Contacts of the helix formed by residues 22 - 35 (chain I) in PDB entry 3GZN
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 22 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I THR 3.3 6.2 + - - +
21I ASP* 1.3 76.7 - - - +
23I VAL* 1.3 66.9 + - - +
24I GLU* 3.1 14.8 - - + +
25I ARG* 2.9 26.0 + - + +
26I ILE* 3.6 4.7 + - - +
52I ASP 3.9 6.7 - - - +
53I GLU* 3.7 37.7 - - - +
54I LYS 3.3 9.0 - - - +
55I THR* 4.0 6.5 - - + +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASP 3.8 0.2 + - - -
22I LYS* 1.3 69.7 - - - +
24I GLU* 1.3 64.1 + - - +
26I ILE* 2.9 22.9 + - + +
27I LYS* 3.2 24.9 + - - +
43I LEU* 4.5 4.0 - - + -
50I MET* 3.6 50.9 - - + +
51I ASN 3.0 24.7 - - - +
52I ASP* 3.2 7.7 + - - +
54I LYS 2.9 14.9 + - - +
55I THR 4.2 7.4 - - - +
59I TYR* 3.8 15.7 - - + -
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LYS* 4.4 14.0 - - + +
23I VAL* 1.3 75.6 - - - +
25I ARG* 1.3 56.8 + - + +
27I LYS* 3.3 8.4 + - - +
28I GLU* 3.1 35.2 + - + +
38I PRO* 5.3 1.2 - - - +
52I ASP* 2.9 41.4 + - + +
53I GLU* 3.3 20.9 - - - +
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Residues in contact with ARG 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 6.3 1.2 - - - +
248A GLU* 5.5 12.9 + - - +
17I ILE* 5.6 2.0 - - - -
21I ASP* 2.9 33.8 + - + +
22I LYS* 2.9 20.5 + - + +
24I GLU* 1.3 75.8 - - + +
26I ILE* 1.3 60.9 + - - +
28I GLU* 3.1 21.1 + - - +
29I ARG* 2.9 66.3 + - - +
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Residues in contact with ILE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ILE* 4.5 10.5 - - + -
5I VAL* 4.9 1.1 - - + -
15I ILE* 4.5 13.5 - - + -
17I ILE* 4.2 22.4 - - + -
21I ASP* 4.8 4.3 - - + +
22I LYS 3.6 5.1 + - - +
23I VAL* 2.9 19.8 + - + +
25I ARG* 1.3 75.5 - - - +
27I LYS* 1.3 62.2 + - - +
29I ARG* 3.0 20.1 + - - +
30I VAL* 3.1 20.8 + - + +
43I LEU* 3.8 20.6 - - + -
50I MET* 4.2 21.8 - - + -
56I ALA* 4.5 21.3 - - + -
61I ILE* 5.0 1.8 - - + -
67I LEU* 4.0 14.4 - - + -
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I VAL* 3.2 20.0 + - - +
24I GLU* 3.4 10.1 - - - +
26I ILE* 1.3 79.9 - - - +
28I GLU* 1.3 56.8 + - - +
30I VAL 3.2 1.6 + - - -
31I GLU* 2.9 16.5 + - - +
38I PRO* 3.6 30.8 + - + +
41I GLN* 2.8 68.0 + - + +
42I ARG* 4.9 4.4 - - - +
43I LEU* 3.8 20.9 - - + +
50I MET 4.6 6.6 + - - -
52I ASP* 2.7 39.5 + - - +
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 3.6 23.0 + - - -
277A LYS* 5.0 9.7 - - - +
280A ASN* 2.8 40.2 + - - +
24I GLU* 3.1 19.6 + - - +
25I ARG* 3.1 28.4 + - - +
27I LYS* 1.3 76.4 - - - +
29I ARG* 1.3 63.5 + - - +
31I GLU* 4.3 3.8 - - - +
32I GLU* 3.1 17.0 + - - +
38I PRO* 4.8 10.5 - - + -
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Residues in contact with ARG 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 3.5 62.2 - - - +
