Contacts of the helix formed by residues 26 - 37 (chain k) in PDB entry 3J9X
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 ASN 26 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28j THR* 4.9 2.8 - - - +
32j THR* 4.0 19.6 + - + +
22k ASN 3.6 2.2 + - - +
23k ALA 3.1 15.6 + - - +
24k PHE 3.0 0.8 + - - -
25k SER* 1.3 79.0 + - - +
27k PRO* 1.4 66.5 - - - +
28k THR* 2.7 34.1 + - - +
29k VAL* 2.7 33.2 + - + -
30k ALA* 2.9 12.2 + - - -
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Residues in contact with PRO 27 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25k SER 3.2 6.4 - - - +
26k ASN* 1.4 93.2 - - - +
28k THR* 1.3 63.7 + - + +
30k ALA* 4.1 2.3 - - + +
31k SER* 2.8 30.0 + - - -
27l PRO* 3.5 33.5 - - + +
28l THR* 5.7 0.2 - - - -
31l SER* 3.5 19.7 - - - +
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Residues in contact with THR 28 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28j THR* 3.1 29.6 - - + +
29j VAL* 4.8 0.7 - - - -
26k ASN* 2.7 20.4 + - - +
27k PRO* 1.3 80.2 - - + +
29k VAL* 1.3 59.4 + - - +
31k SER* 3.2 5.9 + - - -
32k THR* 2.4 40.3 + - - -
27l PRO* 5.5 1.6 - - + -
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Residues in contact with VAL 29 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29j VAL* 3.9 28.5 - - + -
32j THR* 3.7 25.1 - - - +
33j ILE* 4.9 7.2 - - + -
23k ALA 3.5 19.1 - - - +
24k PHE* 4.0 7.9 - - - -
26k ASN* 2.7 31.3 + - + +
28k THR* 1.3 74.7 - - - +
30k ALA* 1.3 64.5 + - - +
32k THR* 3.7 0.7 - - - -
33k ILE* 3.0 43.5 + - + +
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Residues in contact with ALA 30 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24k PHE* 3.3 38.9 + - + +
25k SER 5.0 0.7 - - - -
26k ASN 2.9 10.9 + - - +
27k PRO* 4.1 2.2 - - + +
29k VAL* 1.3 79.2 - - - +
31k SER* 1.3 57.3 + - - +
33k ILE* 3.9 0.5 - - - +
34k LEU* 2.9 38.1 + - + +
30l ALA* 3.6 28.5 - - + -
34l LEU* 4.5 2.9 - - + -
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Residues in contact with SER 31 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27k PRO 2.8 21.1 + - - -
28k THR* 3.2 9.7 + - - -
30k ALA* 1.3 76.1 - - - +
32k THR* 1.3 59.7 + - - +
34k LEU* 4.5 0.7 - - - +
35k SER* 2.6 40.4 + - - -
25l SER 3.4 24.0 - - - -
27l PRO* 3.5 25.1 - - - +
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Residues in contact with THR 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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23j ALA* 3.6 34.8 - - + +
26j ASN* 4.0 19.0 + - + +
29j VAL* 3.8 13.3 - - + +
28k THR* 2.4 26.5 + - - -
29k VAL 3.7 3.8 - - - -
31k SER* 1.3 78.2 + - - +
33k ILE* 1.3 63.3 + - - +
35k SER* 3.2 3.2 + - - -
36k ASN* 3.0 35.6 + - - +
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Residues in contact with ILE 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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1257 A 3.6 43.5 - - - +
1267 T 4.7 8.1 - - - +
2158 A 5.4 2.0 - - - +
20j LYS* 3.9 16.4 - - + -
23j ALA* 3.8 22.4 - - + -
29j VAL* 4.9 8.3 - - + -
33j ILE* 5.3 6.1 - - + -
24k PHE* 4.3 13.9 - - + -
29k VAL* 3.0 33.9 + - + +
30k ALA 3.9 2.0 - - - +
32k THR* 1.3 78.3 - - - +
34k LEU* 1.3 59.9 + - + +
36k ASN* 3.1 2.9 + - - +
37k VAL* 3.0 28.9 + - - +
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Residues in contact with LEU 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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1247 T 4.6 6.3 - - + -
1257 A 4.2 24.0 - - - +
24k PHE* 4.0 14.4 - - + -
30k ALA* 2.9 29.3 + - + +
31k SER 4.3 0.2 - - - +
33k ILE* 1.3 76.8 - - - +
35k SER* 1.3 51.7 + - - +
37k VAL* 3.4 6.1 + - + +
38k SER* 2.6 37.3 + - - -
21l PHE* 3.9 23.9 - - + -
24l PHE* 3.5 38.4 - - + +
25l SER* 3.8 27.4 - - - -
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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 SER* 2.6 26.1 + - - -
32k THR* 3.2 6.6 + - - -
34k LEU* 1.3 78.0 - - - +
36k ASN* 1.3 69.5 + - - +
38k SER* 3.3 19.9 + - - -
39k PRO* 4.0 3.6 - - - +
25l SER* 4.5 8.7 - - - -
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Residues in contact with ASN 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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19j ALA* 3.4 30.3 + - + +
22j ASN* 4.0 10.8 - - - +
23j ALA* 3.5 30.5 - - - +
32k THR* 3.0 27.1 + - - +
33k ILE* 3.1 4.7 + - - +
35k SER* 1.3 88.9 + - - +
37k VAL* 1.3 57.4 - - - +
38k SER 3.3 0.7 + - - -
39k PRO* 3.6 11.6 - - - +
40k VAL* 4.3 2.1 - - - +
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Residues in contact with VAL 37 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247 T 3.9 22.7 - - - +
1257 A 3.9 4.7 - - - +
16j LYS* 4.7 10.8 - - + -
19j ALA* 3.7 17.7 - - + -
20j LYS* 3.6 30.1 - - + -
33k ILE 3.0 19.4 + - - +
34k LEU* 3.5 15.5 - - + +
36k ASN* 1.3 75.7 - - - +
38k SER* 1.3 68.7 + - - +
39k PRO* 3.5 1.3 - - - -
40k VAL* 3.9 7.4 - - + -
41k ALA* 2.9 21.2 + - + +
21l PHE* 4.5 9.0 - - + -
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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