Contacts of the helix formed by residues 34 - 47 (chain A) in PDB entry 3N9Y
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 LYS 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 3.4 35.6 - - + +
31A GLY 3.0 6.7 + - - -
33A HIS* 1.3 90.1 - - + +
35A VAL* 1.3 64.0 + - - +
36A HIS* 3.1 17.0 - - + -
37A LEU* 3.0 33.6 + - + +
38A HIS 3.2 8.8 + - - -
455A GLY* 5.7 0.2 - - - -
456A THR 2.9 21.7 + - - +
457A THR* 5.0 3.1 - - - +
465A GLU* 2.7 36.5 + - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.7 31.2 - - + -
31A GLY 3.9 0.6 + - - -
32A THR 3.7 6.7 + - - +
33A HIS 3.7 1.6 - - - -
34A LYS* 1.3 77.5 - - - +
36A HIS* 1.3 66.4 + - - +
38A HIS* 3.2 7.7 - - + +
39A HIS* 3.1 41.3 + - + +
54A LEU* 5.6 4.3 - - + -
353A VAL* 4.4 12.1 - - + -
458A PHE* 3.6 41.1 - - + -
602A CLR 5.9 0.4 - - + -
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS 3.6 6.9 + - - -
34A LYS* 3.6 26.7 - - + +
35A VAL* 1.3 81.3 + - - +
37A LEU* 1.3 80.7 + - + +
39A HIS* 3.3 7.1 + - - +
40A VAL* 3.2 24.3 + - - +
353A VAL* 4.1 13.9 - - + -
381A TYR* 3.5 51.6 - + + -
456A THR* 3.0 42.2 + - + -
458A PHE* 4.0 4.6 - - - +
462A LEU* 3.8 20.2 - - + +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 4.2 8.3 - - + -
34A LYS* 3.0 36.1 + - + +
36A HIS* 1.3 96.3 - - + +
38A HIS* 1.3 65.1 + - - +
40A VAL* 3.2 10.7 + - + +
41A GLN* 2.9 41.3 + - + +
381A TYR* 4.2 13.7 - - + +
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Residues in contact with HIS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.6 52.8 - + + -
30A THR* 3.8 11.2 + - + +
34A LYS 3.2 5.8 + - - +
35A VAL* 3.2 15.5 - - + +
37A LEU* 1.3 76.9 - - - +
39A HIS* 1.3 68.7 + + - +
41A GLN* 3.3 10.8 + - - +
42A ASN* 3.0 57.5 + - - +
50A TYR* 5.0 0.2 - - - -
52A GLU* 2.8 38.5 + - - -
54A LEU* 4.7 4.9 - - + +
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Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.1 28.3 + - + +
36A HIS 3.4 7.0 - - - +
37A LEU 3.2 0.4 - - - -
38A HIS* 1.3 82.9 - + - +
40A VAL* 1.3 65.3 + - - +
42A ASN* 3.2 3.1 + - - +
43A PHE* 3.0 35.1 + - + -
50A TYR* 3.6 20.9 - - - -
61A TYR* 3.7 19.2 + + - -
353A VAL* 3.4 36.8 - - + +
354A THR* 3.5 22.3 - - + +
377A GLN* 5.3 0.2 - - - -
379A ALA* 4.4 8.2 - - + +
381A TYR* 5.8 0.6 - - - +
382A ALA* 4.4 13.7 - - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A HIS 3.2 13.0 + - - +
37A LEU* 3.2 13.6 + - + +
39A HIS* 1.3 75.8 - - - +
41A GLN* 1.3 66.6 + - + +
43A PHE* 3.4 4.4 + - - +
44A GLN* 3.2 42.3 + - + +
381A TYR* 3.8 25.4 - - + -
382A ALA* 4.0 20.2 - - - +
385A ARG* 5.3 7.6 - - + -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 3.3 24.9 + - - +
37A LEU* 2.9 33.0 + - - +
38A HIS* 3.8 8.2 + - - +
40A VAL* 1.3 79.0 - - + +
42A ASN* 1.3 59.8 + - - +
44A GLN* 3.3 19.9 + - - +
45A LYS* 2.9 44.3 + - - +
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A HIS* 3.0 53.3 + - - +
39A HIS 3.2 2.0 + - - +
41A GLN* 1.3 75.2 - - - +
43A PHE* 1.3 60.0 + - - +
45A LYS* 3.1 20.1 + - - -
46A TYR* 2.8 50.4 + - + +
50A TYR* 3.3 43.1 + - + -
52A GLU* 3.8 6.0 + - - +
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS* 3.0 28.2 + - + -
40A VAL* 4.0 4.7 - - - +
42A ASN* 1.3 71.1 - - - +
44A GLN* 1.3 61.8 + - - +
47A GLY* 2.9 48.1 + - - +
48A PRO 3.8 15.7 - - - -
50A TYR* 3.6 27.1 - + - -
61A TYR* 3.9 13.9 - - + -
62A VAL 3.7 13.0 - - - -
63A ILE* 3.8 29.8 - - + -
379A ALA* 3.4 33.9 - - + -
382A ALA* 3.9 16.6 - - + -
386A GLU* 6.3 0.2 - - + -
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.2 29.6 + - + +
41A GLN* 3.4 24.9 - - - +
43A PHE* 1.3 77.8 - - - +
45A LYS* 1.3 61.4 + - + +
47A GLY 4.5 1.0 + - - -
386A GLU* 5.9 3.1 - - - +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 5.3 6.9 + - - -
41A GLN* 2.9 31.1 + - - +
42A ASN* 3.5 25.4 + - - +
44A GLN* 1.3 80.2 - - + +
46A TYR* 1.3 88.8 + - + +
47A GLY 3.7 0.4 - - - -
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Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.8 38.6 - - + +
14A SER 4.2 12.8 - - - -
15A PRO* 3.3 42.4 - - + +
42A ASN* 2.8 48.6 + - + +
45A LYS* 1.3 100.2 - - + +
47A GLY* 1.3 62.5 + - - +
48A PRO* 4.5 0.9 - - - +
49A ILE 4.1 2.1 - - - +
50A TYR* 3.8 28.3 - + + -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN 4.4 0.3 - - - +
43A PHE* 2.9 37.0 + - - +
44A GLN 4.5 1.4 + - - -
45A LYS 3.7 1.0 - - - -
46A TYR* 1.3 81.5 - - - +
48A PRO* 1.3 66.5 - - - +
49A ILE 3.2 11.6 + - - +
50A TYR* 4.7 0.2 - - - -
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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