Contacts of the helix formed by residues 68 - 78 (chain V) 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 ASN 68 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11V PRO* 3.3 19.3 - - + +
12V LEU 3.7 7.9 - - - +
13V ASN* 3.8 14.2 + - - +
14V SER* 3.4 28.7 + - - +
65V PRO 4.2 3.6 + - - -
66V ARG 3.1 2.0 + - - -
67V ASP* 1.3 92.1 + - - +
69V ILE* 1.3 66.5 + - - +
70V GLU* 3.2 11.4 + - - +
71V GLY* 2.7 30.5 + - - -
72V LEU* 3.0 23.4 + - - +
120V LEU* 3.8 10.0 - - - +
204V GOL 3.9 7.9 + - - -
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Residues in contact with ILE 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V VAL* 4.0 7.4 - - + -
11V PRO 3.0 15.4 + - - +
12V LEU* 3.4 21.3 + - + +
19V ILE* 3.9 22.9 - - + -
21V LEU* 5.1 2.0 - - + -
68V ASN* 1.3 70.9 - - - +
70V GLU* 1.3 56.1 + - - +
72V LEU* 3.3 1.6 + - - +
73V VAL* 2.8 55.1 + - + +
113V VAL* 4.2 25.1 - - + +
116V ALA* 4.0 6.5 - - + -
117V GLY* 3.8 31.0 - - - +
120V LEU* 3.8 14.1 - - + +
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Residues in contact with GLU 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V LEU* 3.0 35.9 + - + +
13V ASN* 4.1 15.5 - - + +
68V ASN* 3.2 7.2 + - - +
69V ILE* 1.3 77.3 - - - +
71V GLY* 1.3 57.2 + - - +
73V VAL* 3.8 10.0 - - - +
74V ASP* 2.9 32.4 + - - +
204V GOL 3.9 21.4 + - - +
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Residues in contact with GLY 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65V PRO 3.7 14.8 - - - -
66V ARG* 2.9 21.9 + - - -
68V ASN* 2.7 21.2 + - - -
70V GLU* 1.3 73.3 - - - +
72V LEU* 1.3 56.1 + - - +
75V TYR 2.9 22.9 + - - -
204V GOL 3.6 19.9 - - - -
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Residues in contact with LEU 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V LEU* 4.3 9.2 - - + -
66V ARG* 3.2 26.0 - - + +
68V ASN 3.0 13.2 + - - +
71V GLY* 1.3 73.9 - - - +
73V VAL* 1.3 64.7 + - - +
75V TYR* 3.2 5.6 + - - +
76V MET* 3.0 32.1 + - + +
116V ALA* 3.6 39.9 - - + +
119V ILE* 4.1 19.5 - - + -
120V LEU* 3.7 22.4 - - + -
201V HEM 3.6 31.0 - - + -
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Residues in contact with VAL 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69V ILE* 2.8 40.4 + - + +
70V GLU* 3.9 10.5 - - - +
72V LEU* 1.3 71.6 - - - +
74V ASP* 1.3 62.5 + - - +
76V MET* 3.2 18.3 + - - +
77V LYS* 3.2 30.3 + - - +
109V GLU* 3.4 25.1 - - - +
112V LEU* 4.1 28.4 - - + +
113V VAL* 4.1 13.9 - - + -
116V ALA* 4.3 1.3 - - + -
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Residues in contact with ASP 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64V PRO* 4.7 1.9 - - - +
66V ARG* 2.8 25.8 + - - -
70V GLU 2.9 18.3 + - - +
71V GLY 3.6 3.1 - - - +
73V VAL* 1.3 75.3 - - - +
75V TYR* 1.3 59.2 + - - +
77V LYS* 3.0 11.2 + - - +
78V ASN* 2.8 41.7 + - - +
204V GOL 3.4 20.7 + - - +
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Residues in contact with TYR 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V ARG* 3.4 35.4 - - + +
71V GLY 2.9 15.6 + - - +
72V LEU* 3.2 12.5 + - - +
74V ASP* 1.3 74.5 - - - +
76V MET* 1.3 61.7 + - + +
78V ASN 4.5 0.2 - - - -
79V PRO* 3.0 43.2 - - + +
80V THR* 3.3 31.2 + - - -
88V ILE* 3.6 13.2 - - - +
92V HIS* 3.5 17.8 - + - -
93V PRO 5.1 0.2 - - - +
94V SER* 4.7 0.2 - - - -
201V HEM 3.2 79.2 + + + +
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Residues in contact with MET 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V LEU* 3.0 31.6 + - + +
73V VAL* 3.2 11.2 + - - +
75V TYR* 1.3 78.7 - - + +
77V LYS* 1.3 57.8 + - - +
92V HIS* 6.3 0.2 - - + -
93V PRO 5.0 3.4 - - - +
94V SER* 3.2 10.5 - - - +
95V LEU* 3.0 24.9 + - - +
104V MET* 4.1 3.1 - - + +
112V LEU* 3.4 50.7 - - + +
115V ILE* 4.0 15.9 - - + -
116V ALA* 3.7 17.9 - - + +
119V ILE* 5.0 1.6 - - + -
201V HEM 3.6 44.2 - - + -
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Residues in contact with LYS 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73V VAL* 3.2 25.7 + - + +
74V ASP* 3.0 12.8 + - - +
76V MET* 1.3 80.6 - - - +
78V ASN* 1.3 61.8 + - + +
79V PRO* 3.8 2.9 - - - -
94V SER* 3.6 1.9 + - - -
95V LEU* 4.2 20.2 - - + +
96V ARG* 3.1 32.2 + - - +
109V GLU* 2.7 42.9 + - - -
112V LEU* 3.9 11.4 - - + -
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Residues in contact with ASN 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V ARG* 4.4 5.7 + - - -
74V ASP* 2.8 24.4 + - - +
75V TYR 3.6 2.0 - - - -
77V LYS* 1.3 82.9 - - + +
79V PRO* 1.4 66.7 - - - +
80V THR* 3.6 11.0 + - - +
87V GLU* 3.0 32.2 + - - +
89V ALA* 5.2 0.9 - - - +
96V ARG* 2.9 31.3 + - - +
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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