Contacts of the helix formed by residues 51 - 62 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C GLU* 2.6 29.9 + - - -
47C VAL 4.5 0.4 + - - +
49C SER* 3.2 11.8 + - - -
50C GLY* 1.3 82.5 - - - +
52C ALA* 1.3 61.5 + - - +
53C ARG* 4.2 4.3 - - - +
54C GLY* 3.2 14.9 + - - -
55C LYS* 3.0 24.6 + - - +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER* 1.3 71.0 - - - +
53C ARG* 1.3 67.3 + - + +
55C LYS* 3.0 20.6 + - - +
56C LYS* 3.1 19.9 + - + +
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Residues in contact with ARG 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 5.1 4.7 - - + +
51C SER* 3.3 5.9 + - - +
52C ALA* 1.3 79.7 - - + +
54C GLY* 1.3 63.0 + - - +
56C LYS* 3.4 14.3 + - + +
57C LEU* 3.0 30.8 + - + +
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 4.0 10.8 - - - +
47C VAL* 3.6 29.6 - - - +
51C SER* 3.2 22.3 + - - -
53C ARG* 1.3 74.7 - - - +
55C LYS* 1.3 63.7 + - - +
57C LEU* 3.3 4.0 + - - +
58C SER* 3.0 23.9 + - - -
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Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 5.4 1.8 + - - -
51C SER 3.0 11.2 + - - +
52C ALA* 3.0 13.8 + - - +
54C GLY* 1.3 75.3 - - - +
56C LYS* 1.3 61.3 - - + +
58C SER* 3.2 9.8 + - - -
59C GLU* 3.2 30.3 + - + +
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA* 3.1 17.6 + - + +
53C ARG* 3.8 15.7 - - + +
54C GLY 3.3 0.2 - - - -
55C LYS* 1.3 73.7 - - + +
57C LEU* 1.3 66.6 + - + +
58C SER 3.4 0.2 + - - -
59C GLU* 3.5 15.3 + - - +
60C ILE* 3.5 22.7 + - + +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.7 23.1 - - + +
46C GLU* 4.1 27.6 - - + -
47C VAL* 4.6 2.9 - - + -
53C ARG* 3.0 21.0 + - + +
54C GLY* 3.3 7.4 + - - +
56C LYS* 1.3 75.5 - - + +
58C SER* 1.3 63.5 + - - +
60C ILE* 3.3 12.8 + - + +
61C MET* 3.1 37.9 + - - +
67C VAL* 3.9 27.5 - - + +
68C PRO* 4.8 4.0 - - + -
71C THR* 4.4 17.0 - - + +
75C MET* 4.6 6.3 - - + -
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.8 22.9 - - - +
54C GLY 3.0 14.2 + - - -
55C LYS* 3.2 11.6 + - - -
57C LEU* 1.3 74.3 - - - +
59C GLU* 1.3 54.1 + - - +
61C MET* 3.2 12.0 + - - +
62C GLU* 2.8 62.1 + - - +
139C VAL* 4.4 7.8 - - - +
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LYS* 3.2 18.8 + - + +
56C LYS* 3.7 11.7 - - - +
57C LEU 3.3 0.2 - - - -
58C SER* 1.3 78.7 - - - +
60C ILE* 1.3 60.0 + - + +
62C GLU* 3.5 12.9 + - - +
63C LYS* 3.5 38.4 + - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 3.5 21.1 - - + +
57C LEU* 3.3 13.3 + - + +
59C GLU* 1.3 74.3 - - + +
61C MET* 1.3 66.5 + - - +
63C LYS* 3.0 23.6 + - - +
65C GLN* 3.4 37.3 + - + +
66C LEU 3.6 23.6 - - - +
67C VAL* 3.8 10.1 - - + -
68C PRO* 4.4 21.1 - - + -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 4.3 2.2 - - - +
43C LEU* 3.7 30.7 - - + -
44C ARG* 3.8 26.0 - - + +
47C VAL* 4.4 7.0 - - - -
57C LEU* 3.1 28.4 + - - +
58C SER* 3.6 10.5 - - - +
60C ILE* 1.3 74.8 - - - +
62C GLU* 1.3 62.9 + - + +
64C GLY* 3.1 14.9 + - - -
67C VAL* 4.1 6.5 - - + -
139C VAL* 5.7 3.1 - - + -
140C ASP* 3.9 21.2 - - + +
149C ARG* 5.4 0.2 - - - -
633C AP5 3.4 51.4 + - - +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 2.8 41.9 + - - +
59C GLU* 3.8 13.2 + - - +
60C ILE 3.2 0.6 - - - -
61C MET* 1.3 72.0 - - - +
63C LYS* 1.3 58.2 + - + +
64C GLY 3.4 0.2 - - - -
139C VAL* 3.2 45.5 - - + +
140C ASP* 4.8 3.4 - - - -
145C THR* 3.1 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