280A ASN* 4.8 4.2 + - - -
15I ILE* 3.7 36.3 - - + +
16I ASP 4.2 12.5 + - - +
17I ILE* 4.7 4.7 - - + +
21I ASP* 5.2 0.6 + - - -
25I ARG* 2.9 55.6 + - + +
26I ILE* 3.0 9.8 + - - +
28I GLU* 1.3 82.6 - - - +
30I VAL* 1.3 62.9 + - - +
32I GLU* 3.6 12.4 + - - +
33I LYS* 3.5 26.2 + - - +
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Residues in contact with VAL 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I VAL* 4.3 16.8 - - + -
7I THR* 5.3 0.9 - - + -
13I ILE* 4.0 19.5 - - + -
15I ILE* 3.7 16.8 - - + -
26I ILE* 3.1 19.9 + - + +
27I LYS 3.2 1.3 + - - +
29I ARG* 1.3 74.7 - - - +
31I GLU* 1.3 60.1 + - - +
33I LYS* 3.0 4.3 + - - +
34I GLU* 2.9 28.8 + - + +
36I ILE* 4.2 22.4 - - + -
41I GLN* 3.3 28.3 - - - +
43I LEU* 5.4 1.6 - - + -
69I LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.6 5.4 - - - +
277A LYS 5.0 2.3 - - - +
278A ASN* 4.7 8.7 - - - +
280A ASN* 3.0 22.4 + - - +
281A THR* 3.6 20.6 + - + +
27I LYS 2.9 14.7 + - - +
28I GLU* 3.8 4.3 - - - +
30I VAL* 1.3 76.0 - - - +
32I GLU* 1.3 60.1 + - - +
35I GLY* 2.7 31.2 + - - -
36I ILE 3.4 30.1 - - - +
37I PRO* 3.9 6.9 - - - +
38I PRO* 3.5 28.3 - - + +
41I GLN* 3.8 1.5 - - - +
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Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.8 15.1 - - - +
244A TYR* 3.3 40.5 + - - -
247A LYS* 4.2 12.9 + - - +
280A ASN* 3.6 31.6 - - - +
281A THR* 4.4 7.7 - - - -
28I GLU 3.1 17.2 + - - +
29I ARG* 3.6 14.6 + - - +
30I VAL 3.2 0.4 - - - -
31I GLU* 1.3 76.8 - - - +
33I LYS* 1.3 65.5 + - + +
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Residues in contact with LYS 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.7 14.1 - - - +
13I ILE* 4.3 20.6 - - + -
14I GLU* 3.6 28.2 + - - +
15I ILE* 5.5 3.1 - - + +
29I ARG 3.5 13.4 + - - +
30I VAL 3.0 7.2 + - - +
32I GLU* 1.3 84.8 - - + +
34I GLU* 1.3 72.7 + - - +
35I GLY 3.9 0.4 - - - -
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Residues in contact with GLU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.9 16.8 - - + +
186A ALA* 3.9 8.4 + - - -
187A LEU* 4.4 5.6 - - - -
7I THR* 4.5 10.3 - - + -
11I LYS* 2.6 40.0 + - - +
13I ILE* 3.8 17.9 - - + +
30I VAL* 2.9 15.9 + - + +
33I LYS* 1.3 92.2 - - + +
35I GLY* 1.3 64.4 + - - +
36I ILE* 3.4 26.0 + - + -
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Residues in contact with GLY 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.9 8.2 + - - +
186A ALA 4.2 14.0 - - - +
187A LEU* 4.0 17.3 - - - +
281A THR* 5.4 0.7 - - - -
31I GLU* 2.7 28.8 + - - +
33I LYS 3.9 0.2 - - - -
34I GLU* 1.3 71.6 - - - +
36I ILE* 1.3 59.3 + - - +
37I PRO* 3.0 15.2 - - - +
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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