Contacts of the helix formed by residues 45 - 59 (chain J) in PDB entry 2ZJQ
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 SER 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J LYS* 3.9 31.7 - - - +
7J ARG* 4.8 0.4 - - - +
43J ILE 3.6 2.4 + - - -
44J LYS* 1.3 70.4 - - - +
46J ASN* 1.3 69.7 + - - +
48J ILE* 2.9 28.7 + - - +
49J GLU* 3.2 8.5 + - - +
71J PRO* 3.8 26.2 - - - +
93J TYR* 5.6 1.9 - - - +
94J TRP* 3.3 28.3 + - - +
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Residues in contact with ASN 46 (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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6J LYS* 5.9 1.3 - - - -
44J LYS* 3.0 18.4 - - - +
45J SER* 1.3 81.0 + - - +
47J GLN* 1.3 68.7 + - - +
48J ILE 3.0 5.4 - - - -
49J GLU* 3.9 11.2 - - + +
50J ALA* 3.1 26.0 + - - +
93J TYR* 5.0 9.3 - - - +
2462X C 4.3 1.6 + - - +
2463X G 3.0 40.7 + - - +
2464X G 5.4 1.2 + - - -
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Residues in contact with GLN 47 (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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42J TRP 3.7 0.2 - - - +
43J ILE* 3.6 7.2 - - + -
44J LYS* 2.5 71.2 + - + +
46J ASN* 1.3 82.2 - - - +
48J ILE* 1.3 57.3 + - - -
50J ALA* 3.9 11.3 - - - +
51J CYS* 3.0 23.9 - - - -
125J LYS 4.3 4.5 - - - +
126J LEU* 3.7 8.1 - - + +
127J PRO* 3.7 22.5 - - - +
2463X G 3.4 14.4 - - - +
2464X G 2.4 42.6 + - - -
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Residues in contact with ILE 48 (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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6J LYS* 6.1 1.1 - - - +
43J ILE* 3.7 12.8 - - + -
44J LYS 3.6 7.9 - - - +
45J SER* 2.9 11.8 + - - +
47J GLN* 1.3 78.7 - - - +
49J GLU* 1.3 58.2 + - + +
50J ALA 3.0 0.9 - - - -
51J CYS* 2.4 28.0 + - - +
52J ARG* 2.6 17.7 + - + -
67J ILE* 3.5 37.0 - - + -
69J ILE* 3.4 34.8 - - + -
70J PHE* 5.2 0.4 - - - -
71J PRO* 3.9 30.1 - - + -
96J SER* 4.7 3.4 - - - -
105J PHE* 4.8 5.2 - - + -
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Residues in contact with GLU 49 (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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6J LYS* 4.8 26.9 + - + +
45J SER 3.2 8.4 + - - +
46J ASN* 3.9 10.8 - - - +
48J ILE* 1.3 80.1 - - + +
50J ALA* 1.3 54.8 + - - +
51J CYS 2.6 12.0 + - - -
52J ARG* 2.4 46.9 + - - +
53J ILE* 2.8 48.3 + - + +
67J ILE* 5.7 1.6 - - - +
2462X C 5.5 1.6 - - - +
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Residues in contact with ALA 50 (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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46J ASN 3.1 16.6 + - - +
47J GLN* 3.9 10.1 - - - +
49J GLU* 1.3 78.6 - - - +
51J CYS* 1.3 54.8 + - - +
53J ILE* 5.3 1.8 - - - -
54J VAL* 2.8 24.9 - - - +
125J LYS* 3.1 19.6 - - + +
2462X C 3.7 17.8 + - - +
2463X G 3.4 29.2 - - - +
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Residues in contact with CYS 51 (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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47J GLN 3.0 23.3 - - - -
48J ILE* 2.4 22.2 + - - +
49J GLU 2.6 0.8 + - - -
50J ALA* 1.3 71.9 - - - +
52J ARG* 1.3 67.6 + - - +
53J ILE 3.4 0.2 - - - -
54J VAL* 3.1 5.0 + - - +
55J MET* 2.9 26.4 + - + +
105J PHE* 3.7 25.4 - - + -
122J ALA* 3.7 16.8 - - + +
125J LYS* 3.7 15.9 - - - -
126J LEU* 3.3 25.6 - - - -
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Residues in contact with ARG 52 (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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48J ILE* 2.6 15.1 + - - +
