Contacts of the helix formed by residues 22 - 35 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J THR 3.3 7.4 + - - +
21J ASP* 1.3 78.9 - - - +
23J VAL* 1.3 66.8 + - - +
24J GLU* 3.2 17.9 - - + +
25J ARG* 3.1 21.5 + - + +
26J ILE* 3.6 5.2 + - - +
52J ASP 3.8 6.1 - - - +
53J GLU* 3.1 41.7 - - - +
54J LYS 3.0 12.8 - - - +
55J THR* 4.1 5.4 - - + +
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Residues in contact with VAL 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LYS* 1.3 70.8 - - - +
24J GLU* 1.3 65.5 + - - +
26J ILE* 3.0 19.3 + - + +
27J LYS* 3.2 25.7 + - - +
43J LEU* 4.4 4.7 - - + -
50J MET* 3.7 49.4 - - + +
51J ASN 3.1 25.4 - - - +
52J ASP* 3.0 12.1 + - - +
54J LYS 3.0 7.2 + - - +
55J THR 4.5 5.2 - - - +
56J ALA 5.1 0.2 - - - +
59J TYR* 4.0 17.3 - - + -
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Residues in contact with GLU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LYS* 4.3 16.0 - - + -
23J VAL* 1.3 76.1 - - - +
25J ARG* 1.3 56.5 + - - +
27J LYS* 3.3 8.1 + - - +
28J GLU* 3.0 36.1 + - + +
38J PRO* 5.3 1.2 - - - +
52J ASP* 2.9 42.4 + - + +
53J GLU* 2.9 23.8 - - - +
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Residues in contact with ARG 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR* 5.9 3.2 - - - +
248C GLU* 5.6 10.7 + - - +
17J ILE* 5.5 1.8 - - - -
21J ASP* 2.8 34.4 + - + +
22J LYS* 3.1 15.6 + - + +
23J VAL 3.1 0.2 + - - -
24J GLU* 1.3 76.2 - - + +
26J ILE* 1.3 61.1 + - - +
28J GLU* 3.1 21.8 + - - +
29J ARG* 2.9 66.4 + - - +
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Residues in contact with ILE 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ILE* 4.3 21.5 - - + -
5J VAL* 5.1 1.1 - - + -
15J ILE* 4.9 4.9 - - + -
17J ILE* 4.0 32.5 - - + -
21J ASP* 5.1 3.1 - - + +
22J LYS 3.6 8.0 + - - +
23J VAL* 3.0 14.1 + - + +
25J ARG* 1.3 77.7 - - - +
27J LYS* 1.3 60.7 + - - +
29J ARG* 3.1 18.3 + - - +
30J VAL* 3.2 21.1 + - + +
43J LEU* 3.7 23.3 - - + -
50J MET* 4.4 17.9 - - + -
56J ALA* 4.6 13.2 - - + -
61J ILE* 4.8 2.5 - - + -
67J LEU* 4.2 9.4 - - + -
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Residues in contact with LYS 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J VAL* 3.2 21.4 + - - +
24J GLU* 3.5 10.3 - - - +
25J ARG 3.2 0.2 - - - -
26J ILE* 1.3 73.7 - - - +
28J GLU* 1.3 58.6 + - - +
30J VAL* 3.2 1.5 + - - -
31J GLU* 2.9 27.2 + - - +
38J PRO* 3.7 29.3 + - + +
41J GLN* 3.0 62.2 + - + +
42J ARG* 4.9 3.6 - - - +
43J LEU* 4.0 19.7 - - + +
50J MET 4.5 8.3 + - - -
52J ASP* 2.5 38.4 + - - +
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Residues in contact with GLU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 3.7 23.9 + - - -
277C LYS 5.4 0.3 - - - +
280C ASN* 2.8 43.1 + - + +
24J GLU* 3.0 21.3 + - + +
25J ARG* 3.1 31.4 + - - +
27J LYS* 1.3 77.0 - - - +
29J ARG* 1.3 63.3 + - - +
31J GLU* 4.4 3.6 - - - +
32J GLU* 3.1 12.8 + - - +
