Contacts of the helix formed by residues 51 - 63 (chain B) in PDB entry 1Z83
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 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B GLU* 2.7 26.7 + - - -
47B VAL 4.6 0.6 + - - +
49B SER* 3.1 13.4 + - - -
50B GLY* 1.3 82.3 - - - +
52B ALA* 1.3 58.9 + - - +
53B ARG* 3.8 5.1 + - - -
54B GLY* 2.9 23.5 + - - -
55B LYS* 3.0 27.1 + - - +
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Residues in contact with ALA 52 (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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702A SO4 5.1 0.7 - - - -
50B GLY 3.9 0.6 + - - -
51B SER* 1.3 70.2 - - - +
53B ARG* 1.3 65.7 + - - +
55B LYS* 3.3 10.3 + - - +
56B LYS* 3.2 27.7 + - + +
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Residues in contact with ARG 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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2A GLU* 6.1 4.6 - - - +
107A ARG* 3.0 30.7 + - - +
108A ARG* 4.5 7.1 - - - +
702A SO4 2.8 56.5 + - - +
46B GLU* 3.8 26.3 + - + +
51B SER* 3.2 8.2 - - - +
52B ALA* 1.3 78.3 - - - +
54B GLY* 1.3 56.2 + - - +
56B LYS* 3.2 6.9 + - - +
57B LEU* 2.9 43.6 + - + +
71B THR* 3.9 18.6 + - - +
75B MET* 4.5 3.4 - - - -
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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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46B GLU* 4.1 7.9 - - - -
47B VAL* 3.5 35.8 - - - +
51B SER* 2.9 22.3 + - - -
53B ARG* 1.3 74.2 - - - +
55B LYS* 1.3 58.8 + - - +
57B LEU* 3.3 2.0 + - - -
58B SER* 2.9 27.4 + - - -
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Residues in contact with LYS 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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47B VAL* 5.7 0.7 - - - -
50B GLY 5.3 3.4 - - - +
51B SER 3.0 14.6 + - - +
52B ALA* 3.6 12.3 - - - +
53B ARG 3.3 0.4 - - - -
54B GLY* 1.3 75.3 - - - +
56B LYS* 1.3 61.6 + - + +
58B SER* 3.3 8.0 + - - -
59B GLU* 3.2 31.5 + - - +
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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
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702A SO4 5.4 6.3 - - - +
52B ALA* 3.2 16.4 + - + +
53B ARG* 3.2 7.2 + - - +
55B LYS* 1.3 73.0 - - + +
57B LEU* 1.3 67.8 + - + +
59B GLU* 3.3 20.0 + - - +
60B ILE* 3.3 23.9 + - + +
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Residues in contact with LEU 57 (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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43B LEU* 3.9 20.4 - - + +
46B GLU* 3.9 21.5 - - + -
47B VAL* 4.4 0.7 - - + -
53B ARG* 2.9 37.8 + - + +
54B GLY* 3.7 4.9 - - - +
56B LYS* 1.3 75.0 - - + +
58B SER* 1.3 62.8 + - - +
60B ILE* 3.2 9.8 + - + +
61B MET* 3.0 39.2 + - + +
67B VAL* 3.8 30.6 - - + +
68B PRO* 4.7 7.9 - - + -
71B THR* 4.1 15.9 - - + +
75B MET* 4.1 6.3 - - + -
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Residues in contact with SER 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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47B VAL* 4.0 20.4 - - - +
54B GLY 2.9 17.3 + - - -
55B LYS* 3.6 8.3 - - - -
56B LYS 3.2 0.2 - - - -
57B LEU* 1.3 75.6 - - - +
59B GLU* 1.3 53.3 + - - +
61B MET* 3.2 12.7 + - - +
62B GLU* 2.8 62.4 + - - +
139B VAL* 4.4 9.4 - - - +
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Residues in contact with GLU 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 LYS* 3.2 18.1 + - - +
56B LYS* 3.3 13.0 + - - +
58B SER* 1.3 77.4 - - - +
60B ILE* 1.3 61.2 + - + +
62B GLU* 3.7 9.4 + - - +
63B LYS* 3.1 37.8 + - + +
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Residues in contact with ILE 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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56B LYS* 3.4 21.3 - - + +
57B LEU* 3.2 11.4 + - + +
59B GLU* 1.3 76.1 - - + +
61B MET* 1.3 64.0 + - - +
62B GLU 3.2 0.4 - - - -
63B LYS* 3.3 12.5 + - + -
65B GLN* 3.1 51.5 + - + +
66B LEU 3.6 18.8 - - - +
67B VAL* 4.0 6.7 - - + -
68B PRO* 4.2 23.3 - - + -
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Residues in contact with MET 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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40B GLY 5.1 0.4 - - - +
43B LEU* 4.0 24.0 - - + +
44B ARG* 4.4 16.8 - - + -
47B VAL* 3.5 31.2 - - + -
57B LEU* 3.0 35.0 + - + +
58B SER* 3.7 5.8 - - - +
60B ILE* 1.3 76.3 - - - +
62B GLU* 1.3 62.9 + - + +
64B GLY* 3.4 12.0 + - - -
67B VAL* 4.3 4.7 - - + -
140B ASP* 3.6 24.4 - - + +
145B THR* 4.0 0.3 - - - +
149B ARG* 5.3 0.3 - - - +
632B AP5 3.4 47.3 + - - +
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Residues in contact with GLU 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 SER* 2.8 39.2 + - - +
59B GLU* 3.9 10.2 + - - +
60B ILE 3.2 0.2 - - - -
61B MET* 1.3 79.4 - - + +
63B LYS* 1.3 56.3 + - + +
64B GLY 3.4 1.1 - - - -
139B VAL* 3.0 40.1 - - + +
140B ASP* 5.5 0.2 - - + -
145B THR* 3.0 27.8 + - - +
148B LYS* 5.2 0.9 - - - +
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Residues in contact with LYS 63 (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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59B GLU* 3.1 26.8 + - + +
60B ILE* 3.3 11.5 + - + +
61B MET 3.3 0.6 - - - -
62B GLU* 1.3 75.5 - - - +
64B GLY* 1.3 62.4 + - - +
65B GLN* 3.3 37.0 + - - +
145B THR* 4.8 0.2 - - - -
148B LYS* 3.6 34.9 - - + +
152B THR* 5.2 0.2 + - - -
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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