Contacts of the helix formed by residues 33 - 45 (chain L) in PDB entry 4GGF
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 33 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26L LEU* 3.8 24.2 + - - +
32L LEU* 1.3 76.4 - - - +
34L GLN* 1.3 65.6 + - - +
35L GLY* 3.2 6.1 + - - -
36L GLU* 2.8 39.1 + - - +
37L PHE* 3.0 21.0 + - - +
63L MET* 3.9 2.5 - - - -
72L LYS 4.1 5.6 - - - +
73L GLN* 3.6 14.9 + - - +
203L SO4 3.2 40.2 + - - +
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Residues in contact with GLN 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ASN* 1.3 76.0 - - - +
35L GLY* 1.3 57.2 + - - +
37L PHE* 3.4 1.8 + - + +
38L LYS* 2.9 57.3 + - + +
60L GLU* 3.5 37.7 + - + +
63L MET* 3.7 28.0 - - + +
72L LYS 4.4 2.7 + - - +
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Residues in contact with GLY 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LEU* 5.7 5.6 - - - -
33L ASN* 3.2 6.4 + - - -
34L GLN* 1.3 78.8 - - - +
36L GLU* 1.3 58.5 + - - +
38L LYS* 3.4 10.1 + - - +
39L GLU* 3.0 28.6 + - - +
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Residues in contact with GLU 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L TYR* 3.0 28.3 - - + +
23L SER 3.0 3.5 - - - +
25L LYS* 4.5 6.3 - - + -
26L LEU* 2.7 38.1 + - + +
31L THR 3.0 4.7 - - - +
32L LEU* 3.2 11.6 - - + -
33L ASN* 2.8 41.8 + - - +
35L GLY* 1.3 73.0 - - - +
37L PHE* 1.3 65.4 + - - +
39L GLU* 3.3 9.1 + - - +
40L LEU* 3.0 23.4 + - - +
205L CA 2.4 30.8 - - - -
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Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU* 4.2 19.9 - - + +
33L ASN 3.0 16.8 + - - +
34L GLN* 3.7 4.3 - - + +
36L GLU* 1.3 77.5 - - - +
38L LYS* 1.3 59.9 + - + +
40L LEU* 3.2 6.5 + - + +
41L VAL* 2.9 58.9 + - + +
59L ILE* 3.8 23.6 - - + -
62L ILE* 3.9 22.4 - - + -
63L MET* 3.7 35.0 - - + -
66L LEU* 4.0 4.5 - - + -
74L LEU* 3.6 25.4 - - + -
79L PHE* 4.4 8.3 - + - -
82L LEU* 3.9 17.7 - - + -
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Residues in contact with LYS 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLN* 2.9 40.8 + - + +
35L GLY* 3.6 8.1 - - - +
37L PHE* 1.3 78.7 - - + +
39L GLU* 1.3 57.2 + - - +
41L VAL* 3.5 1.4 + - - +
42L ARG* 2.9 33.1 + - - +
53L ASN* 4.8 0.7 - - - +
56L GLU* 2.7 40.0 + - + +
59L ILE* 3.8 25.3 - - + +
60L GLU* 2.8 40.2 + - - +
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Residues in contact with GLU 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L TYR* 3.5 15.1 - - + -
25L LYS* 3.0 38.9 + - - +
35L GLY 3.0 16.7 + - - +
36L GLU* 3.6 7.3 - - - +
38L LYS* 1.3 73.4 - - - +
40L LEU* 1.3 66.8 + - - +
42L ARG* 3.3 26.5 + - - +
43L LYS* 2.7 53.8 + - - +
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Residues in contact with LEU 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K LEU* 4.2 13.0 - - + -
18L THR* 4.0 14.8 - - + +
19L PHE* 4.2 5.8 - - - -
22L TYR* 3.6 40.2 - - + -
32L LEU* 4.2 15.5 - - + -
36L GLU 3.0 11.5 + - - +
37L PHE* 3.6 8.3 - - + +
39L GLU* 1.3 76.3 - - - +
41L VAL* 1.3 60.4 + - + +
44L ASP* 2.7 31.1 + - + -
45L LEU* 4.1 17.5 - - + -
79L PHE* 3.8 40.6 - - + -
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Residues in contact with VAL 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 2.9 55.4 + - + +
38L LYS* 3.9 5.2 - - - +
40L LEU* 1.3 76.4 - - + +
42L ARG* 1.3 62.0 + - - +
45L LEU* 3.2 35.9 + - + -
49L LEU* 3.8 24.0 - - + -
53L ASN* 3.1 35.7 + - - +
59L ILE* 3.9 15.3 - - + -
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Residues in contact with ARG 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LYS 2.9 18.2 + - - +
39L GLU* 3.7 21.2 + - - +
41L VAL* 1.3 75.8 - - - +
43L LYS* 1.3 92.6 + - + +
46L GLN* 3.4 21.0 - - - +
53L ASN* 3.4 19.2 + - + +
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Residues in contact with LYS 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K THR* 3.5 4.7 - - - +
22L TYR* 3.7 20.8 - - - +
25L LYS* 4.8 1.2 - - - +
39L GLU* 2.7 43.0 + - + +
42L ARG* 1.3 109.2 - - - +
44L ASP* 1.3 67.0 + - - +
45L LEU 3.4 0.4 - - - -
46L GLN* 3.0 31.1 - - - +
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Residues in contact with ASP 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K THR* 2.7 34.0 + - - +
4K GLU* 5.5 0.5 + - - +
5K LEU* 4.0 24.3 + - + +
6K GLU* 3.5 6.2 - - - +
18L THR* 3.6 13.4 - - + +
21L GLN* 4.9 2.1 - - - +
22L TYR* 2.6 40.7 + - - -
40L LEU 2.7 15.6 + - - +
43L LYS* 1.3 76.5 - - - +
45L LEU* 1.3 61.2 + - - +
46L GLN 3.5 0.4 - - - -
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K LEU* 3.9 19.3 - - + -
6K GLU* 3.2 17.7 - - + -
9K LEU* 4.7 4.3 - - + -
40L LEU* 3.5 16.1 + - + -
41L VAL* 3.2 20.4 + - + +
44L ASP* 1.3 83.6 - - - +
46L GLN* 1.3 64.3 + - - +
47L ASN 3.2 3.8 - - - -
48L PHE* 4.2 8.1 - - + -
49L LEU* 2.9 44.8 + - + +
53L ASN* 3.5 2.1 + - - -
82L LEU* 4.1 14.1 - - + -
83L MET* 4.1 8.7 - - + -
86L LEU* 3.7 31.6 - - + -
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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