Contacts of the helix formed by residues 57 - 64 (chain u) in PDB entry 4IL6
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 57 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55u TYR* 3.7 6.8 - - - +
56u GLU* 1.3 78.9 - - - +
58u VAL* 1.3 65.7 + - - +
59u GLU* 3.4 32.3 + - - +
60u ASP* 2.6 39.7 + - - +
84u VAL* 3.8 11.0 - - - -
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Residues in contact with VAL 58 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27u LEU* 3.9 7.8 - - - +
57u SER* 1.3 71.4 - - - +
59u GLU* 1.3 64.9 + - - +
61u VAL* 3.0 35.2 + - - +
79u LEU* 3.6 33.0 - - + +
82u PHE* 3.7 24.5 - - + +
83u THR* 3.4 40.8 - - - +
84u VAL* 3.9 6.3 - - + +
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Residues in contact with GLU 59 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57u SER* 3.4 24.7 + - - +
58u VAL* 1.3 84.2 + - - +
60u ASP* 1.3 60.8 + - - +
61u VAL 3.1 0.7 - - - -
62u LEU* 3.2 33.8 + - + +
63u ASN* 4.5 3.7 + - - +
79u LEU* 4.5 14.8 - - + +
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Residues in contact with ASP 60 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55u TYR* 3.9 21.5 - - + -
56u GLU* 3.8 12.4 - - - +
57u SER* 2.6 45.7 + - - +
59u GLU* 1.3 73.4 - - - +
61u VAL* 1.3 63.6 + - - +
62u LEU 3.1 2.7 - - - -
63u ASN* 3.0 37.2 + - - +
64u ILE 4.2 2.1 + - - -
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Residues in contact with VAL 61 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27u LEU* 3.8 21.3 - - + -
49u ILE* 3.7 37.0 - - + -
55u TYR* 3.9 13.6 - - + -
58u VAL 3.0 22.9 + - - +
60u ASP* 1.3 78.6 - - - +
62u LEU* 1.3 65.0 + - + +
63u ASN 3.1 1.3 + - - -
64u ILE* 3.4 25.2 + - + +
67u LEU* 3.6 6.1 - - - +
75u LEU* 3.8 18.1 - - + +
79u LEU* 3.9 21.5 - - + -
82u PHE* 4.6 2.9 - - + -
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Residues in contact with LEU 62 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59u GLU* 3.4 28.7 - - + +
60u ASP 3.1 0.8 - - - -
61u VAL* 1.3 78.4 - - + +
63u ASN* 1.3 63.3 + - - +
64u ILE 3.5 1.0 - - - +
67u LEU* 3.4 17.2 - - - +
72u LYS* 3.8 23.3 - - + +
75u LEU* 3.7 29.4 - - + -
76u ARG* 3.8 43.5 - - + +
79u LEU* 4.4 11.4 - - + -
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Residues in contact with ASN 63 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59u GLU 4.7 2.5 + - - +
60u ASP* 3.0 34.6 + - - +
62u LEU* 1.3 86.3 - - - +
64u ILE* 1.3 65.8 + - - +
65u PRO* 3.1 9.5 - - - +
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Residues in contact with ILE 64 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45u LEU* 6.1 0.2 - - + -
48u LEU* 3.9 26.0 - - + +
49u ILE* 4.0 8.3 - - + +
52u ASN* 3.6 30.3 - - + +
55u TYR* 3.3 34.3 - - + +
60u ASP 4.2 0.6 + - - -
61u VAL* 3.4 28.5 - - + +
62u LEU 3.5 2.1 - - - +
63u ASN* 1.3 76.5 - - - +
65u PRO* 1.3 80.8 - - + +
66u GLY 3.4 1.2 + - - -
67u LEU* 3.2 34.6 + - + +
72u LYS* 5.8 0.3 - - - -
75u LEU* 5.3 0.7 - - + -
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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