Contacts of the helix formed by residues 4 - 17 (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 SER 4 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3T PHE* 1.3 70.7 - - - +
5T GLU* 1.3 65.2 + - - +
6T GLU* 3.3 28.5 + - - +
7T GLN* 2.6 41.8 + - - +
8T THR 2.8 4.5 + - - -
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Residues in contact with GLU 5 (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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3T PHE 3.3 1.6 + - - -
4T SER* 1.3 73.1 - - - +
6T GLU* 1.3 55.1 + - - +
8T THR* 3.1 27.4 - - - +
9T ALA* 2.5 44.6 + - + +
12T LYS* 4.3 13.4 + - - +
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Residues in contact with GLU 6 (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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4T SER* 2.9 16.9 + - - +
5T GLU* 1.3 80.4 - - - +
7T GLN* 1.3 66.8 + - - +
9T ALA* 3.6 6.0 - - - +
10T GLU* 3.6 25.5 + - - +
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Residues in contact with GLN 7 (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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3T PHE* 3.0 36.5 - - + +
4T SER* 2.6 55.4 + - - +
6T GLU* 1.3 80.3 - - + +
8T THR* 1.3 56.7 + - - +
9T ALA 3.0 1.8 - - - -
10T GLU* 2.6 13.6 + - - +
11T PHE* 2.6 52.7 + - + -
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Residues in contact with THR 8 (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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3T PHE* 2.6 36.6 + - - +
4T SER 2.8 4.3 + - - -
5T GLU* 3.1 23.1 - - - +
7T GLN* 1.3 77.3 - - - +
9T ALA* 1.3 57.8 + - - +
11T PHE* 3.3 17.8 + - - +
12T LYS* 2.9 27.8 - - - +
66T PHE* 3.7 7.1 - - + -
70T LEU* 3.5 29.4 - - + -
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Residues in contact with ALA 9 (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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5T GLU* 2.5 27.8 + - + +
6T GLU* 3.6 7.6 - - - +
8T THR* 1.3 73.8 - - - +
10T GLU* 1.3 58.5 + - - +
12T LYS* 3.0 40.9 - - - +
13T GLU* 3.4 15.0 - - - +
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Residues in contact with GLU 10 (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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6T GLU* 3.6 19.7 + - - +
7T GLN* 2.6 17.4 + - - +
9T ALA* 1.3 72.8 - - - +
11T PHE* 1.3 58.6 + - + +
12T LYS 3.0 2.2 - - - -
13T GLU* 2.5 60.9 + - - +
14T ALA* 3.0 5.6 + - - +
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Residues in contact with PHE 11 (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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3T PHE* 3.3 57.7 - + + -
7T GLN* 2.6 40.0 + - + -
8T THR* 3.4 16.8 - - - +
10T GLU* 1.3 71.8 - - + +
12T LYS* 1.3 51.6 + - - +
14T ALA* 2.8 10.0 + - - +
15T PHE* 2.7 33.6 + - - +
38T LEU* 3.6 32.5 - - + +
66T PHE* 3.4 13.5 - + + -
69T PHE* 5.6 0.8 - + + -
70T LEU* 4.1 14.4 - - + -
73T MET* 3.4 22.9 - - + -
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Residues in contact with LYS 12 (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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5T GLU* 4.3 16.5 + - - -
8T THR* 2.9 25.8 - - - +
9T ALA* 3.0 30.0 - - - +
11T PHE* 1.3 73.5 - - - +
13T GLU* 1.3 55.3 + - + +
16T GLN* 2.7 46.3 + - + +
66T PHE* 3.0 28.5 - - + -
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Residues in contact with GLU 13 (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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9T ALA* 3.4 9.8 - - - +
10T GLU* 2.5 56.9 + - + +
12T LYS* 1.3 73.4 - - + +
14T ALA* 1.3 54.5 + - - +
16T GLN* 4.1 4.9 - - - +
17T LEU* 3.1 28.3 + - - +
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Residues in contact with ALA 14 (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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812S PHE* 5.5 7.9 - - + -
10T GLU 3.0 6.3 + - - +
11T PHE* 2.8 9.1 + - - +
13T GLU* 1.3 75.9 - - - +
15T PHE* 1.3 66.2 + - - +
17T LEU* 3.0 19.2 + - - +
18T PHE* 3.1 24.4 - - + -
34T VAL* 5.0 0.4 - - + -
38T LEU* 3.2 35.7 - - + -
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Residues in contact with PHE 15 (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 2.7 11.3 + - - +
12T LYS* 3.7 1.1 - - - +
14T ALA* 1.3 71.5 - - - +
16T GLN* 1.3 70.5 + - + +
18T PHE* 3.0 21.7 - - - +
24T GLY* 4.1 11.0 - - - -
26T ILE* 3.4 43.9 - - + +
34T VAL* 4.2 15.6 - - + +
64T LEU* 3.6 21.3 - - + -
65T LYS 4.0 0.4 - - - -
66T PHE* 3.6 48.0 - + + -
69T PHE* 3.2 52.7 - + + -
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Residues in contact with GLN 16 (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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12T LYS* 2.7 31.9 + - + +
13T GLU* 4.1 5.2 - - - +
15T PHE* 1.3 74.7 - - + +
17T LEU* 1.3 52.9 + - - +
18T PHE 2.6 18.1 + - - -
19T ASP* 3.6 13.3 + - - +
24T GLY* 5.0 14.6 - - - -
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Residues in contact with LEU 17 (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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812S PHE* 3.9 27.4 - - + -
816S GLN* 4.0 28.3 - - + +
819S LEU* 4.7 22.4 - - + -
13T GLU 3.1 19.0 + - - +
14T ALA* 3.0 11.1 + - - +
16T GLN* 1.3 74.6 - - - +
18T PHE* 1.3 68.3 + - - +
19T ASP 4.0 0.4 - - - -
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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