Contacts of the helix formed by residues 68 - 79 (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 THR 68 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66u GLY 4.6 4.5 - - - +
67u LEU* 1.3 76.5 - - - +
69u GLU* 1.3 64.5 + - - +
70u ARG* 3.6 9.7 + - - +
71u GLN* 2.9 45.5 + - - +
72u LYS* 3.1 24.1 + - - +
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Residues in contact with GLU 69 (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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67u LEU 5.2 0.9 - - - +
68u THR* 1.3 73.3 - - - +
70u ARG* 1.3 61.2 + - - +
72u LYS* 3.4 35.1 + - - +
73u GLN* 3.2 27.5 + - - +
76u ARG* 4.7 2.1 + - - -
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Residues in contact with ARG 70 (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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68u THR* 3.2 9.8 - - - +
69u GLU* 1.3 78.9 - - - +
71u GLN* 1.3 57.3 - - + +
73u GLN* 3.1 40.5 + - - +
74u ILE* 3.0 56.3 + - + +
77u GLU* 5.1 7.5 + - - -
85v GLU* 6.1 0.4 - - - +
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Residues in contact with GLN 71 (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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44u THR* 3.7 28.5 - - - +
45u LEU* 3.8 31.9 - - + +
48u LEU* 4.4 6.1 - - - +
66u GLY 4.4 1.7 - - - +
67u LEU* 3.5 14.7 - - + +
68u THR* 2.9 46.5 + - - +
70u ARG* 1.3 77.1 - - + +
72u LYS* 1.3 57.9 + - - +
74u ILE* 3.2 13.6 + - + +
75u LEU* 2.9 35.0 + - - +
85v GLU* 3.9 17.0 + - - +
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Residues in contact with LYS 72 (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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62u LEU* 3.8 18.8 - - + +
64u ILE 5.8 0.4 - - - -
67u LEU* 3.7 42.4 + - + -
68u THR 3.1 9.6 + - - +
69u GLU* 3.4 40.8 + - - +
70u ARG 3.3 0.2 - - - -
71u GLN* 1.3 73.7 - - - +
73u GLN* 1.3 57.2 - - - +
75u LEU* 3.5 10.4 + - - +
76u ARG* 3.0 53.2 + - - +
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Residues in contact with GLN 73 (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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69u GLU 3.2 16.9 + - - +
70u ARG* 3.1 39.7 + - - +
72u LYS* 1.3 74.3 - - - +
74u ILE* 1.3 64.2 + - - +
76u ARG* 3.3 23.9 + - - +
77u GLU* 3.2 23.7 + - - +
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Residues in contact with ILE 74 (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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39u ARG 4.2 7.4 - - - +
40u GLY* 4.1 19.7 - - - +
41u LEU* 4.1 6.7 - - + -
45u LEU* 3.9 17.7 - - + -
70u ARG* 3.0 54.9 + - + +
71u GLN* 3.2 13.4 + - + +
73u GLN* 1.3 74.5 - - - +
75u LEU* 1.3 64.2 + - - +
77u GLU* 3.2 15.4 + - - +
78u ASN* 3.0 34.5 + - - +
85v GLU* 5.9 3.1 - - - +
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Residues in contact with LEU 75 (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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41u LEU* 4.3 5.2 - - + -
45u LEU* 4.1 25.6 - - + -
49u ILE* 3.9 27.8 - - + -
61u VAL* 3.8 24.0 - - + +
62u LEU* 3.7 12.6 - - + -
64u ILE* 5.3 0.9 - - + -
67u LEU* 3.7 31.0 - - + -
71u GLN 2.9 20.3 + - - +
72u LYS* 3.7 4.3 - - - +
73u GLN 3.3 0.2 - - - -
74u ILE* 1.3 75.9 - - - +
76u ARG* 1.3 58.3 + - - +
78u ASN* 2.9 20.9 + - - +
79u LEU* 3.0 18.3 + - - +
82u PHE* 4.1 14.2 - - + -
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Residues in contact with ARG 76 (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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62u LEU* 3.8 30.8 - - + +
69u GLU* 4.7 2.2 + - - -
72u LYS* 3.0 36.4 + - - +
73u GLN* 3.3 35.5 + - - +
75u LEU* 1.3 75.1 - - - +
77u GLU* 1.3 61.3 + - - +
78u ASN 3.2 0.9 + - - -
79u LEU* 3.5 27.7 + - + +
80u GLU* 4.9 0.9 + - - +
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Residues in contact with GLU 77 (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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70u ARG* 5.1 8.1 + - - -
73u GLN 3.2 13.2 + - - +
74u ILE* 3.4 15.7 - - - +
75u LEU 3.2 0.4 - - - -
76u ARG* 1.3 77.0 - - - +
78u ASN* 1.3 67.0 + - - +
79u LEU 3.7 0.2 - - - -
80u GLU* 4.0 18.4 - - - +
81u HIS* 4.6 1.0 - - - -
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Residues in contact with ASN 78 (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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38u TYR* 3.5 14.8 - - - +
39u ARG 3.8 17.8 + - - -
41u LEU* 3.9 12.6 - - + +
74u ILE* 3.0 28.8 + - - +
75u LEU 2.9 7.5 + - - +
77u GLU* 1.3 86.3 - - - +
79u LEU* 1.3 57.7 + - - +
80u GLU 3.2 2.9 - - - -
81u HIS* 2.8 45.0 + - + +
82u PHE* 3.4 31.4 - - + -
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Residues in contact with LEU 79 (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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58u VAL* 3.6 30.5 - - + +
59u GLU* 4.5 10.5 - - + +
61u VAL* 3.9 23.3 - - + -
62u LEU* 4.4 12.8 - - + -
75u LEU 3.0 22.1 + - - +
76u ARG* 3.5 31.2 + - + +
78u ASN* 1.3 76.9 - - - +
80u GLU* 1.3 56.2 + - - +
82u PHE* 2.9 34.7 + - + +
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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