Contacts of the helix formed by residues 29 - 35 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP 3.5 4.3 - - - -
55A THR 4.1 0.4 - - - -
57A ARG 3.3 8.1 - - - -
58A GLN 3.5 5.8 - - - -
59A ARG* 3.4 35.2 - - + +
24B VAL* 3.5 17.9 - - + +
25B ALA 3.6 8.1 - - - +
26B TYR* 2.7 22.4 + - - +
28B GLN* 1.3 77.9 - - - +
30B LEU* 1.3 60.9 - - - +
31B ASP* 3.4 12.7 + - - +
32B GLY 3.0 10.7 + - - -
33B THR* 2.7 33.1 + - - -
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Residues in contact with LEU 30 (chain B).
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* 5.2 7.4 - - + -
34A VAL* 3.8 21.3 - - + -
55A THR* 3.0 28.8 + - + +
56A LEU* 4.4 1.6 - - - +
57A ARG 2.8 16.2 + - - +
64A HIS* 3.6 39.9 - - + +
66A GLY 4.6 0.4 - - - -
67A ALA* 4.2 18.6 - - + +
29B THR* 1.3 70.3 - - - +
31B ASP* 1.3 64.2 + - - +
33B THR* 3.2 4.8 + - + -
34B VAL* 3.1 42.3 + - + +
36B PHE* 5.6 0.4 - - + -
70B ALA* 4.4 12.6 - - + -
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 3.9 8.8 - - - +
59A ARG 4.7 0.5 + - - -
64A HIS* 2.8 36.8 + - - -
371A 4CA 4.3 2.5 + - - -
15B LEU* 5.4 5.3 - - + +
26B TYR* 4.2 11.0 - - + -
29B THR* 3.1 15.8 + - - +
30B LEU* 1.3 78.0 - - - +
32B GLY* 1.3 56.7 + - - +
34B VAL* 3.6 0.9 - - - +
35B GLY 3.0 8.1 + - - -
36B PHE* 2.9 50.6 + - + -
74B MET* 3.3 29.4 - - + +
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.1 45.7 - - - -
27B GLU* 4.1 6.7 - - - +
29B THR* 3.0 10.7 + - - -
31B ASP* 1.3 75.0 - - - +
33B THR* 1.3 66.4 + - - +
35B GLY* 3.5 9.0 + - - -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 3.7 30.3 - - + -
34A VAL* 6.0 0.4 - - + -
55A THR* 3.9 19.4 + - + +
27B GLU 3.9 8.5 + - - -
28B GLN* 3.9 6.2 + - - -
29B THR 2.7 25.5 + - - -
30B LEU* 3.2 6.3 + - + -
32B GLY* 1.3 81.6 - - - +
34B VAL* 1.4 61.1 + - + +
55B THR* 3.9 13.4 + - + +
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Residues in contact with VAL 34 (chain B).
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* 4.8 9.2 - - + -
33A THR* 6.2 0.2 - - + -
34A VAL* 6.2 0.4 - - + -
30B LEU* 3.1 34.0 + - + +
31B ASP 3.6 4.5 - - - +
33B THR* 1.4 77.9 - - + +
35B GLY* 1.3 59.9 + - - +
36B PHE* 3.6 37.5 - - + -
50B VAL* 3.3 16.3 - - - +
51B GLU 4.3 5.2 - - - +
53B THR* 4.9 6.8 + - - +
55B THR* 4.0 32.1 - - + +
56B LEU* 3.6 17.2 - - + +
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Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.8 7.0 - - - -
31B ASP 3.0 9.6 + - - -
32B GLY 3.5 7.8 + - - -
33B THR 3.3 3.2 - - - -
34B VAL* 1.3 83.4 - - - +
36B PHE* 1.3 62.7 + - - -
37B VAL* 3.6 9.2 + - - +
49B SER 3.8 2.8 - - - +
50B VAL* 3.6 14.1 - - - +
51B GLU* 4.7 1.7 + - - +
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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