Contacts of the helix formed by residues 21 - 33 (chain T) in PDB entry 1G3I
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 ALA 21 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19T GLY 3.5 1.1 + - - -
20T GLN* 1.3 85.8 - - - +
22T ASP* 1.3 65.2 + - - +
23T ALA* 2.6 15.1 + - - +
24T LYS* 3.0 20.8 + - - +
25T ARG* 3.1 18.6 + - - +
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Residues in contact with ASP 22 (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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21T ALA* 1.3 84.5 - - - +
23T ALA* 1.3 65.0 + - - +
25T ARG* 3.9 23.0 + - - +
26T ALA* 3.3 16.3 + - - +
331T VAL* 3.4 13.0 - - + +
332T GLU* 4.4 17.2 - - + +
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Residues in contact with ALA 23 (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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20T GLN* 3.5 37.9 - - + +
21T ALA 2.6 0.8 + - - +
22T ASP* 1.3 81.7 - - - +
24T LYS* 1.3 69.0 + - - +
26T ALA* 3.2 2.8 + - - +
27T VAL* 3.0 24.4 + - + +
55T MET* 5.8 0.9 - - - -
66T ILE* 3.9 10.5 - - + -
331T VAL* 3.3 14.0 - - - +
332T GLU 4.9 1.8 + - - -
333T LEU* 3.7 14.8 - - + -
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Residues in contact with LYS 24 (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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10T VAL* 4.7 16.8 - - + -
13T LEU* 4.3 25.1 - - + +
14T ASP* 2.8 31.6 + - - +
17T ILE* 2.6 37.7 + - - -
18T ILE* 4.1 2.2 - - - +
19T GLY 3.0 29.3 + - - +
20T GLN* 4.0 9.6 - - + -
21T ALA* 3.0 10.1 + - - +
23T ALA* 1.3 76.2 - - - +
25T ARG* 1.3 56.7 + - - +
27T VAL* 2.6 34.2 + - - +
28T ALA* 2.7 15.4 + - - +
66T ILE* 3.8 15.0 - - + +
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Residues in contact with ARG 25 (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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10T VAL* 5.0 8.0 - - + +
21T ALA 3.1 15.6 + - - +
22T ASP* 3.9 21.1 + - - +
24T LYS* 1.3 79.4 - - - +
26T ALA* 1.3 59.4 + - - +
28T ALA* 3.1 7.5 + - - +
29T ILE* 3.0 34.4 + - - +
405U ASP* 3.2 39.4 + - - -
406U LYS* 5.1 1.6 - - - +
409U PHE* 4.1 49.6 - - + +
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Residues in contact with ALA 26 (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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22T ASP 3.3 14.1 + - - +
23T ALA 3.2 4.6 + - - +
25T ARG* 1.3 77.2 - - - +
27T VAL* 1.3 64.3 + - + +
29T ILE* 3.1 28.4 - - + +
30T ALA 3.4 2.6 + - - -
53T ILE* 3.1 19.3 - - + +
329T ILE* 4.1 23.1 - - + -
331T VAL* 4.4 12.1 - - + -
405U ASP* 6.1 0.2 - - - +
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Residues in contact with VAL 27 (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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13T LEU* 5.1 3.8 - - + -
23T ALA* 3.0 19.3 + - - +
24T LYS* 2.6 15.9 + - - +
26T ALA* 1.3 73.8 - - + +
28T ALA* 1.3 58.9 + - - +
30T ALA* 3.2 15.8 - - - +
31T LEU 3.7 3.1 + - - -
53T ILE* 4.0 13.0 - - + -
55T MET* 5.2 13.5 - - + -
66T ILE* 3.3 36.8 - - + +
70T LEU* 3.3 42.5 - - + +
306T ILE* 5.0 6.7 - - + -
331T VAL* 5.7 0.9 - - + -
