Contacts of the helix formed by residues 45 - 62 (chain B) in PDB entry 5ZJS
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 THR 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA* 3.5 7.0 - - - +
44B ILE* 1.3 78.1 - - - +
46B VAL* 1.3 75.0 + - + +
47B SER* 3.2 25.4 + - - +
48B GLN* 3.3 31.1 + - - +
49B VAL* 3.5 9.5 + - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 4.2 7.9 - - + +
36B GLU* 4.0 28.7 - - + +
39B ALA* 3.7 20.6 - - + -
45B THR* 1.3 75.4 - - + +
47B SER* 1.3 56.2 + - - +
48B GLN 2.9 5.9 + - - -
49B VAL* 3.1 5.3 + - - +
50B SER* 2.8 37.8 + - - -
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.4 22.4 + - - +
46B VAL* 1.3 84.4 - - - +
48B GLN* 1.3 53.7 + - - +
50B SER* 3.5 10.7 + - - -
51B ASN* 2.5 37.4 + - - -
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.1 30.6 - - + -
44B ILE* 4.0 13.3 - - + +
45B THR* 3.3 40.8 + - - +
46B VAL 2.9 0.4 - - - -
47B SER* 1.3 84.5 - - - +
49B VAL* 1.3 60.6 + - - +
51B ASN* 3.3 3.8 + - - +
52B TRP* 2.9 28.1 + - - +
6D A 3.0 36.5 + - - +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 6.2 0.2 - - - -
17B LEU* 4.3 12.6 - - + -
30B PRO* 5.6 0.7 - - + -
35B LYS* 4.2 13.7 - - + +
38B LEU* 4.0 23.1 - - + +
39B ALA* 3.8 27.6 - - + +
42B CYS* 5.5 2.7 - - + -
44B ILE* 5.1 6.1 - - + -
45B THR 3.5 15.3 - - - +
46B VAL 3.1 4.8 + - - +
48B GLN* 1.3 73.9 - - - +
50B SER* 1.3 65.8 + - - +
52B TRP* 3.0 7.0 + - - +
53B PHE* 3.0 53.9 + - + -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 6.1 3.4 - - - -
35B LYS* 5.8 4.0 - - - +
46B VAL 2.8 19.4 + - - -
47B SER* 3.5 11.8 + - - -
49B VAL* 1.3 75.3 - - - +
51B ASN* 1.3 57.8 + - - +
53B PHE* 3.5 7.2 + - - +
54B GLY* 2.9 24.3 + - - -
5C T 5.3 8.3 - - - -
6C T 5.8 0.7 - - - +
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.5 25.2 + - - -
48B GLN* 3.3 10.1 + - - +
50B SER* 1.3 77.9 + - - +
52B TRP* 1.3 65.1 + - - +
54B GLY* 3.0 4.1 + - - -
55B ASN* 3.0 29.5 + - - +
5D G 5.4 0.9 - - + -
6D A 3.8 41.6 + - + +
7D T 3.5 27.4 + - - +
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Residues in contact with TRP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 4.3 14.5 - + + -
14B SER* 4.7 8.3 - - - +
17B LEU* 3.4 58.7 - - + +
18B ASN* 3.2 28.5 - - - -
21B PHE* 4.1 11.7 - + + -
48B GLN 2.9 15.1 + - - +
49B VAL* 3.0 8.3 + - - +
51B ASN* 1.3 75.1 - - - +
53B PHE* 1.3 79.1 + + - +
55B ASN* 3.5 6.3 + - + +
56B LYS* 2.9 65.0 + - + +
5D G 3.6 28.4 + - - +
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 4.3 7.4 - - + -
20B TYR* 3.3 44.6 - + + -
21B PHE* 4.2 24.2 - + + -
28B PRO 3.6 21.3 - - - +
30B PRO* 4.4 17.9 - - + -
38B LEU* 4.1 9.6 - - + -
49B VAL* 3.0 48.6 + - + +
50B SER* 4.0 5.6 - - - +
52B TRP* 1.3 93.5 - + - +
54B GLY* 1.3 65.6 + - - +
55B ASN 3.1 0.7 - - - -
56B LYS* 4.3 2.0 - - - +
