Contacts of the helix formed by residues 54 - 63 (chain F) in PDB entry 2WJZ
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 PHE 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F GLY 3.9 0.2 + - - -
53F HIS* 1.3 71.0 - - - +
55F GLY* 1.3 61.6 + - - +
56F GLU 3.1 4.0 - - - +
58F MET* 3.1 41.7 - - + +
85F LEU* 6.2 2.0 - - - +
88F GLN* 3.1 45.5 - - + -
89F LEU* 3.6 22.3 - - + +
91F PHE 4.6 0.9 - - - -
93F GLU* 4.3 3.6 - - - -
94F SER* 3.2 42.2 - - - +
96F GLU* 3.0 17.4 + - + +
97F ALA* 3.6 21.1 - - + -
100F VAL* 4.2 15.0 - - + -
101F LYS 4.4 0.9 - - - -
102F GLY* 3.9 25.4 - - - -
110F VAL* 4.4 1.1 - - + -
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Residues in contact with GLY 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F HIS* 2.9 22.2 + - - -
54F PHE* 1.3 77.2 - - - +
56F GLU* 1.3 63.9 + - - -
58F MET* 3.4 4.4 - - - +
59F ARG* 3.0 27.9 + - - +
97F ALA* 3.9 6.0 - - - +
100F VAL* 4.7 13.1 - - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PRO* 3.9 18.4 - - + +
53F HIS* 2.6 35.7 + - + +
54F PHE* 3.1 3.5 - - - +
55F GLY* 1.3 74.4 - - - +
57F GLY* 1.3 57.8 + - - +
58F MET 2.9 5.9 + - - -
59F ARG* 2.8 46.0 + - - +
60F ARG* 2.8 48.5 + - - +
89F LEU* 5.4 1.9 - - - +
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Residues in contact with GLY 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 5.3 1.6 - - - +
9F GLY 3.5 24.5 - - - -
10F PRO* 3.8 3.5 - - - +
56F GLU* 1.3 72.4 - - - +
58F MET* 1.3 59.1 + - - +
59F ARG 3.1 2.3 - - - +
60F ARG* 3.5 20.2 - - - +
61F LEU* 2.9 24.4 + - - -
89F LEU* 4.5 14.3 - - - +
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Residues in contact with MET 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 3.1 37.7 - - + +
55F GLY 3.4 3.6 - - - +
56F GLU 2.9 5.1 + - - -
57F GLY* 1.3 76.7 - - - +
59F ARG* 1.3 61.5 + - - +
61F LEU* 3.8 3.3 + - - -
62F ARG* 3.5 13.9 + - - -
89F LEU* 3.8 21.4 - - + +
100F VAL* 4.5 11.9 - - + -
101F LYS 3.3 24.0 - - - +
102F GLY* 3.4 18.6 - - - -
103F LEU* 3.8 32.5 - - + +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 3.7 38.9 - - + +
30D VAL 5.6 1.3 - - - +
31D SER* 5.6 11.3 - - - -
55F GLY 3.0 12.0 + - - +
56F GLU* 2.8 60.3 + - - +
58F MET* 1.3 77.3 - - - +
60F ARG* 1.3 60.7 + - - +
61F LEU 3.2 0.2 - - - -
62F ARG* 3.0 5.2 + - - +
63F GLU* 2.8 27.0 + - - -
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Residues in contact with ARG 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 2.8 55.2 + - + +
9F GLY* 3.8 11.5 - - - -
10F PRO* 3.7 24.3 - - - +
56F GLU* 2.8 44.2 + - - +
57F GLY* 3.4 13.5 + - - +
59F ARG* 1.3 79.4 - - + +
61F LEU* 1.3 60.7 + - - +
63F GLU* 3.9 2.2 - - - +
64F ASN* 3.0 34.5 + - - +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 6.5 0.7 - - - -
8F VAL* 5.2 2.9 - - - +
57F GLY 2.9 17.2 + - - -
58F MET* 4.3 4.7 - - - +
60F ARG* 1.3 74.3 - - - +
62F ARG* 1.3 62.8 + - - +
64F ASN* 3.7 0.4 + - - -
65F ASP 3.6 1.4 + - - -
66F LEU* 3.0 40.4 + - - +
67F ILE* 3.6 9.2 + - - +
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 6.0 2.2 - - - -
58F MET 3.5 9.9 + - - -
59F ARG* 3.0 7.0 + - - +
61F LEU* 1.3 73.3 - - - +
63F GLU* 1.3 51.1 + - - +
64F ASN 2.6 16.2 + - - -
65F ASP* 2.9 15.6 + - - +
67F ILE* 5.5 0.9 - - - +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET 6.4 0.4 - - - +
59F ARG 2.8 17.2 + - - -
60F ARG* 3.8 3.1 + - - +
62F ARG* 1.3 68.6 - - - +
64F ASN* 1.3 71.4 + - - +
65F ASP 3.8 0.4 - - - -
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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