Contacts of the helix formed by residues 17 - 25 (chain D) in PDB entry 5IRC
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 GLY 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ALA 3.2 3.4 - - - -
16D CYS* 1.3 80.2 - - - +
18D LYS* 1.3 66.0 + - - +
20D CSX 3.7 1.7 + - - +
21D LEU* 3.1 23.6 + - - +
117D ASN* 3.6 10.0 + - - -
118D LYS* 4.2 0.4 - - - -
161D ALA* 5.4 0.5 - - - +
201D GDP 3.0 41.5 + - - -
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Residues in contact with LYS 18 (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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10D ILE* 3.7 26.4 - - + +
11D VAL* 3.4 34.3 - - - +
12D GLY* 3.0 10.2 + - - +
13D ASP 2.8 18.0 + - - -
16D CYS* 4.0 12.3 - - - -
17D GLY* 1.3 69.6 - - - +
19D THR* 1.3 63.8 + - - +
21D LEU* 3.3 4.3 + - - +
22D LEU* 3.1 26.2 + - - +
59D ASP* 4.1 7.6 - - - +
60D THR* 3.5 20.0 - - - -
62D GLY 4.3 1.6 - - - +
83D CYS* 4.3 4.9 - - + -
117D ASN* 4.5 1.8 - - - +
201D GDP 2.7 29.6 + - - +
203D MGF 2.6 34.6 - - - -
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Residues in contact with THR 19 (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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18D LYS* 1.3 73.5 - - - +
20D CSX 1.3 60.7 + - - +
22D LEU* 3.1 4.2 + - - +
23D ILE* 2.8 50.4 + - + +
35D VAL 5.9 2.0 - - - +
37D THR* 2.8 5.3 + - - +
42D TYR* 4.4 9.9 - - + +
59D ASP* 2.5 26.2 + - - +
201D GDP 3.1 13.0 + - - +
202D MG 2.1 29.8 - - - -
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Residues in contact with CSX 20 (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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17D GLY 3.9 0.9 - - - +
19D THR* 1.3 78.0 + - - +
21D LEU* 1.3 62.0 + - - +
23D ILE* 4.5 4.9 - - - -
24D VAL* 3.0 33.1 + - + +
33D VAL 5.9 2.5 - - - -
161D ALA* 3.9 8.1 - - + -
201D GDP 2.8 70.4 + - + +
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Residues in contact with LEU 21 (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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10D ILE* 3.8 21.3 - - + -
17D GLY 3.1 14.9 + - - +
18D LYS 3.5 7.6 - - - +
19D THR 3.2 0.2 - - - -
20D CSX 1.3 76.7 + - - +
22D LEU* 1.3 62.4 + - - +
24D VAL* 3.5 5.0 - - - +
25D ASN 3.3 14.4 + - - -
81D LEU* 4.1 14.8 - - + -
83D CYS* 4.3 2.9 - - - -
115D VAL* 4.2 13.5 - - + -
117D ASN* 3.8 17.7 - - - +
159D CYS* 3.7 24.5 - - - -
161D ALA* 4.1 8.4 - - + +
167D VAL* 3.8 17.3 - - + -
170D VAL* 4.5 4.7 - - + -
171D PHE* 3.6 28.6 - - + -
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Residues in contact with LEU 22 (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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8D LEU* 4.2 7.6 - - + -
10D ILE* 3.6 28.5 - - + -
18D LYS 3.1 11.5 + - - +
19D THR* 3.1 6.7 + - - +
21D LEU* 1.3 76.0 - - - +
23D ILE* 1.3 59.7 + - - +
25D ASN* 3.1 28.8 + - - -
42D TYR* 4.2 20.8 - - + +
57D LEU* 4.2 27.0 - - + +
58D TRP 4.7 0.4 - - - -
59D ASP* 3.6 41.5 - - + +
171D PHE* 3.8 27.1 - - + -
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Residues in contact with ILE 23 (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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19D THR* 2.8 34.1 + - + +
20D CSX 4.1 4.9 - - - +
22D LEU* 1.3 75.3 - - - +
24D VAL* 1.3 68.5 + - + +
25D ASN* 2.9 17.6 + - - +
42D TYR* 3.6 41.7 - - + +
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Residues in contact with VAL 24 (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 CSX 3.0 22.3 + - + +
21D LEU 3.5 8.1 - - - +
23D ILE* 1.3 74.6 - - + +
25D ASN* 1.3 70.4 + - - +
161D ALA* 3.6 29.4 - - + +
164D LYS* 4.9 13.8 - - + +
167D VAL* 3.5 31.9 - - + +
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Residues in contact with ASN 25 (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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21D LEU 3.3 1.6 + - - -
22D LEU 3.1 20.9 + - - +
23D ILE* 2.9 15.5 + - - +
24D VAL* 1.3 85.3 - - - +
42D TYR* 5.9 2.0 - - - +
43D VAL 4.7 4.8 + - - -
44D ALA* 4.3 27.4 - - + +
57D LEU* 4.5 5.5 - - - +
167D VAL* 4.3 7.4 - - - -
168D ARG* 6.1 2.0 - - - -
171D PHE* 3.7 39.8 - - - +
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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