Contacts of the helix formed by residues 21 - 33 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19X GLY 3.5 1.3 + - - -
20X GLN* 1.3 86.5 - - - +
22X ASP* 1.3 65.4 + - - +
23X ALA* 2.6 14.7 + - - +
24X LYS* 3.0 19.2 + - - +
25X ARG* 3.1 19.3 + - - +
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Residues in contact with ASP 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ALA* 1.3 83.5 - - - +
23X ALA* 1.3 64.4 + - - +
25X ARG* 3.9 22.8 + - - +
26X ALA* 3.3 15.2 + - - +
331X VAL* 3.3 13.4 - - + +
332X GLU* 4.4 17.3 - - + +
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Residues in contact with ALA 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLN* 3.5 40.2 - - + +
21X ALA 2.6 1.0 + - - +
22X ASP* 1.3 81.8 - - - +
24X LYS* 1.3 69.9 + - - +
26X ALA* 3.1 2.4 + - - +
27X VAL* 3.0 25.1 + - + +
55X MET* 5.8 0.7 - - - -
66X ILE* 4.0 8.7 - - + -
331X VAL* 3.3 14.5 - - - +
332X GLU 4.9 1.8 + - - -
333X LEU* 3.7 14.4 - - + -
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Residues in contact with LYS 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 4.6 17.9 - - + -
13X LEU* 4.3 26.3 - - + +
14X ASP* 2.8 31.6 + - - +
17X ILE* 2.7 36.7 + - - -
18X ILE* 4.1 1.4 - - - +
19X GLY 3.0 29.3 + - - +
20X GLN* 4.0 10.1 - - + -
21X ALA* 3.0 10.2 + - - +
23X ALA* 1.3 76.5 - - - +
25X ARG* 1.3 56.3 + - - +
27X VAL* 2.6 34.4 + - - +
28X ALA* 2.7 15.0 + - - +
66X ILE* 3.8 15.0 - - + -
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Residues in contact with ARG 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405S ASP* 3.4 37.2 + - - -
406S LYS* 5.2 1.6 - - - +
409S PHE* 4.1 49.6 - - + +
10X VAL* 5.0 8.7 - - + +
21X ALA* 3.1 16.1 + - - +
22X ASP* 3.9 21.7 + - - +
24X LYS* 1.3 78.7 - - - +
26X ALA* 1.3 56.7 + - - +
28X ALA* 3.1 8.0 + - - +
29X ILE* 3.0 34.7 + - - +
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Residues in contact with ALA 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X ASP 3.3 13.9 + - - +
23X ALA 3.1 4.5 + - - +
25X ARG* 1.3 76.7 - - - +
27X VAL* 1.3 65.5 + - + +
29X ILE* 3.2 29.4 - - + +
30X ALA* 3.5 2.6 + - - +
53X ILE* 3.0 19.3 - - + +
329X ILE* 4.1 22.9 - - + -
330X ARG 6.0 0.2 - - - +
331X VAL* 4.3 11.7 - - + -
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Residues in contact with VAL 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 5.1 3.8 - - + -
23X ALA* 3.0 19.5 - - - +
24X LYS* 2.6 16.5 + - - +
26X ALA* 1.3 72.5 - - + +
28X ALA* 1.3 59.6 + - - +
30X ALA* 3.2 15.2 - - - +
31X LEU 3.7 3.1 + - - -
53X ILE* 4.1 12.8 - - + -
55X MET* 5.3 13.5 - - + -
66X ILE* 3.3 38.1 - - + +
70X LEU* 3.4 41.2 - - + +
306X ILE* 5.0 6.5 - - + -
331X VAL* 5.7 1.1 - - + -
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Residues in contact with ALA 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409S PHE* 5.2 0.9 - - + -
