Contacts of the helix formed by residues 29 - 39 (chain k) in PDB entry 6AH0
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 LEU 29 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23k GLU 4.8 1.2 + - - -
24k PHE* 3.5 13.3 - - - +
27k GLY* 3.1 2.0 - - - -
28k PRO* 1.3 71.7 - - - +
30k SER* 1.3 52.4 + - - +
31k VAL 3.0 5.4 - - - -
32k LEU* 2.7 26.2 + - - +
33k THR 2.9 9.0 + - - -
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Residues in contact with SER 30 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24k PHE 3.0 19.3 + - - -
25k ASN* 4.1 11.9 - - - +
27k GLY 3.0 14.5 + - - -
29k LEU* 1.3 76.6 - - - +
31k VAL* 1.3 53.0 + - - +
32k LEU 3.2 0.2 - - - -
33k THR* 3.7 3.8 - - - +
34k GLN* 2.7 30.3 + - - -
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Residues in contact with VAL 31 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27k GLY 4.7 0.2 + - - -
28k PRO 3.2 11.7 + - - -
29k LEU 3.0 2.2 - - - -
30k SER* 1.3 77.0 - - - +
32k LEU* 1.3 55.1 + - - +
34k GLN* 4.0 0.7 - - - -
35k SER* 3.2 20.8 + - - -
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Residues in contact with LEU 32 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28k PRO 4.8 0.2 + - - -
29k LEU* 2.7 15.0 + - - +
31k VAL* 1.3 68.8 - - - +
33k THR* 1.3 63.1 + - - +
35k SER* 3.1 2.8 + - - +
36k VAL* 3.0 21.5 + - - -
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Residues in contact with THR 33 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24k PHE 4.8 5.4 - - - -
25k ASN* 6.2 0.4 - - - +
29k LEU 2.9 11.9 + - - -
30k SER* 3.6 6.1 - - - +
32k LEU* 1.3 75.2 - - - +
34k GLN* 1.3 59.8 + - - +
36k VAL* 3.6 1.3 + - - +
37k LYS* 3.2 19.2 + - - -
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Residues in contact with GLN 34 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30k SER 2.7 21.0 + - - -
31k VAL 4.0 1.6 - - - -
33k THR* 1.3 73.5 - - - +
35k SER* 1.3 57.4 + - - +
37k LYS* 4.6 0.7 - - - +
38k ASN* 3.1 23.6 + - - -
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Residues in contact with SER 35 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31k VAL 3.2 11.2 + - - -
32k LEU* 3.1 6.7 + - - +
34k GLN* 1.3 75.1 - - - +
36k VAL* 1.3 60.2 + - - +
39k ASN* 2.9 25.3 + - - -
40k THR* 3.1 24.0 + - - +
56k VAL* 4.4 6.8 + - - +
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Residues in contact with VAL 36 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32k LEU 3.0 14.3 + - - -
33k THR 4.1 1.3 - - - -
35k SER* 1.3 75.6 - - - +
37k LYS* 1.3 63.7 + - - +
39k ASN* 3.4 7.4 + - - -
56k VAL* 3.6 21.6 + - - +
57k LYS 5.6 2.9 - - - -
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Residues in contact with LYS 37 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33k THR 3.2 15.7 + - - -
34k GLN* 4.1 1.6 - - - +
35k SER 3.4 0.2 - - - -
36k VAL* 1.3 77.9 - - - +
38k ASN* 1.3 59.4 + - - +
39k ASN 3.6 0.2 + - - -
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Residues in contact with ASN 38 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34k GLN 3.1 16.5 + - - -
37k LYS* 1.3 75.1 - - - +
39k ASN* 1.3 66.2 + - - +
40k THR* 3.2 4.8 + - - +
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Residues in contact with ASN 39 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35k SER 2.9 10.4 + - - -
36k VAL* 3.4 7.1 + - - +
37k LYS 3.4 3.8 + - - -
38k ASN* 1.3 77.1 - - - +
40k THR* 1.3 61.0 + - - +
55k ARG* 5.7 3.8 - - - +
56k VAL 5.6 2.7 - - - +
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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