Contacts of the helix formed by residues 33 - 38 (chain B) in PDB entry 1QAJ
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 TRP 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B TRP* 2.8 40.4 + - + -
26B LEU* 3.7 21.5 - - + -
29B PHE* 2.9 29.3 + - + +
30B PRO 3.7 1.0 + - - -
31B GLN 3.4 0.2 - - - -
32B ALA* 1.3 79.7 - - - +
34B ALA* 1.3 54.0 + - - +
35B GLU* 3.9 9.4 - - - +
36B THR* 3.7 9.4 - - - +
37B GLY* 2.6 37.1 + - - -
149B LEU* 3.9 5.6 - - + -
244B LEU* 3.3 34.1 - - + -
253B ARG* 3.6 3.2 - - - -
254B ALA* 3.3 32.1 - - + -
255B SER 3.9 0.2 - - - -
256B ALA* 3.3 40.6 - - + -
259B ALA* 3.8 23.3 - - + -
261B ILE* 4.2 7.4 - - + -
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Residues in contact with ALA 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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33B TRP* 1.3 72.5 - - - +
35B GLU* 1.3 64.9 + - - +
38B GLY* 2.8 34.6 + - - +
39B MET* 6.2 0.2 - - - -
152B LYS* 3.9 32.5 - - + +
253B ARG* 3.8 20.3 - - + +
254B ALA 2.9 15.3 + - - +
255B SER* 5.1 0.2 - - - -
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Residues in contact with GLU 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 LEU* 4.5 17.3 - - + -
33B TRP* 3.2 1.1 - - - +
34B ALA* 1.3 85.7 + - + +
36B THR* 1.3 60.6 + - + +
38B GLY 5.0 0.5 + - - -
152B LYS* 5.4 8.8 + - - +
254B ALA 3.6 1.0 - - - +
255B SER* 3.9 4.6 + - - -
256B ALA* 3.2 27.7 + - + +
257B LYS* 3.1 35.9 + - - +
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Residues in contact with THR 36 (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 LEU* 3.6 40.1 + - + +
29B PHE 3.9 0.7 + - - -
30B PRO* 2.6 44.0 + - - +
33B TRP* 3.3 11.2 + - - +
35B GLU* 1.3 80.0 - - + +
37B GLY* 1.3 58.7 + - - +
38B GLY 3.7 0.7 - - - -
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Residues in contact with GLY 37 (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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30B PRO 3.1 11.4 + - - -
31B GLN* 4.4 3.4 - - - -
33B TRP 2.6 20.9 + - - -
36B THR* 1.3 76.7 - - - +
38B GLY* 1.3 61.8 + - - +
39B MET 4.3 1.4 - - - +
253B ARG* 3.1 26.6 + - - -
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Residues in contact with GLY 38 (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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34B ALA* 2.8 25.7 + - - +
35B GLU 4.8 0.2 - - - -
36B THR 3.7 1.0 - - - -
37B GLY* 1.3 72.5 - - - +
39B MET* 1.3 68.5 + - - +
253B ARG* 3.0 23.6 - - - +
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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