6X PRO* 3.7 31.9 - - + +
9X ILE* 4.4 24.5 - - + +
10X VAL* 4.8 5.4 - - + +
13X LEU* 6.1 0.9 - - + -
24X LYS 2.7 10.0 + - - +
25X ARG* 3.1 12.8 + - - +
27X VAL* 1.3 73.5 - - - +
29X ILE* 1.3 53.3 + - - +
30X ALA 2.5 17.0 + - - -
31X LEU* 2.7 18.1 + - - +
32X ARG* 3.1 8.8 + - - +
70X LEU* 5.5 0.2 - - - -
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Residues in contact with ILE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401S GLU* 4.1 20.4 - - - +
405S ASP* 4.2 23.8 - - - +
408S SER* 4.2 16.4 - - - +
409S PHE* 4.0 40.4 - - + +
6X PRO* 4.6 2.6 - - + +
25X ARG* 3.5 11.0 - - + +
26X ALA* 3.2 33.7 - - + +
28X ALA* 1.3 76.7 - - - +
30X ALA* 1.3 57.1 + - - +
32X ARG* 4.0 11.2 - - - -
33X ASN* 2.7 35.3 + - - +
329X ILE* 5.0 5.4 - - + -
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Residues in contact with ALA 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X ALA 3.5 10.3 - - - +
27X VAL 3.2 14.8 + - - +
28X ALA 2.5 6.1 + - - -
29X ILE* 1.3 77.7 - - - +
31X LEU* 1.3 61.6 + - - +
33X ASN* 3.7 5.1 + - - +
34X ARG* 3.7 17.7 + - - +
50X PRO* 5.9 2.1 - - - +
51X LYS* 4.8 6.1 - - - +
53X ILE* 3.7 17.9 - - + -
70X LEU* 5.7 2.7 - - + -
304X LEU* 4.7 27.3 - - + +
306X ILE* 6.2 0.7 - - + -
329X ILE* 5.1 2.5 - - + -
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Residues in contact with LEU 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLU* 4.9 20.3 - - + +
4X MET* 6.2 2.2 - - + -
9X ILE* 3.6 26.9 - - + -
27X VAL 3.7 5.3 + - - +
28X ALA 2.7 14.5 + - - +
30X ALA* 1.3 72.8 - - - +
32X ARG* 1.3 62.6 + - - +
34X ARG* 3.4 40.4 + - - +
35X TRP* 3.7 10.4 + - - +
70X LEU* 4.4 20.1 - - + +
73X LEU 4.5 3.6 - - - +
74X ALA* 3.6 33.4 - - + +
253X ILE* 5.8 2.0 - - + -
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Residues in contact with ARG 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360S MET* 6.2 1.3 - - + -
363S GLU* 2.4 38.6 + - + +
408S SER* 4.9 9.4 - - - +
412S SER* 3.6 10.0 + - - -
4X MET 2.6 33.2 + - - -
5X THR* 3.3 14.1 + - - +
6X PRO* 3.4 26.1 - - + +
9X ILE* 5.2 3.2 - - + +
28X ALA 3.1 11.9 + - - +
29X ILE* 4.3 9.9 - - - +
31X LEU* 1.3 78.4 - - - +
33X ASN* 1.3 58.8 + - - +
34X ARG 3.2 0.2 - - - -
35X TRP* 3.0 32.4 + - - +
36X ARG* 3.1 54.5 + - + +
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Residues in contact with ASN 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356S TYR* 5.2 11.4 - - - -
359S LEU* 4.7 17.6 - - + +
360S MET* 4.0 16.3 - - - +
401S GLU* 5.2 9.3 + - - -
408S SER* 3.3 24.6 + - - -
29X ILE* 2.7 27.5 + - - +
30X ALA* 3.7 5.6 + - - +
31X LEU 3.3 0.6 - - - -
32X ARG* 1.3 78.4 - - - +
34X ARG* 1.3 55.9 + - - +
35X TRP 3.2 3.6 - - - -
36X ARG* 4.2 8.5 - - - +
37X ARG* 3.3 20.8 + - - +
50X PRO* 5.9 6.4 - - + +
51X LYS* 5.5 12.7 - - + +
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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