49J GLU* 2.4 43.0 + - - +
51J CYS* 1.3 75.2 - - - +
53J ILE* 1.3 62.8 + - - +
54J VAL 2.8 2.4 + - - -
55J MET* 2.9 13.1 + - - +
56J SER* 2.7 47.3 + - - +
65J ILE* 4.8 8.3 - - + +
67J ILE* 3.4 32.0 - - + +
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Residues in contact with ILE 53 (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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49J GLU* 2.8 52.5 + - + +
50J ALA* 5.3 1.8 - - - -
52J ARG* 1.3 85.1 - - - +
54J VAL* 1.3 61.2 + - + +
56J SER* 3.6 9.6 - - - -
57J ARG* 3.3 44.7 + - - +
2461X G 5.1 15.5 - - - +
2462X C 6.0 1.6 - - - +
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Residues in contact with VAL 54 (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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50J ALA* 2.8 27.1 - - - +
51J CYS* 3.1 8.7 + - - +
52J ARG 2.8 1.4 + - - -
53J ILE* 1.3 75.5 - - + +
55J MET* 1.3 71.8 + - - +
56J SER 2.9 2.1 + - - -
57J ARG* 3.1 18.8 + - - +
58J HIS* 3.4 8.7 + - - +
118J ALA* 4.9 0.7 - - - +
121J LEU* 3.5 42.2 - - + +
122J ALA 3.9 8.3 - - - +
125J LYS* 3.9 13.9 - - - -
2461X G 5.5 7.4 - - - +
2462X C 4.4 8.5 - - - +
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Residues in contact with MET 55 (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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51J CYS* 2.9 24.4 + - + +
52J ARG* 3.5 5.6 - - - +
54J VAL* 1.3 76.9 - - - +
56J SER* 1.3 69.8 + - - +
58J HIS* 3.1 11.8 + - - +
59J PHE* 3.2 12.6 + - - -
65J ILE* 3.4 39.9 - - + -
105J PHE* 3.4 38.8 - - + -
107J VAL* 4.4 2.5 - - - -
118J ALA* 2.7 40.8 - - + +
119J PHE* 3.5 30.1 - - - -
122J ALA* 4.2 5.2 - - + -
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Residues in contact with SER 56 (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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52J ARG* 2.7 33.3 + - - -
53J ILE* 3.6 15.3 - - - -
54J VAL 2.9 0.4 + - - -
55J MET* 1.3 69.8 - - - +
57J ARG* 1.3 70.2 + - - +
59J PHE* 2.4 30.2 + - - +
65J ILE* 4.0 10.2 - - - +
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Residues in contact with ARG 57 (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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53J ILE* 3.3 33.0 + - - +
54J VAL* 3.4 8.5 - - - +
56J SER* 1.3 84.2 - - - +
58J HIS* 1.3 55.0 + - - +
59J PHE 2.8 15.6 + - - +
60J ARG* 3.9 13.2 + - - -
2448X A 4.7 27.8 + - - +
2461X G 5.4 6.3 - - - +
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Residues in contact with HIS 58 (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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54J VAL 3.4 5.2 + - - +
55J MET* 3.1 13.9 + - - +
56J SER 2.7 3.8 + - - -
57J ARG* 1.3 76.5 - - - +
59J PHE* 1.3 65.2 + + + +
60J ARG* 3.9 5.0 + - - -
114J GLN* 3.9 42.4 + - - +
117J GLU* 3.7 30.8 - - + +
118J ALA* 4.4 15.0 - - - -
121J LEU* 4.8 14.3 - - + +
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Residues in contact with PHE 59 (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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55J MET 3.7 3.1 - - - -
56J SER* 2.4 36.2 + - - +
57J ARG 3.5 2.7 - - - +
58J HIS* 1.3 76.8 - + - +
60J ARG* 1.3 68.9 + - - +
61J ARG* 3.0 15.8 + - - +
63J GLY* 5.2 2.5 - - - +
64J LYS* 4.0 15.9 - - + +
65J ILE* 3.3 43.5 - - + -
107J VAL* 3.6 19.5 - - + -
110J VAL* 3.9 24.2 - - + -
114J GLN 3.3 24.2 - - - -
118J ALA* 3.4 27.4 - - + -
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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