Contacts of the helix formed by residues 58 - 69 (chain A) in PDB entry 1I4W
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 GLY 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.4 0.2 - - - -
55A PRO* 3.4 12.9 + - - -
56A GLY 3.5 2.0 - - - -
57A VAL* 1.3 77.7 - - - +
59A ILE* 1.3 59.5 + - - +
60A GLN 3.3 2.0 - - - -
61A SER* 3.4 21.3 - - - -
62A ALA* 2.8 31.5 + - - +
75A LEU* 5.1 0.4 - - - -
86A LEU* 3.6 12.1 - - - +
90A PHE* 3.4 10.9 - - - -
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 6.0 0.9 - - - -
8A ILE* 3.5 45.5 - - + +
9A LYS 5.1 3.1 - - - +
12A SER* 5.2 2.7 - - - +
23A LEU 4.4 0.9 - - - +
24A TRP* 3.4 44.4 - - + +
26A PRO* 4.9 3.1 - - + -
29A TYR* 3.6 22.0 - - + +
57A VAL* 2.9 26.4 + - + +
58A GLY* 1.3 76.4 - - - +
60A GLN* 1.3 64.6 + - - +
62A ALA* 3.3 4.4 + - - +
63A ILE* 3.0 42.4 + - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.0 48.6 + - + +
33A PHE* 4.3 9.2 - - + -
52A ASP* 5.4 1.6 - - - +
55A PRO 6.1 0.7 - - - +
58A GLY* 4.4 0.4 - - - -
59A ILE* 1.3 81.0 - - - +
61A SER* 1.3 59.3 + - - +
63A ILE* 3.4 2.6 + - - +
64A PHE* 2.8 30.2 + - + +
73A TYR* 5.0 4.9 - - - +
135A VAL* 2.9 35.9 - - + +
171A TRP* 3.0 26.1 + - - +
343A XE 3.1 19.3 - - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.9 1.6 - - - +
52A ASP* 3.0 18.0 + - - -
55A PRO* 4.1 2.9 + - - +
58A GLY* 3.4 22.0 - - - -
60A GLN* 1.3 77.5 - - - +
62A ALA* 1.3 64.6 + - - +
64A PHE* 4.0 0.9 - - - +
65A TYR* 3.1 26.3 + - - +
73A TYR* 3.6 29.5 - - - -
75A LEU* 3.9 15.2 - - - +
95A LEU* 4.5 8.2 - - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.3 17.2 - - + +
6A PRO 3.7 15.3 - - - +
7A GLY* 4.5 7.0 - - - -
8A ILE* 5.1 0.2 - - + -
58A GLY 2.8 16.8 + - - +
59A ILE* 3.8 4.0 - - - +
61A SER* 1.3 74.8 - - - +
63A ILE* 1.3 60.1 + - + +
66A ASN* 2.9 39.2 + - - +
90A PHE* 3.7 21.9 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 5.9 5.2 - - - -
26A PRO* 3.9 26.5 - - + +
29A TYR* 3.7 28.0 - - + -
30A ASN* 4.3 7.4 - - - +
33A PHE* 4.0 17.0 - - + -
59A ILE* 3.0 27.2 + - + +
60A GLN 3.9 2.9 - - - +
62A ALA* 1.3 76.8 - - + +
64A PHE* 1.3 67.2 + - - +
66A ASN* 3.3 6.1 + - - +
67A LYS* 3.0 52.0 + - + +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.6 29.1 - + + -
38A LEU* 3.7 17.9 - - + -
48A LEU* 4.0 6.7 - - + -
50A VAL* 3.8 18.2 - - + -
60A GLN* 2.8 23.2 + - + +
61A SER 4.0 2.7 - - - +
63A ILE* 1.3 73.9 - - - +
65A TYR* 1.3 59.5 + - - +
67A LYS* 3.0 4.1 + - - -
68A TYR* 2.8 63.5 + + + -
70A PRO* 4.1 11.2 - - + -
73A TYR* 3.3 28.5 - + + +
133A LEU* 3.9 20.9 - - + -
342A XE 3.9 9.9 - - - -
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO 5.7 4.9 - - - -
5A ILE* 3.4 27.6 - - + -
61A SER 3.1 17.7 + - - +
64A PHE* 1.3 84.0 - - - +
66A ASN* 1.3 65.9 + - - +
69A CYS* 2.7 55.3 + - - +
70A PRO* 3.3 42.9 + - + -
73A TYR* 4.1 9.0 - - + -
94A PRO* 3.3 41.9 - - + +
95A LEU* 4.1 15.0 - - + -
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.2 17.1 - - - +
5A ILE* 2.8 52.1 - - - +
7A GLY* 5.3 0.7 + - - -
62A ALA* 2.9 28.4 + - - +
63A ILE* 3.7 6.3 - - - +
65A TYR* 1.3 80.5 - - - +
67A LYS* 1.3 60.8 + - + +
69A CYS* 5.0 5.3 + - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASN* 3.1 55.7 + - - +
33A PHE* 4.2 22.0 - - + +
34A ASP* 4.8 4.4 + - - -
63A ILE* 3.0 32.6 + - + +
64A PHE 3.5 3.1 - - - +
66A ASN* 1.3 82.1 - - + +
68A TYR* 1.3 81.0 + - + +
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Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 4.1 33.3 + + - +
37A ASP* 5.5 0.3 - - - -
38A LEU* 4.3 13.3 + - + +
39A THR* 3.8 24.2 - - + +
45A PRO* 3.4 24.9 - - + +
46A GLU* 6.0 0.2 - - - +
48A LEU* 5.8 0.4 - - + -
64A PHE* 2.8 69.6 + + + +
67A LYS* 1.3 98.2 - - + +
69A CYS* 1.3 72.6 + - - +
70A PRO* 3.1 2.8 - - + -
342A XE 3.6 17.3 - - - -
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Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO 3.4 5.0 - - - +
46A GLU* 3.8 9.9 - - - +
65A TYR* 2.7 48.1 + - - +
66A ASN* 5.3 4.5 - - - -
67A LYS 3.9 0.4 - - - -
68A TYR* 1.3 72.1 - - - +
70A PRO* 1.3 72.3 - - - +
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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