Contacts of the helix formed by residues 22 - 36 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20V PRO 4.5 5.2 - - - +
21V LEU* 1.3 78.3 - - - +
23V THR* 1.3 66.4 + - - +
24V ASP* 3.7 7.7 + - - +
25V GLN* 3.0 41.3 + - - +
26V LEU* 3.0 18.9 + - - +
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Residues in contact with THR 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 1.3 73.5 - - - +
24V ASP* 1.3 69.2 + - - +
26V LEU* 3.4 11.8 + - + +
27V ALA* 3.0 23.2 + - - +
84V LEU* 6.1 0.2 - - - +
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Residues in contact with ASP 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 3.2 7.0 + - - +
23V THR* 1.3 86.3 + - - +
25V GLN* 1.3 59.7 + - + +
27V ALA* 3.3 8.0 + - - +
28V ARG* 2.9 36.2 + - + +
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Residues in contact with GLN 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D GLN* 3.7 23.5 + - - +
433D GLU* 3.9 22.4 + - - +
19V PRO 5.0 1.2 - - - +
20V PRO 3.7 4.9 - - - +
21V LEU* 3.4 20.1 - - + +
22V THR* 3.0 45.5 + - - +
24V ASP* 1.3 75.5 - - + +
26V LEU* 1.3 65.4 + - - +
28V ARG* 3.4 3.6 + - - +
29V GLN* 3.3 28.3 + - - +
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Residues in contact with LEU 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V LEU* 4.3 16.7 - - + +
22V THR 3.0 14.0 + - - +
23V THR* 3.6 13.9 - - + +
24V ASP 3.3 0.2 - - - -
25V GLN* 1.3 75.8 - - - +
27V ALA* 1.3 65.0 + - - +
29V GLN* 3.1 14.8 + - - +
30V VAL* 3.3 13.0 + - + +
84V LEU* 3.9 23.1 - - + -
87V LEU* 4.0 16.8 - - + -
101V ILE* 4.4 6.3 - - + -
115V PHE* 3.4 33.2 - - + -
117V ALA* 4.3 17.7 - - + +
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Residues in contact with ALA 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V THR 3.0 17.3 + - - +
24V ASP* 3.3 9.6 + - - +
26V LEU* 1.3 79.3 - - - +
28V ARG* 1.3 55.6 + - - +
30V VAL* 3.2 9.1 + - - +
31V ASP* 3.0 35.5 + - - +
80V PRO* 5.1 2.2 - - + +
84V LEU* 4.4 21.5 - - + +
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Residues in contact with ARG 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D ASN 4.1 5.1 - - - +
433D GLU* 3.0 60.9 + - + +
435D ARG* 6.2 0.6 - - - +
24V ASP* 2.9 24.4 + - + +
25V GLN 3.7 7.0 - - - +
26V LEU 3.2 0.2 - - - -
27V ALA* 1.3 78.0 - - + +
29V GLN* 1.3 59.7 + - - +
31V ASP* 3.3 13.5 + - - +
32V TYR* 3.0 28.2 + - - +
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Residues in contact with GLN 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D GLN* 4.1 22.1 + - - +
432D ASN* 3.0 41.5 + - - +
433D GLU* 4.4 6.6 - - - +
15V LEU* 4.0 30.4 - - + +
21V LEU* 4.6 9.0 - - + -
25V GLN 3.3 16.0 - - - +
26V LEU 3.1 9.0 + - - +
28V ARG* 1.3 76.2 - - - +
30V VAL* 1.3 57.6 + - - +
32V TYR* 3.4 9.4 + - - +
33V LEU* 3.1 25.8 + - - +
113V VAL* 5.4 3.7 - - - +
115V PHE* 3.8 25.8 - - + -
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Residues in contact with VAL 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 3.3 12.8 + - + +
27V ALA* 3.2 8.5 + - - +
28V ARG 3.2 0.2 - - - -
29V GLN* 1.3 76.2 - - - +
31V ASP* 1.3 60.4 + - - +
33V LEU* 3.2 12.8 + - + +
34V LEU* 3.0 30.1 + - + +
40V PRO* 6.0 0.2 - - + -
80V PRO* 3.8 29.8 - - + +
83V VAL* 4.0 24.7 - - + -
84V LEU* 4.2 21.1 - - + -
101V ILE* 4.4 21.5 - - + -
115V PHE* 4.7 5.6 - - + -
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Residues in contact with ASP 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ALA* 3.0 23.0 + - - +
28V ARG* 3.6 18.9 - - - +
30V VAL* 1.3 72.6 - - - +
32V TYR* 1.3 57.1 + - - +
34V LEU* 3.3 4.3 + - - +
35V ASN* 2.8 54.6 + - - +
80V PRO* 3.8 28.5 - - - +
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Residues in contact with TYR 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D ASP* 4.5 4.2 + - - -
431D ARG* 3.5 26.9 + - + -
432D ASN* 3.3 61.5 - - + +
28V ARG 3.0 13.5 + - - +
29V GLN* 3.4 12.3 - - - +
30V VAL 3.2 0.2 - - - -
31V ASP* 1.3 78.6 - - - +
33V LEU* 1.3 62.3 + - - +
35V ASN* 4.0 5.1 - - + +
36V ASN* 2.7 53.5 + - - -
38V TRP* 3.6 28.8 - + - -
112V CYS 5.3 1.3 - - - -
113V VAL* 4.2 11.9 - - + -
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Residues in contact with LEU 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V GLN 3.1 13.6 + - - +
30V VAL* 3.4 13.5 - - + +
32V TYR* 1.3 81.3 - - - +
34V LEU* 1.3 68.0 + - + +
36V ASN 3.4 3.6 + - - -
38V TRP* 3.2 65.8 + - + +
39V VAL 4.2 0.7 - - - -
40V PRO* 3.8 24.9 - - + -
101V ILE* 4.2 11.9 - - + -
102V ILE 3.8 10.5 - - - +
103V GLY* 3.7 26.5 - - - +
113V VAL* 4.0 20.4 - - + -
115V PHE* 5.6 0.7 - - + -
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Residues in contact with LEU 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V VAL* 3.0 25.2 + - + +
31V ASP* 4.0 5.4 - - - +
33V LEU* 1.3 81.2 - - + +
35V ASN* 1.3 59.9 + - - +
37V LYS* 3.0 26.7 + - - +
38V TRP 4.2 5.8 - - - +
40V PRO* 4.0 25.6 - - + -
77V CYS* 3.4 32.7 - - - +
78V THR* 4.1 9.9 - - - +
79V ASP 3.8 5.8 - - - +
80V PRO* 3.4 44.2 - - + -
83V VAL* 4.6 1.8 - - + -
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Residues in contact with ASN 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V ASP* 2.8 46.2 + - - +
32V TYR* 3.5 6.6 + - - +
33V LEU 3.4 0.2 - - - -
34V LEU* 1.3 75.3 - - - +
36V ASN* 1.3 60.8 + - - +
37V LYS* 3.1 14.5 + - - +
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Residues in contact with ASN 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V TYR* 2.7 56.1 + - - +
33V LEU 3.4 0.2 + - - -
34V LEU 3.2 0.8 - - - -
35V ASN* 1.3 79.4 - - - +
37V LYS* 1.3 71.1 + - - +
38V TRP* 3.2 47.7 + - + -
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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