Contacts of the helix formed by residues 49 - 60 (chain P) in PDB entry 2ZJR
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 49 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48P LYS* 1.3 71.8 - - - +
50P VAL* 1.3 53.3 - - - +
51P GLN* 2.2 48.9 + - - +
52P ASP* 2.4 38.9 + - - +
53P ALA 3.2 5.2 + - - -
90P LEU 4.4 7.7 + - - -
91P PHE* 4.4 2.8 - - - +
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Residues in contact with VAL 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P LYS 2.7 10.5 + - - -
49P SER* 1.3 67.6 - - - +
51P GLN* 1.3 63.3 + - + +
53P ALA* 3.8 11.4 - - - +
54P GLU* 3.2 26.0 + - + +
72P LEU* 4.1 31.4 - - + +
76P LYS* 5.0 17.3 - - + -
87P GLU 4.4 4.7 - - - +
90P LEU* 3.2 42.8 + - + +
91P PHE* 4.1 7.9 - - - -
92P VAL* 4.4 4.3 - - - +
128P VAL* 4.8 9.0 - - + -
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Residues in contact with GLN 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P SER* 2.2 30.6 + - - +
50P VAL* 1.3 73.2 - - + +
52P ASP* 1.3 64.3 - - - +
54P GLU* 2.8 37.3 + - - +
55P ASP* 2.9 27.6 + - - +
88P ASP* 6.6 0.2 - - - -
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Residues in contact with ASP 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P LYS* 3.8 28.0 - - - +
49P SER* 2.4 41.7 + - - +
51P GLN* 1.3 75.0 - - - +
53P ALA* 1.3 52.7 + - - +
55P ASP* 2.6 16.8 + - - +
56P LEU* 2.5 40.5 + - + -
39Z LYS* 3.8 17.9 + - - +
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Residues in contact with ALA 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P ILE* 3.4 35.2 - - + +
48P LYS* 4.9 3.4 - - + +
49P SER 3.2 3.1 + - - +
50P VAL* 3.8 12.8 - - - +
52P ASP* 1.3 79.2 - - - +
54P GLU* 1.3 62.5 + - - +
56P LEU* 4.7 0.9 - - - -
57P LEU* 3.1 28.9 + - - +
72P LEU* 3.2 26.2 - - + -
92P VAL* 4.3 5.2 - - + -
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Residues in contact with GLU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P VAL* 3.2 16.2 + - + +
51P GLN* 2.8 33.5 + - - +
53P ALA* 1.3 79.4 - - - +
55P ASP* 1.3 65.7 + - - +
57P LEU* 4.0 6.1 - - - +
58P ARG* 3.5 31.1 + - - +
72P LEU* 4.6 10.1 - - + -
73P ASN* 4.5 9.0 - - + +
76P LYS* 3.2 31.7 + - + -
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Residues in contact with ASP 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P GLN* 2.9 31.0 + - - +
52P ASP* 2.6 11.4 + - - +
54P GLU* 1.3 73.9 - - - +
56P LEU* 1.3 65.5 + - - +
57P LEU 3.2 1.3 - - - -
58P ARG* 3.1 38.2 + - - +
59P PHE* 3.5 2.6 + - - -
30Z LEU* 3.5 16.3 - - + +
39Z LYS* 3.0 50.9 + - + +
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Residues in contact with LEU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P VAL* 4.5 10.8 - - + +
45P ILE* 4.7 7.2 - - + -
48P LYS* 2.9 38.4 - - + +
52P ASP* 2.5 23.5 + - + +
53P ALA 4.3 2.5 - - - +
55P ASP* 1.3 72.4 - - - +
57P LEU* 1.3 57.6 + - - +
59P PHE* 3.1 2.8 + - - +
60P ILE* 2.8 44.1 + - + +
27Z ALA* 4.1 15.9 - - + -
28Z PRO* 4.1 28.0 - - + +
30Z LEU* 4.3 16.4 - - + +
39Z LYS* 5.0 7.2 - - - +
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P VAL* 3.8 18.8 - - + -
45P ILE* 3.1 33.0 - - + -
53P ALA 3.1 22.6 + - - +
54P GLU* 4.0 6.1 - - - +
56P LEU* 1.3 79.4 - - - +
58P ARG* 1.3 65.1 + - - +
59P PHE 2.8 1.6 + - - -
60P ILE* 3.5 15.8 + - + +
65P SER* 3.7 26.8 - - - +
68P VAL* 3.7 19.3 - - + +
69P ALA* 3.4 36.8 - - + +
72P LEU* 4.4 8.1 - - + -
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Residues in contact with ARG 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P GLU* 3.5 19.5 + - - +
55P ASP* 3.1 35.6 + - - +
57P LEU* 1.3 79.3 - - - +
59P PHE* 1.3 80.7 - - + +
60P ILE 5.0 0.3 - - - +
39Z LYS* 5.4 4.2 + - - +
47Z PRO* 5.2 5.6 - - - -
48Z ASN* 4.4 21.0 - - - +
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Residues in contact with PHE 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K THR* 4.8 7.4 + - - +
55P ASP 3.5 11.9 - - - +
56P LEU 3.1 5.2 + - - +
57P LEU 2.8 1.6 + - - -
58P ARG* 1.3 106.9 - - + +
60P ILE* 1.3 67.1 + - - +
61P PRO* 3.0 13.6 - - - +
28Z PRO* 4.0 17.6 - - + +
30Z LEU* 3.6 15.3 - - + -
39Z LYS* 3.6 24.7 - - + -
40Z LYS* 4.0 5.6 - - - -
41Z LEU* 3.6 53.0 - - + +
47Z PRO* 4.1 21.3 - - + -
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Residues in contact with ILE 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P VAL* 4.3 18.2 - - + -
44P VAL* 3.1 42.2 - - + -
56P LEU* 2.8 28.9 + - + +
57P LEU* 3.5 6.9 + - + +
58P ARG 5.0 0.5 - - - +
59P PHE* 1.3 72.1 - - - +
61P PRO* 1.3 66.7 - - + +
62P ARG* 3.8 14.2 - - + +
65P SER* 3.0 33.4 + - - +
25Z LEU* 5.0 8.1 - - + -
26Z THR 5.4 1.8 - - - +
27Z ALA* 4.8 1.3 - - - -
28Z PRO* 3.6 25.0 - - + +
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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