Contacts of the helix formed by residues 22 - 36 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20T PRO 4.5 4.7 - - - +
21T LEU* 1.3 77.3 - - - +
23T THR* 1.3 65.9 + - - +
24T ASP* 3.5 6.8 + - - +
25T GLN* 2.9 41.7 + - - +
26T LEU* 3.0 21.9 + - - +
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Residues in contact with THR 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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22T THR* 1.3 74.8 - - - +
24T ASP* 1.3 71.9 + - - +
26T LEU* 3.6 10.9 + - - +
27T ALA* 3.2 21.9 + - + +
84T LEU* 5.6 4.3 - - + +
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Residues in contact with ASP 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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22T THR* 3.2 7.5 + - - +
23T THR* 1.3 84.9 - - - +
25T GLN* 1.3 65.4 + - + +
27T ALA* 3.4 7.7 + - - +
28T ARG* 3.0 39.8 + - - +
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Residues in contact with GLN 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLN* 3.8 22.0 + - - +
433B GLU* 4.2 16.3 + - - +
19T PRO 5.0 1.0 - - - +
20T PRO 3.7 4.0 - - - +
21T LEU* 3.4 19.7 - - + +
22T THR* 2.9 46.9 + - - +
24T ASP* 1.3 76.8 - - + +
26T LEU* 1.3 66.1 + - - +
28T ARG* 3.2 10.7 + - - +
29T GLN* 3.1 27.9 + - - +
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Residues in contact with LEU 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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21T LEU* 4.4 19.6 - - + +
22T THR 3.0 16.4 + - - +
23T THR* 3.7 9.2 - - - +
25T GLN* 1.3 78.3 - - - +
27T ALA* 1.3 62.7 + - - +
29T GLN* 3.1 14.2 + - - +
30T VAL* 3.2 21.5 + - + +
84T LEU* 5.1 11.4 - - + -
87T LEU* 4.0 23.6 - - + -
101T ILE* 4.5 4.7 - - + -
115T PHE* 3.6 31.2 - - + -
117T ALA* 4.3 18.4 - - + +
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Residues in contact with ALA 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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23T THR* 3.2 12.4 + - + +
24T ASP* 3.6 12.1 - - - +
26T LEU* 1.3 79.2 - - - +
28T ARG* 1.3 59.9 + - - +
30T VAL* 3.3 9.8 + - - +
31T ASP* 3.0 37.1 + - - +
80T PRO* 5.0 3.3 - - + +
84T LEU* 4.4 22.0 - - + +
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Residues in contact with ARG 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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432B ASN 4.2 5.4 - - - +
433B GLU* 4.4 40.4 + - + +
24T ASP* 3.0 31.5 + - - +
25T GLN* 3.5 9.2 - - - +
26T LEU 3.2 0.4 - - - -
27T ALA* 1.3 76.4 - - - +
29T GLN* 1.3 65.5 + - - +
31T ASP* 3.4 16.9 + - + +
32T TYR* 3.1 22.0 + - - +
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Residues in contact with GLN 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLN* 3.9 28.9 + - - +
432B ASN* 3.0 41.9 + - - +
433B GLU* 4.2 8.9 + - - +
15T LEU* 4.1 25.3 - - + +
21T LEU* 4.5 10.5 - - + -
25T GLN* 3.1 15.0 + - - +
26T LEU 3.1 7.7 + - - +
28T ARG* 1.3 75.1 - - - +
30T VAL* 1.3 64.1 + - - +
32T TYR* 3.3 9.9 + - - +
33T LEU* 3.2 21.1 + - - +
113T VAL* 5.5 1.9 - - - +
115T PHE* 3.9 24.2 - - + -
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Residues in contact with VAL 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 LEU* 3.2 15.6 + - + +
27T ALA 3.6 6.7 - - - +
28T ARG 3.3 0.2 - - - -
29T GLN* 1.3 74.8 - - - +
31T ASP* 1.3 63.9 + - - +
33T LEU* 3.3 13.7 + - + +
34T LEU* 3.0 25.8 + - + +
80T PRO* 3.9 23.3 - - + +
83T VAL* 4.0 28.5 - - + -
84T LEU* 3.7 22.2 - - + -
101T ILE* 4.6 21.1 - - + -
115T PHE* 4.8 6.1 - - + -
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Residues in contact with ASP 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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27T ALA* 3.0 26.3 + - - +
28T ARG* 3.7 18.9 + - + +
29T GLN 3.3 0.2 - - - -
30T VAL* 1.3 76.5 - - - +
32T TYR* 1.3 57.3 + - - +
34T LEU* 3.7 4.5 - - - +
35T ASN* 2.8 47.5 + - - +
80T PRO* 3.1 32.5 - - - +
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Residues in contact with TYR 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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396B ASP* 4.4 4.7 + - - -
431B ARG* 3.5 23.5 + - + -
432B ASN* 3.2 71.2 + - + +
28T ARG 3.1 9.4 + - - +
29T GLN* 3.3 13.9 - - - +
31T ASP* 1.3 78.2 - - - +
33T LEU* 1.3 62.1 + - - +
35T ASN* 3.5 5.2 + - - +
36T ASN* 2.7 54.4 + - - -
38T TRP* 3.7 27.2 - + - -
112T CYS 5.4 0.8 + - - -
113T VAL* 4.0 15.0 - - + -
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Residues in contact with LEU 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 GLN 3.2 8.0 + - - +
30T VAL* 3.3 18.1 + - + +
32T TYR* 1.3 81.2 - - - +
34T LEU* 1.3 62.8 + - + +
36T ASN 3.6 3.5 + - - -
38T TRP* 3.1 62.4 + - + +
40T PRO* 4.0 22.9 - - + -
101T ILE* 4.3 18.2 - - + -
102T ILE 4.0 19.3 - - - +
103T GLY* 4.2 7.6 - - - -
113T VAL* 4.2 24.7 - - + -
115T PHE* 5.5 0.7 - - + -
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Residues in contact with LEU 34 (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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30T VAL* 3.0 21.6 + - + +
31T ASP* 3.8 4.7 - - - +
33T LEU* 1.3 76.5 - - + +
35T ASN* 1.3 63.2 + - - +
36T ASN 3.1 1.6 - - - -
37T LYS* 2.9 28.8 + - - +
38T TRP 4.3 4.5 - - - +
40T PRO* 4.1 29.4 - - + -
77T CYS* 3.6 24.9 - - - +
78T THR* 3.9 11.7 - - - +
79T ASP 3.7 6.3 - - - +
80T PRO* 3.3 48.0 - - + -
83T VAL* 4.8 0.7 - - + -
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Residues in contact with ASN 35 (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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31T ASP* 2.8 33.4 + - - +
32T TYR* 3.5 6.9 + - - +
34T LEU* 1.3 78.5 - - - +
36T ASN* 1.3 61.6 + - - +
37T LYS* 3.2 18.9 + - - +
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Residues in contact with ASN 36 (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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32T TYR* 2.7 54.3 + - - +
33T LEU 4.0 0.2 - - - +
34T LEU 3.1 1.0 - - - -
35T ASN* 1.3 79.6 - - - +
37T LYS* 1.3 71.1 + - - +
38T TRP* 3.2 48.5 + - + -
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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