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Residues in contact with ALA 28 (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 PRO* 3.8 32.1 - - + +
9T ILE* 4.4 22.9 - - + +
10T VAL* 4.8 5.4 - - + +
13T LEU* 6.0 1.1 - - + +
24T LYS 2.7 10.6 + - - +
25T ARG* 3.2 12.8 - - - +
27T VAL* 1.3 74.3 - - - +
29T ILE* 1.3 54.2 + - - +
30T ALA 2.5 16.8 + - - -
31T LEU* 2.6 18.5 + - - +
32T ARG* 3.1 8.7 + - - +
409U PHE* 5.4 0.9 - - + -
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Residues in contact with ILE 29 (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 PRO* 4.6 2.9 - - + +
25T ARG* 3.0 10.7 + - + +
26T ALA* 3.1 34.3 - - + +
28T ALA* 1.3 72.1 - - - +
30T ALA* 1.3 58.4 + - - +
32T ARG* 4.0 11.0 - - - -
33T ASN* 2.7 35.0 + - - +
329T ILE* 5.0 4.7 - - + -
401U GLU* 3.9 21.5 - - - +
405U ASP* 4.3 22.9 - - - +
408U SER* 4.2 18.4 - - - +
409U PHE* 4.2 38.4 - - + +
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Residues in contact with ALA 30 (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 ALA 3.4 10.3 + - - +
27T VAL 3.2 13.7 - - - +
28T ALA 2.5 6.1 + - - -
29T ILE* 1.3 76.8 - - - +
31T LEU* 1.3 61.7 + - - +
32T ARG 3.3 0.2 - - - -
33T ASN* 3.7 4.8 + - - +
34T ARG* 3.7 18.0 + - - +
50T PRO* 6.0 1.6 - - - +
51T LYS* 4.8 6.1 - - - +
53T ILE* 3.7 18.8 - - + -
70T LEU* 5.7 2.7 - - + -
304T LEU* 4.7 26.7 - - + +
306T ILE* 6.2 0.7 - - + -
329T ILE* 5.1 2.7 - - + -
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Residues in contact with LEU 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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3T GLU* 4.9 20.2 - - + +
4T MET* 6.3 2.0 - - + -
9T ILE* 3.6 27.1 - - + -
27T VAL 3.7 5.5 + - - +
28T ALA 2.6 13.2 + - - +
30T ALA* 1.3 74.8 - - - +
32T ARG* 1.3 62.4 + - - +
34T ARG* 3.3 40.5 + - - +
35T TRP* 3.7 10.9 + - - +
70T LEU* 4.4 20.6 - - + +
73T LEU 4.5 4.0 - - - +
74T ALA* 3.5 34.1 - - + +
253T ILE* 5.7 2.0 - - + -
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Residues in contact with ARG 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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4T MET 2.7 32.7 + - - -
5T THR* 3.3 18.2 + - - +
6T PRO* 3.4 26.9 - - + +
9T ILE* 5.2 3.3 - - + +
28T ALA 3.1 11.2 + - - +
29T ILE* 4.2 10.1 - - - +
31T LEU* 1.3 79.2 - - - +
33T ASN* 1.3 59.1 + - - +
34T ARG 3.2 0.2 - - - -
35T TRP* 3.0 31.3 + - - +
36T ARG* 3.0 60.7 + - + +
360U MET* 6.3 1.3 - - + -
363U GLU* 2.7 32.8 + - + +
408U SER* 5.1 8.5 - - - +
412U SER* 3.8 4.4 + - - -
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Residues in contact with ASN 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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29T ILE* 2.7 27.9 + - - +
30T ALA* 3.7 5.8 + - - +
31T LEU 3.3 0.4 - - - -
32T ARG* 1.3 79.4 - - - +
34T ARG* 1.3 56.7 + - - +
35T TRP 3.2 3.8 - - - -
36T ARG* 4.3 10.4 - - - +
37T ARG* 3.4 20.4 + - - +
50T PRO* 5.9 6.1 - - + +
51T LYS* 5.5 13.3 - - + +
356U TYR* 5.3 10.5 - - - -
359U LEU* 4.8 17.1 - - + +
360U MET* 4.2 15.6 - - - +
401U GLU* 5.3 8.5 + - - -
408U SER* 3.5 23.4 + - - -
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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