Contacts of the helix formed by residues 40 - 45 (chain B) in PDB entry 3QJQ
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 HIS 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B THR* 1.3 84.8 - - + +
41B THR* 1.3 85.4 + - + +
42B ALA 2.8 11.6 + - - -
43B GLY* 3.0 13.9 + - - -
136B ARG 5.1 0.5 - - - +
138B THR* 6.5 0.7 - - - -
140B LYS* 4.2 27.0 - - - -
31C PHE* 4.3 15.0 + + - -
34C GLY* 4.4 10.4 + - - -
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 5.4 0.6 - - - +
36B THR* 3.5 17.7 + - - +
39B THR* 3.9 7.1 + - - -
40B HIS* 1.3 101.6 + - + +
42B ALA* 1.3 62.2 + - - +
43B GLY 3.1 1.7 + - - -
44B VAL* 3.4 25.8 + - - +
122B ASN* 5.4 0.8 - - - +
30C PHE* 3.8 31.4 - - + +
31C PHE* 3.7 18.7 - - + -
34C GLY* 3.8 26.7 - - - -
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Residues in contact with ALA 42 (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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370A THR* 5.2 2.7 - - - -
36B THR 3.7 6.7 - - - +
37B LEU* 3.6 19.1 - - - +
39B THR 3.1 15.5 + - - +
40B HIS 2.8 4.4 + - - -
41B THR* 1.3 70.0 + - - +
43B GLY* 1.3 65.5 + - - +
44B VAL 2.9 5.3 + - - -
45B ILE* 3.0 40.0 + - + +
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Residues in contact with GLY 43 (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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40B HIS 3.0 12.1 + - - -
41B THR 3.1 1.2 - - - -
42B ALA* 1.3 76.9 - - - +
44B VAL* 1.3 56.7 + - - +
45B ILE 3.2 9.6 + - - +
135B VAL* 3.7 1.2 - - - -
136B ARG* 2.8 58.4 + - - +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 6.1 0.4 - - + -
373A TYR* 3.9 32.1 - - + -
41B THR 3.4 18.8 - - - +
42B ALA 2.9 0.8 + - - +
43B GLY* 1.3 74.9 - - - +
45B ILE* 1.3 67.8 + - + +
46B PRO* 3.2 10.7 - - - +
122B ASN* 3.9 39.7 - - + +
123B ILE* 4.1 8.3 - - + +
124B ASN 5.6 2.1 + - - -
125B VAL* 5.4 1.6 - - - +
135B VAL* 3.7 14.8 - - + +
136B ARG 4.3 4.0 - - - +
137B TYR* 3.9 24.9 - - + -
30C PHE* 5.1 4.3 - - + -
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Residues in contact with ILE 45 (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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292A PRO* 4.6 16.4 - - + -
295A LYS* 4.5 9.4 - - + -
369A PHE* 3.8 24.5 - - + -
370A THR* 4.3 15.9 - - + -
373A TYR* 3.5 29.2 - - + +
37B LEU* 4.3 13.2 - - + -
42B ALA* 3.0 37.0 + - + +
43B GLY 3.4 10.3 - - - +
44B VAL* 1.3 79.4 - - + +
46B PRO* 1.3 82.5 - - + +
134B THR 4.0 2.1 - - - +
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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