Contacts of the helix formed by residues 25 - 34 (chain B) in PDB entry 1AQJ
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 PRO 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 5.8 2.9 - - - +
23B THR 3.6 2.6 - - - +
24B PRO* 1.3 82.8 - - + +
26B GLU* 1.3 73.8 + - - +
28B VAL* 3.1 10.0 + - + +
29B ASP* 2.8 39.9 + - - +
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Residues in contact with GLU 26 (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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24B PRO* 3.9 11.0 - - + +
25B PRO* 1.3 94.9 - - - +
27B VAL* 1.3 59.3 + - + +
29B ASP* 3.2 13.1 + - - +
30B PHE* 2.8 28.6 + - - +
222B GLU* 4.5 11.4 - - - +
226B GLY* 4.3 18.2 - - - -
227B PHE* 4.2 23.2 + - + -
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Residues in contact with VAL 27 (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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23B THR* 4.2 10.3 - - + -
24B PRO* 3.0 32.8 + - + +
26B GLU* 1.3 75.3 - - + +
28B VAL* 1.3 64.7 + - - +
30B PHE* 2.9 10.4 + - + +
31B MET* 2.9 40.6 + - + +
163B VAL* 4.4 8.7 - - + -
192B LEU* 3.9 20.0 - - + -
195B VAL* 4.1 21.1 - - + -
196B PHE* 5.9 0.7 - - + -
205B VAL* 4.9 0.2 - - + -
227B PHE* 4.0 19.7 - - + -
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Residues in contact with VAL 28 (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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23B THR* 3.5 29.8 - - + +
24B PRO 3.0 16.4 + - - +
25B PRO* 3.3 9.2 - - + +
27B VAL* 1.3 76.8 - - - +
29B ASP* 1.3 63.9 + - - +
31B MET* 3.3 1.4 + - - +
32B VAL* 3.0 24.1 + - + +
52B PRO* 4.5 11.7 - - + +
53B PHE* 3.9 28.3 - - + -
56B ALA* 3.8 27.6 - - + -
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Residues in contact with ASP 29 (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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25B PRO* 2.8 27.8 + - - +
26B GLU* 3.4 12.1 - - - +
27B VAL 3.2 0.2 - - - -
28B VAL* 1.3 80.0 - - - +
30B PHE* 1.3 62.1 + - - +
32B VAL* 3.7 6.2 + - - +
33B SER* 3.2 22.2 + - - -
56B ALA* 5.6 3.5 - - - +
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Residues in contact with PHE 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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26B GLU 2.8 13.0 + - - +
27B VAL* 2.9 11.4 + - - +
29B ASP* 1.3 76.1 - - - +
31B MET* 1.3 63.8 + - - +
33B SER* 2.5 26.0 + - - -
34B LEU* 3.4 31.9 + - + +
190B TYR* 3.8 39.9 - + + -
192B LEU* 4.2 16.4 - - + -
205B VAL* 4.0 20.9 - - + -
220B THR* 4.2 8.5 - - + -
227B PHE* 4.1 32.3 - - + +
229B PRO* 3.7 23.8 - - + -
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Residues in contact with MET 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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27B VAL* 2.9 23.1 + - - +
28B VAL 3.8 3.8 - - - +
30B PHE* 1.3 76.2 - - - +
32B VAL* 1.3 62.1 + - - +
34B LEU* 3.1 17.3 + - - +
35B ALA* 3.1 12.5 + - - +
53B PHE* 3.5 35.0 - - + -
103B LEU* 4.6 2.7 - - + -
104B GLY 3.6 15.0 - - - +
161B VAL* 3.6 44.6 - - + +
162B PHE 3.9 0.2 - - - -
163B VAL* 3.7 31.6 - - + +
205B VAL* 3.8 21.8 - - + -
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Residues in contact with VAL 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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28B VAL* 3.0 20.8 + - + +
29B ASP* 4.1 6.1 - - - +
31B MET* 1.3 75.5 - - - +
33B SER* 1.3 59.6 + - - +
34B LEU 3.2 0.2 - - - -
35B ALA* 3.3 13.2 + - - +
53B PHE* 4.6 6.1 - - + +
56B ALA* 3.8 25.8 - - + +
57B PHE* 3.9 14.8 - - + +
60B ALA* 3.8 18.4 - - + -
61B HIS* 2.8 49.2 + - + +
103B LEU* 4.5 12.6 - - + -
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Residues in contact with SER 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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29B ASP 3.2 14.7 + - - -
30B PHE* 2.5 31.2 + - - -
32B VAL* 1.3 76.9 - - - +
34B LEU* 1.3 63.1 + - - +
35B ALA 3.4 2.9 - - - +
61B HIS* 4.9 4.0 - - - -
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Residues in contact with LEU 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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30B PHE* 3.5 41.3 - - + +
31B MET* 3.1 9.9 + - - +
33B SER* 1.3 80.5 - - - +
35B ALA* 1.3 62.0 + - - +
36B GLU* 4.6 1.1 - - - +
161B VAL* 4.5 11.3 - - + +
190B TYR* 3.5 46.2 - - + +
205B VAL* 3.9 14.6 - - + -
207B ARG* 2.7 40.4 + - + +
229B PRO* 5.4 3.8 - - + -
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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