4.4 5.0 - - - +
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Residues in contact with ALA 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808S ALA 5.9 0.2 - - - -
809S ARG* 4.2 19.5 - - - +
812S PHE* 3.8 35.8 - - + -
14T ALA* 5.8 0.4 - - + -
18T PHE* 4.0 18.6 - - + -
33T ASP 2.6 20.3 + - - +
34T VAL 3.8 5.6 - - - +
35T MET 3.4 0.2 - - - -
36T ARG* 1.3 72.3 - - - +
38T LEU* 1.3 63.5 + - + +
39T GLY 3.0 4.5 + - - -
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Residues in contact with LEU 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T PHE* 3.6 38.9 - - + +
14T ALA* 3.2 33.2 - - + -
34T VAL* 3.1 23.5 + - + +
35T MET 3.1 9.8 + - - +
36T ARG 2.9 1.2 + - - -
37T ALA* 1.3 79.1 - - + +
39T GLY* 1.3 60.4 + - - +
40T GLN* 3.4 6.5 + - - -
69T PHE* 4.7 5.8 - - + -
73T MET* 3.4 39.7 - - + +
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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