Contacts of the helix formed by residues 29 - 35 (chain A) in PDB entry 1Q4U
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 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.5 18.8 - - + +
25A ALA 3.4 14.6 - - - +
26A TYR* 2.7 20.8 + - - -
28A GLN* 1.3 80.4 - - - +
30A LEU* 1.3 60.9 + - - +
31A ASP* 3.5 13.6 + - - +
32A GLY 3.2 10.4 + - - -
33A THR* 2.7 32.6 + - - -
54B ASP 3.4 7.2 - - - -
55B THR 4.2 0.2 - - - -
57B ARG 3.4 7.2 - - - +
58B GLN 3.7 2.2 - - - -
59B ARG* 3.5 31.0 - - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 1.3 71.4 - - - +
31A ASP* 1.3 68.7 + - - +
33A THR* 3.1 5.1 + - - -
34A VAL* 2.9 42.8 + - + +
36A PHE* 4.4 11.4 - - + -
70A ALA* 4.7 7.6 - - + -
30B LEU* 5.2 5.2 - - + -
34B VAL* 4.8 13.0 - - + -
54B ASP 3.7 0.2 + - - -
55B THR 3.1 25.6 + - - +
56B LEU* 4.4 2.5 - - - +
57B ARG 2.9 17.2 + - - +
64B HIS* 3.8 31.2 - - + +
66B GLY 4.7 2.2 - - - -
67B ALA* 4.3 22.4 - - + +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.4 5.5 - - + +
26A TYR* 4.2 11.0 - - + -
29A THR* 3.1 10.4 + - - +
30A LEU* 1.3 77.2 - - - +
32A GLY* 1.3 57.2 + - - +
34A VAL* 3.4 1.4 + - - +
35A GLY 2.9 9.2 + - - -
36A PHE* 2.9 60.3 + - + -
74A MET* 3.2 21.0 - - + +
370A 4CA 4.0 2.9 + - - -
58B GLN* 4.0 13.0 - - - +
59B ARG 4.8 0.9 + - - -
64B HIS* 2.6 37.2 + - - -
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.2 43.7 + - - -
27A GLU* 4.2 8.4 - - - -
29A THR* 3.2 7.9 + - - -
31A ASP* 1.3 76.2 - - - +
33A THR* 1.3 67.5 + - - +
35A GLY* 3.2 10.9 + - - -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU 3.9 10.5 + - - -
28A GLN 4.0 3.1 + - - -
29A THR 2.7 23.1 + - - -
30A LEU* 3.1 4.9 + - - -
32A GLY* 1.3 79.7 - - - +
34A VAL* 1.3 63.3 + - + +
55A THR* 4.0 12.8 + - + +
33B THR* 3.7 30.1 - - + -
34B VAL* 6.2 0.2 - - + -
55B THR* 3.8 20.5 + - + +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 2.9 26.4 + - + +
31A ASP 3.5 5.2 - - - +
33A THR* 1.3 81.6 - - + +
35A GLY* 1.3 59.3 + - - +
36A PHE* 3.6 33.2 - - + -
50A VAL* 3.2 16.6 - - - +
51A GLU 4.5 3.8 - - - +
53A THR* 5.2 5.2 + - - +
55A THR* 3.9 21.7 - - + +
56A LEU* 3.8 18.1 - - + +
30B LEU* 3.8 28.0 - - + -
33B THR* 6.0 0.4 - - + -
34B VAL* 6.2 0.7 - - + -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.8 6.7 - - - -
31A ASP 2.9 8.2 + - - -
32A GLY 3.2 11.8 + - - -
34A VAL* 1.3 80.0 - - - +
36A PHE* 1.3 64.3 + - - -
37A VAL* 3.4 10.8 + - - +
49A SER 3.7 2.4 - - - +
50A VAL* 3.5 14.4 - - - +
51A GLU 4.7 1.2 + - - -
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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