38J PRO* 4.8 8.5 - - + -
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Residues in contact with ARG 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR* 3.5 61.7 - - - +
280C ASN* 4.5 7.7 + - - -
15J ILE* 3.7 32.0 - - + +
16J ASP 4.2 17.3 + - - +
17J ILE* 4.6 5.1 - - + +
25J ARG* 2.9 57.1 + - + +
26J ILE* 3.1 9.8 + - - +
28J GLU* 1.3 78.4 + - - +
30J VAL* 1.3 63.7 + - - +
32J GLU* 3.5 15.0 + - - +
33J LYS* 3.4 25.5 + - - +
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Residues in contact with VAL 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J VAL* 4.1 18.4 - - + -
7J THR* 5.5 1.6 - - + -
13J ILE* 4.0 19.5 - - + -
15J ILE* 3.6 18.2 - - + -
26J ILE* 3.2 17.9 + - + +
27J LYS* 3.2 1.1 + - - +
29J ARG* 1.3 73.9 - - - +
31J GLU* 1.3 65.2 - - - +
33J LYS* 2.9 4.7 + - - +
34J GLU* 2.9 24.4 + - + +
36J ILE* 4.3 13.2 - - + -
41J GLN* 3.2 28.3 - - - +
43J LEU* 5.5 1.6 - - + -
69J LEU* 4.3 16.4 - - + -
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Residues in contact with GLU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 3.8 0.7 - - - +
277C LYS 4.9 2.9 - - - +
278C ASN* 4.2 12.9 - - - +
280C ASN* 2.8 31.3 + - - +
281C THR* 3.6 21.6 + - + +
27J LYS 2.9 15.4 + - - +
28J GLU* 4.6 1.9 - - - +
30J VAL* 1.3 75.7 - - - +
32J GLU* 1.3 60.2 + - - +
35J GLY* 2.9 29.2 + - - +
36J ILE 3.3 33.4 - - - +
37J PRO* 4.3 3.9 - - + +
38J PRO* 3.7 25.3 - - + +
41J GLN* 4.0 1.0 - - - +
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 3.7 8.3 - - - +
244C TYR* 3.3 37.7 + - - -
247C LYS* 3.5 18.2 + - - -
280C ASN* 3.6 20.3 - - - +
281C THR* 4.2 3.1 - - - -
284C ASN* 3.0 41.7 + - - +
28J GLU 3.1 15.7 + - - +
29J ARG* 3.5 20.9 + - - +
31J GLU* 1.3 77.0 - - - +
33J LYS* 1.3 64.4 + - + +
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Residues in contact with LYS 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 3.6 14.8 - - - +
244C TYR* 6.2 0.2 - - - -
13J ILE* 4.3 20.2 - - + -
14J GLU* 3.6 26.4 + - - +
15J ILE* 5.3 3.6 - - + +
29J ARG 3.4 13.4 + - - +
30J VAL 2.9 6.9 + - - +
32J GLU* 1.3 86.2 - - + +
34J GLU* 1.3 72.3 + - - +
35J GLY 3.7 0.4 - - - -
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASN* 4.0 7.6 - - + +
186C ALA* 3.9 18.7 + - - -
187C LEU* 4.2 4.6 + - - -
7J THR* 4.3 17.0 - - + -
11J LYS* 2.7 47.7 + - - +
13J ILE* 3.6 18.3 - - + +
30J VAL* 2.9 14.8 + - + +
33J LYS* 1.3 88.3 - - + +
35J GLY* 1.3 62.9 + - - +
36J ILE* 3.4 18.5 + - + -
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Residues in contact with GLY 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASN* 3.9 8.2 + - - +
186C ALA 4.2 13.9 - - - +
187C LEU* 4.1 16.1 - - - +
281C THR* 5.4 0.2 - - - -
31J GLU* 2.9 23.1 + - - +
33J LYS 3.7 0.4 - - - -
34J GLU* 1.3 79.3 - - - +
36J ILE* 1.3 61.3 + - - +
37J PRO* 3.1 14.7 - - - +
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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