Contacts of the helix formed by residues 22 - 36 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20S PRO 4.5 4.7 - - - +
21S LEU* 1.3 77.4 - - - +
23S THR* 1.3 65.2 + - - +
24S ASP* 3.5 8.8 + - - +
25S GLN* 3.1 38.1 + - - +
26S LEU* 2.9 20.5 + - - +
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Residues in contact with THR 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S THR* 1.3 74.3 - - - +
24S ASP* 1.3 64.6 + - - +
26S LEU* 3.6 13.6 + - + +
27S ALA* 3.1 27.2 + - - +
84S LEU* 5.7 1.4 - - - +
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Residues in contact with ASP 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S THR* 3.1 8.5 + - - +
23S THR* 1.3 82.8 + - - +
25S GLN* 1.3 60.9 + - + +
27S ALA* 3.3 7.3 + - - +
28S ARG* 3.0 35.5 + - + +
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Residues in contact with GLN 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLN* 3.8 23.2 + - - +
433A GLU* 4.0 20.7 + - - +
19S PRO 4.9 1.2 - - - +
20S PRO 3.7 5.9 - - - +
21S LEU* 3.4 21.8 - - + +
22S THR* 3.1 40.4 + - - +
24S ASP* 1.3 75.5 - - + +
26S LEU* 1.3 65.5 + - - +
28S ARG* 3.4 3.4 + - - +
29S GLN* 3.2 28.3 + - - +
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Residues in contact with LEU 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S LEU* 4.3 19.9 - - + +
22S THR 2.9 16.0 + - - +
23S THR* 3.7 13.0 - - + +
25S GLN* 1.3 75.8 - - - +
27S ALA* 1.3 63.9 + - - +
29S GLN* 3.1 12.3 + - - +
30S VAL* 3.2 19.5 + - + +
84S LEU* 4.1 12.6 - - + -
87S LEU* 4.0 22.9 - - + -
101S ILE* 4.2 9.6 - - + -
115S PHE* 3.8 26.7 - - + -
117S ALA* 4.8 11.0 - - + +
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Residues in contact with ALA 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S THR 3.1 15.2 + - - +
24S ASP* 3.5 9.9 - - - +
26S LEU* 1.3 80.3 - - - +
28S ARG* 1.3 57.1 + - + +
30S VAL* 3.2 9.8 + - - +
31S ASP* 3.0 36.3 + - - +
80S PRO* 5.2 2.4 - - + +
84S LEU* 4.6 19.4 - - + +
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Residues in contact with ARG 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ASN 4.1 5.4 - - - +
433A GLU* 4.1 50.6 + - + +
24S ASP* 3.0 20.0 + - - +
25S GLN 3.7 7.9 - - - +
26S LEU 3.3 0.4 - - - -
27S ALA* 1.3 76.3 - - - +
29S GLN* 1.3 63.0 + - - +
31S ASP* 3.3 15.7 + - - +
32S TYR* 3.0 23.0 + - - +
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Residues in contact with GLN 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLN* 3.9 24.2 + - - +
432A ASN* 3.0 41.4 - - - +
433A GLU* 4.4 5.2 - - - +
15S LEU* 4.1 28.3 - - + +
21S LEU* 4.7 6.5 - - + -
25S GLN 3.2 16.3 + - - +
26S LEU* 3.1 10.3 + - - +
28S ARG* 1.3 77.4 - - - +
30S VAL* 1.3 61.4 + - - +
32S TYR* 3.3 9.6 + - - +
33S LEU* 3.1 21.0 + - - +
113S VAL* 5.4 3.8 - - - +
115S PHE* 3.8 28.1 - - + -
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Residues in contact with VAL 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S LEU* 3.2 26.9 + - + +
27S ALA* 3.2 8.2 + - - +
29S GLN* 1.3 75.2 - - - +
31S ASP* 1.3 63.2 + - - +
33S LEU* 3.3 11.8 + - + +
34S LEU* 3.0 31.2 + - + +
40S PRO* 6.0 0.4 - - + -
80S PRO* 3.9 23.3 - - + +
83S VAL* 4.1 24.2 - - + -
84S LEU* 4.4 15.0 - - + -
101S ILE* 4.4 16.2 - - + -
115S PHE* 4.8 4.3 - - + -
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Residues in contact with ASP 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ALA* 3.0 24.6 + - - +
28S ARG* 3.6 20.9 + - - +
30S VAL* 1.3 73.4 - - - +
32S TYR* 1.3 60.0 + - - +
34S LEU* 3.3 5.7 + - - +
35S ASN* 2.8 49.6 + - - +
80S PRO* 3.7 28.6 - - - +
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Residues in contact with TYR 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ASP* 4.4 4.3 + - - -
431A ARG* 3.7 24.5 + - + -
432A ASN* 3.2 70.6 + - + +
28S ARG 3.0 8.9 + - - +
29S GLN* 3.4 11.0 - - - +
31S ASP* 1.3 77.0 - - - +
33S LEU* 1.3 62.6 + - - +
35S ASN* 3.4 6.4 + - + +
36S ASN* 2.9 52.4 + - - -
38S TRP* 3.6 29.1 - + - -
112S CYS 5.4 1.3 - - - -
113S VAL* 4.2 12.3 - - + -
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Residues in contact with LEU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S GLN 3.1 9.6 + - - +
30S VAL* 3.4 14.8 - - + +
31S ASP 3.2 0.2 - - - -
32S TYR* 1.3 83.4 - - - +
34S LEU* 1.3 66.9 + - + +
36S ASN 3.4 3.3 + - - -
37S LYS 3.5 0.2 + - - -
38S TRP* 3.2 66.0 + - + +
39S VAL 4.2 0.4 - - - -
40S PRO* 3.9 23.1 - - + -
101S ILE* 4.2 14.6 - - + -
102S ILE 3.8 22.2 - - - +
103S GLY* 3.8 12.1 - - - -
113S VAL* 4.0 22.2 - - + -
115S PHE* 5.5 0.9 - - + -
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Residues in contact with LEU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S VAL* 3.0 23.3 + - + +
31S ASP* 3.9 5.4 - - - +
33S LEU* 1.3 75.1 - - + +
35S ASN* 1.3 62.0 + - - +
36S ASN 3.1 2.0 - - - -
37S LYS* 3.0 27.6 + - - +
38S TRP 4.3 5.2 - - - +
40S PRO* 4.2 21.8 - - + -
77S CYS* 3.5 35.9 - - - +
78S THR* 4.3 8.7 - - - +
79S ASP 3.9 5.6 - - - +
80S PRO* 3.4 47.6 - - + -
83S VAL* 4.8 0.7 - - + -
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Residues in contact with ASN 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ASP* 2.8 46.1 + - - +
32S TYR* 4.0 6.7 - - - +
34S LEU* 1.3 74.7 - - - +
36S ASN* 1.3 60.9 + - - +
37S LYS* 3.0 25.1 + - - +
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Residues in contact with ASN 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S TYR* 2.9 58.1 + - - +
34S LEU 3.1 0.8 - - - -
35S ASN* 1.3 77.4 - - - +
37S LYS* 1.3 71.8 + - - +
38S TRP* 3.3 43.8 + - + -
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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