57B ARG* 3.0 29.5 + - - +
6C T 5.0 1.0 + - - -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER 2.9 15.9 + - - -
51B ASN* 3.0 6.7 + - - -
53B PHE* 1.3 76.9 - - - +
55B ASN* 1.3 60.5 + - - +
57B ARG* 4.4 2.4 - - - +
58B ILE* 3.8 15.6 + - - +
6C T 4.2 36.5 + - - +
7C A 4.8 7.0 - - - +
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ASN* 3.0 21.6 + - - +
52B TRP* 4.0 4.9 - - + +
54B GLY* 1.3 77.7 - - - +
56B LYS* 1.3 60.1 + - - +
57B ARG 3.2 2.2 + - - -
58B ILE* 3.2 9.7 - - - +
59B ARG* 3.0 56.1 + - - +
7C A 5.8 0.7 - - - +
8C A 4.2 5.7 + - - -
5D G 3.7 13.5 + - + +
6D A 2.6 51.3 + - - +
7D T 5.0 0.7 - - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN* 4.5 10.1 - - - -
21B PHE* 3.8 19.1 - - + -
22B TYR* 3.6 21.7 + - - -
52B TRP* 2.9 56.0 + - + +
53B PHE* 4.2 2.5 - - - +
55B ASN* 1.3 76.5 - - - +
57B ARG* 1.3 57.5 + - - +
59B ARG* 4.6 9.6 + - + +
60B TYR* 2.9 37.7 + - - +
68B GLN* 3.3 25.0 - - - +
4D T 5.7 3.2 + - - -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 4.4 16.2 + - + +
21B PHE* 4.3 13.8 - - + -
28B PRO* 6.0 4.5 - - + -
29B TYR* 6.2 1.6 - - + -
53B PHE 3.0 18.6 + - - +
54B GLY 4.4 4.0 - - - +
56B LYS* 1.3 79.6 - - - +
58B ILE* 1.3 58.5 + - + +
60B TYR* 3.2 5.0 - - - +
61B LYS* 3.0 27.0 + - - +
6C T 4.8 17.7 - - - +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY 3.8 13.5 - - - +
55B ASN* 3.2 15.3 - - - +
57B ARG* 1.3 77.1 - - - +
59B ARG* 1.3 67.6 + - + +
61B LYS* 3.0 12.2 + - + +
62B LYS* 2.8 59.7 + - + +
6C T 5.7 1.6 - - + -
7C A 3.8 55.2 - - + +
8C A 5.3 1.1 - - - +
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASN* 3.0 41.2 + - - +
56B LYS* 4.4 12.3 + - + +
58B ILE* 1.3 83.3 - - + +
60B TYR* 1.3 61.3 + - - +
62B LYS* 3.9 13.6 + - + +
63B ASN* 4.3 8.1 + - - +
68B GLN* 4.7 4.9 - - - +
9C T 4.0 8.3 + - - +
10C C 4.9 0.2 - - - +
4D T 3.6 35.8 + - - +
5D G 2.6 50.9 + - - -
6D A 3.7 8.9 - - - +
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 4.0 30.9 - + - -
21B PHE* 3.6 27.1 - + + -
22B TYR* 4.1 13.9 - + - -
25B LEU* 5.0 11.6 - - + +
56B LYS* 2.9 24.3 + - - +
57B ARG 3.2 3.8 - - - +
58B ILE 3.1 0.2 - - - -
59B ARG* 1.3 78.1 - - - +
61B LYS* 1.3 63.6 - - - +
62B LYS 3.1 0.9 - - - -
63B ASN* 3.0 28.1 + - - +
68B GLN* 3.7 38.8 + - + +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 4.3 19.1 - - + +
57B ARG 3.0 13.9 + - - +
58B ILE* 3.0 16.4 + - + +
60B TYR* 1.3 84.1 - - + +
62B LYS* 1.3 56.9 + - - +
63B ASN 3.1 11.3 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 2.8 38.8 + - + +
59B ARG* 4.4 11.9 - - + +
60B TYR 3.0 1.0 + - - -
61B LYS* 1.3 76.4 - - - +
63B ASN* 1.3 58.1 + - - +
64B ILE* 5.6 0.5 - - - +
8C A 3.7 24.7 + - - -
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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