Contacts of the helix formed by residues 22 - 36 (chain U) in PDB entry 1IR1
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 THR 22 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20U PRO 4.4 4.3 - - - +
21U LEU* 1.3 77.1 - - - +
23U THR* 1.3 66.7 + - - +
24U ASP* 3.7 5.5 + - - +
25U GLN* 2.9 44.3 + - - +
26U LEU* 3.0 21.2 + - - +
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Residues in contact with THR 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U THR* 1.3 75.5 - - - +
24U ASP* 1.3 71.1 + - - +
26U LEU* 3.3 10.6 + - + +
27U ALA* 3.1 21.1 + - + +
84U LEU* 5.8 2.3 - - + +
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Residues in contact with ASP 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U THR* 3.3 5.6 + - - +
23U THR* 1.3 83.3 - - - +
25U GLN* 1.3 64.3 + - + +
27U ALA* 3.2 9.2 + - - +
28U ARG* 2.9 34.9 + - + +
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Residues in contact with GLN 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C GLN* 3.8 22.6 + - - +
433C GLU* 4.0 20.4 + - - +
19U PRO 5.1 0.9 - - - +
20U PRO 3.7 4.2 - - - +
21U LEU* 3.5 19.5 - - + +
22U THR* 2.9 45.0 + - - +
24U ASP* 1.3 78.2 - - + +
26U LEU* 1.3 61.3 + - - +
28U ARG* 3.4 4.9 + - - +
29U GLN* 3.3 27.3 + - - +
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Residues in contact with LEU 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U LEU* 4.2 18.1 - - + +
22U THR 3.0 12.9 + - - +
23U THR* 3.5 13.7 - - + +
25U GLN* 1.3 75.5 - - - +
27U ALA* 1.3 66.0 + - - +
29U GLN* 3.1 14.1 + - - +
30U VAL* 3.2 13.5 + - + +
84U LEU* 4.1 23.1 - - + -
87U LEU* 4.2 16.2 - - + -
101U ILE* 4.5 5.4 - - + -
115U PHE* 3.5 32.8 - - + -
117U ALA* 4.4 17.5 - - + +
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Residues in contact with ALA 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U THR* 3.1 11.7 + - + +
24U ASP* 3.5 13.2 - - - +
26U LEU* 1.3 80.3 - - - +
28U ARG* 1.3 57.5 + - + +
30U VAL* 3.2 6.4 + - - +
31U ASP* 2.9 34.7 + - - +
80U PRO* 5.1 3.2 - - + +
84U LEU* 4.3 25.1 - - + +
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Residues in contact with ARG 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C ASN 4.1 5.5 - - - +
433C GLU* 2.9 60.4 + - + +
435C ARG* 6.2 1.4 - - - +
24U ASP* 2.9 23.6 + - + +
25U GLN* 3.7 7.9 - - - +
26U LEU 3.2 0.4 - - - -
27U ALA* 1.3 75.5 - - + +
29U GLN* 1.3 61.1 + - - +
31U ASP* 3.3 13.5 + - - +
32U TYR* 3.0 27.2 + - - +
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Residues in contact with GLN 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C GLN* 4.0 25.2 + - - +
432C ASN* 3.0 40.7 - - - +
433C GLU* 4.3 5.5 - - - +
15U LEU* 4.2 26.5 - - + +
21U LEU* 4.4 11.2 - - + -
25U GLN 3.4 15.1 - - - +
26U LEU 3.1 8.4 + - - +
28U ARG* 1.3 77.7 - - - +
30U VAL* 1.3 62.3 + - - +
32U TYR* 3.3 9.7 + - - +
33U LEU* 3.1 22.2 + - - +
113U VAL* 5.4 3.6 - - - +
115U PHE* 3.8 26.2 - - + -
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Residues in contact with VAL 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U LEU* 3.2 13.8 + - + +
27U ALA* 3.2 8.3 + - - +
29U GLN* 1.3 75.6 - - - +
31U ASP* 1.3 60.1 + - - +
33U LEU* 3.3 12.0 + - + +
34U LEU* 3.0 32.9 + - + +
80U PRO* 3.8 29.8 - - + +
83U VAL* 4.0 21.1 - - + -
84U LEU* 4.2 20.9 - - + -
101U ILE* 4.4 22.2 - - + -
115U PHE* 4.8 5.4 - - + -
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Residues in contact with ASP 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U ALA* 2.9 23.0 + - - +
28U ARG* 3.5 18.6 - - - +
29U GLN 3.3 0.2 - - - -
30U VAL* 1.3 75.8 - - - +
32U TYR* 1.3 51.6 + - - +
34U LEU* 3.3 4.9 + - - +
35U ASN* 2.7 55.6 + - - +
80U PRO* 3.9 25.3 - - - +
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Residues in contact with TYR 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C ASP* 4.3 4.7 + - - -
431C ARG* 3.5 23.3 + - + -
432C ASN* 3.2 67.2 + - + +
28U ARG 3.0 13.5 + - - +
29U GLN* 3.3 13.5 - - - +
31U ASP* 1.3 77.0 - - - +
33U LEU* 1.3 63.2 + - - +
35U ASN* 3.4 7.7 + - + +
36U ASN* 2.9 52.0 + - - -
38U TRP* 3.6 26.6 - + - -
112U CYS 5.4 1.3 + - - -
113U VAL* 4.1 13.7 - - + -
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Residues in contact with LEU 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U GLN 3.1 9.4 + - - +
30U VAL* 3.6 14.8 - - + +
32U TYR* 1.3 82.2 - - - +
34U LEU* 1.3 68.9 + - + +
36U ASN* 3.3 7.3 + - - +
38U TRP* 3.2 62.7 + - + +
40U PRO* 4.1 16.4 - - + -
101U ILE* 4.2 13.9 - - + -
102U ILE 3.8 24.2 - - - +
103U GLY* 3.8 12.8 - - - +
113U VAL* 4.2 16.8 - - + -
115U PHE* 5.7 0.9 - - + -
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U VAL* 3.0 22.8 + - + +
31U ASP* 3.8 5.8 - - - +
33U LEU* 1.3 80.1 - - + +
35U ASN* 1.3 61.5 + - - +
37U LYS* 3.0 30.7 + - - +
38U TRP 4.1 6.7 - - - +
40U PRO* 4.0 31.0 - - + -
77U CYS* 3.9 24.2 - - - +
78U THR* 4.2 8.7 - - - +
79U ASP 3.9 6.3 - - - +
80U PRO* 3.5 44.2 - - + -
83U VAL* 4.5 3.8 - - + -
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Residues in contact with ASN 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U ASP* 2.7 49.1 + - - +
32U TYR* 3.9 7.5 - - + +
34U LEU* 1.3 74.4 - - - +
36U ASN* 1.3 60.2 + - - +
37U LYS* 3.1 15.8 + - - +
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Residues in contact with ASN 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U TYR* 2.9 54.8 + - - +
34U LEU 3.2 1.0 - - - -
35U ASN* 1.3 77.6 - - - +
37U LYS* 1.3 71.3 + - - +
38U TRP* 3.3 46.7 + - + +
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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