Contacts of the helix formed by residues 31 - 45 (chain A) in PDB entry 3OQN
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 1.3 71.1 - - - +
32A PRO* 1.3 64.0 - - + +
33A THR* 2.7 35.9 + - - +
34A THR* 2.5 46.9 + - - +
35A ARG 2.9 9.9 + - - -
700B A 3.5 17.5 - - - +
701B T 2.9 13.5 + - - +
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Residues in contact with PRO 32 (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 VAL 3.4 8.9 - - - +
31A LYS* 1.3 88.0 - - + +
33A THR* 1.3 62.4 + - - +
35A ARG* 4.2 9.6 - - + +
36A LYS* 3.4 21.7 + - - +
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Residues in contact with THR 33 (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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31A LYS* 2.7 33.1 + - - +
32A PRO* 1.3 75.8 - - - +
34A THR* 1.3 63.2 + - - -
36A LYS* 3.6 5.6 - - + +
37A LYS* 3.2 21.9 + - - +
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Residues in contact with THR 34 (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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15A VAL* 4.0 25.1 - - + +
19A THR* 4.2 15.7 - - + -
23A VAL* 5.7 0.2 - - + -
30A VAL* 5.3 1.1 - - + -
31A LYS* 2.5 27.7 + - - +
33A THR* 1.3 71.7 - - - +
35A ARG* 1.3 67.2 + - - +
37A LYS* 3.0 26.6 + - - +
38A VAL* 3.2 7.5 + - + +
701B T 2.7 41.2 + - - +
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Residues in contact with ARG 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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23A VAL* 3.4 27.3 + - + +
26A GLY* 3.1 34.6 + - - -
27A ASN 3.4 6.3 + - - -
28A PRO* 4.8 2.6 - - - +
30A VAL* 2.9 40.2 - - + +
31A LYS 2.9 11.6 + - - +
32A PRO* 4.3 8.5 - - + +
34A THR* 1.3 75.6 - - - +
36A LYS* 1.3 66.0 + - - +
38A VAL* 2.8 26.2 - - - +
39A LEU* 2.8 35.3 + - + +
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Residues in contact with LYS 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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32A PRO 3.4 18.6 + - - +
33A THR* 3.6 8.3 - - + +
34A THR 3.2 0.4 - - - -
35A ARG* 1.3 79.5 - - - +
37A LYS* 1.3 65.1 + - - +
39A LEU* 3.2 12.6 + - + +
40A GLU* 3.0 61.7 + - + +
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Residues in contact with LYS 37 (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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12A GLU 5.6 0.2 - - - +
13A ALA* 3.0 24.4 + - - +
14A ASN* 2.9 39.7 + - + +
15A VAL* 3.9 8.7 - - + +
33A THR 3.2 9.5 + - - +
34A THR* 3.0 18.2 + - - +
36A LYS* 1.3 82.2 - - - +
38A VAL* 1.3 58.7 + - - +
40A GLU* 3.4 9.3 + - - +
41A ALA* 3.1 22.9 + - - +
44A ARG* 4.7 2.6 + - - -
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Residues in contact with VAL 38 (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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9A VAL* 3.4 24.9 - - + -
13A ALA* 3.3 18.6 - - + +
15A VAL* 4.9 6.7 - - + -
20A VAL* 3.9 13.7 - - + -
23A VAL* 3.3 35.4 - - + -
34A THR* 3.4 10.8 - - + +
35A ARG 2.8 21.3 - - - +
37A LYS* 1.3 73.4 - - - +
39A LEU* 1.3 54.3 + - - +
41A ALA* 3.0 0.5 + - - +
42A ILE* 2.6 53.5 + - + +
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Residues in contact with LEU 39 (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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23A VAL* 3.5 23.3 - - + +
24A VAL* 6.0 0.4 - - - -
35A ARG* 2.8 49.9 + - + +
36A LYS* 3.7 13.5 - - + +
38A VAL* 1.3 71.5 - - - +
40A GLU* 1.3 59.5 + - + +
42A ILE* 3.4 14.2 + - + +
43A GLU* 2.9 27.0 + - - +
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Residues in contact with GLU 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 LYS* 3.0 53.1 + - + +
37A LYS* 3.6 9.0 + - - +
39A LEU* 1.3 74.6 - - + +
41A ALA* 1.3 55.9 + - - +
43A GLU* 3.3 10.1 - - + +
44A ARG* 2.7 51.0 + - - +
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Residues in contact with ALA 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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9A VAL* 4.3 6.1 - - + +
12A GLU* 3.6 20.2 - - + +
13A ALA* 3.5 32.1 - - + +
37A LYS 3.1 7.9 + - - +
38A VAL 3.0 7.5 + - - +
40A GLU* 1.3 73.2 - - - +
42A ILE* 1.3 66.3 + - - +
44A ARG* 3.2 12.3 + - - +
45A LEU* 2.8 32.4 + - - +
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Residues in contact with ILE 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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9A VAL* 3.6 26.9 - - + -
24A VAL* 4.0 28.9 - - + +
38A VAL* 2.6 42.9 + - + +
39A LEU* 3.6 18.8 - - + +
41A ALA* 1.3 71.3 - - - +
43A GLU* 1.3 62.2 + - - +
45A LEU 3.4 0.3 + - - -
46A GLY* 3.1 17.2 + - - -
47A TYR* 3.1 44.7 + - + +
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Residues in contact with GLU 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 LEU 2.9 14.8 + - - +
40A GLU* 3.3 14.4 - - + +
42A ILE* 1.3 77.3 - - - +
44A ARG* 1.3 67.2 + - + +
46A GLY* 3.0 14.6 + - - -
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Residues in contact with ARG 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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12A GLU* 3.0 36.0 + - - -
13A ALA* 5.7 0.6 - - - +
37A LYS 4.7 2.4 + - - -
40A GLU* 2.7 32.4 + - - +
41A ALA* 3.7 18.8 - - - +
43A GLU* 1.3 77.7 - - + +
45A LEU* 1.3 65.1 + - + +
46A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 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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4A ILE* 3.2 29.7 - - + +
8A ASP* 3.9 13.0 - - + -
9A VAL* 3.8 39.7 - - + +
12A GLU* 3.5 36.3 - - + +
41A ALA 2.8 27.6 + - - +
42A ILE 4.2 2.7 - - - +
44A ARG* 1.3 88.0 - - + +
46A GLY* 1.3 68.6 + - - +
47A TYR* 4.5 5.6 - - + +
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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