Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 1TE6
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 VAL 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU* 3.0 20.3 + - + -
17A PRO* 4.2 4.0 - - + +
18A THR* 3.6 36.6 - - - +
19A VAL* 3.9 12.1 - - + -
48A LEU 3.7 21.1 - - - +
49A ARG* 3.8 23.1 - - - +
50A ASP* 3.6 2.9 - - - -
59A LYS 4.0 0.4 - - - +
60A GLY* 1.3 77.8 - - - +
62A LEU* 1.3 65.4 + - - +
63A LYS 3.2 2.2 - - - -
64A ALA* 3.4 4.0 + - + +
65A VAL* 3.1 22.5 + - + +
108A ASN* 3.8 10.8 - - - +
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Residues in contact with LEU 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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9A GLU* 3.5 32.3 - - + +
50A ASP* 2.7 21.0 + - - +
55A ARG* 3.6 35.9 - - - +
61A VAL* 1.3 71.0 - - - +
63A LYS* 1.3 59.4 + - + +
65A VAL* 3.2 9.0 + - + +
66A ASP* 2.8 43.5 + - - +
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Residues in contact with LYS 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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48A LEU* 3.9 23.6 - - + +
49A ARG 4.5 5.4 + - - +
50A ASP* 2.8 49.5 + - - +
62A LEU* 1.3 77.2 - - + +
64A ALA* 1.3 61.9 + - - +
66A ASP* 3.3 7.7 + - - +
67A HIS* 3.0 34.1 + - + +
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Residues in contact with ALA 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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19A VAL* 3.9 9.2 - - + -
48A LEU* 4.1 9.5 - - + +
61A VAL* 3.4 8.7 + - + +
62A LEU 3.3 0.4 - - - -
63A LYS* 1.3 78.2 - - - +
65A VAL* 1.3 62.5 + - - +
67A HIS* 3.4 1.3 + - - +
68A ILE* 3.2 27.3 + - - +
105A PHE 4.0 16.2 - - - +
108A ASN* 3.8 26.0 - - - +
109A ALA* 3.6 18.2 - - + +
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Residues in contact with VAL 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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6A TRP* 6.0 0.2 - - + -
7A ALA* 3.3 35.0 - - + +
8A ARG* 3.7 28.9 - - - +
9A GLU* 4.1 7.6 - - + +
19A VAL* 4.5 7.6 - - + -
61A VAL* 3.1 22.0 + - + +
62A LEU* 3.5 14.4 - - + +
64A ALA* 1.3 77.5 - - - +
66A ASP* 1.3 63.0 + - - +
68A ILE* 3.2 4.1 + - - +
69A ASN* 3.1 28.7 + - - +
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Residues in contact with ASP 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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62A LEU* 2.8 30.6 + - - +
63A LYS* 3.7 6.9 - - - +
65A VAL* 1.3 78.2 - - - +
67A HIS* 1.3 60.0 + - + +
69A ASN* 4.6 4.8 + - - +
70A SER* 2.9 44.3 + - - +
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Residues in contact with HIS 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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48A LEU* 3.9 9.6 - - + +
63A LYS* 3.0 28.0 + - - +
64A ALA 3.7 5.4 - - - +
65A VAL 3.3 0.2 - - - -
66A ASP* 1.3 76.0 - - + +
68A ILE* 1.3 57.6 + - - +
71A THR* 3.0 19.2 + - - -
72A ILE* 2.9 26.5 + - - +
104A LYS* 3.3 28.3 + - + -
105A PHE* 3.7 47.3 - + + -
109A ALA* 4.8 1.1 - - + -
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Residues in contact with ILE 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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5A ILE* 3.8 17.5 - - + -
7A ALA* 3.6 24.0 - - + -
19A VAL* 5.2 1.8 - - + -
21A VAL* 4.6 4.0 - - + -
64A ALA 3.2 14.3 + - - +
65A VAL* 3.5 8.1 - - - +
66A ASP 3.2 0.6 - - - -
67A HIS* 1.3 79.3 - - - +
69A ASN* 1.3 59.7 + - - +
72A ILE* 3.1 25.1 + - + -
73A ALA* 2.8 32.9 + - - +
109A ALA* 2.9 37.0 - - + +
113A VAL* 3.1 33.4 - - + -
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Residues in contact with ASN 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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5A ILE 3.5 3.7 - - - +
6A TRP* 3.2 41.3 - - + -
7A ALA* 2.6 48.2 + - - +
65A VAL* 3.1 23.9 + - - +
66A ASP* 4.3 5.2 + - - +
68A ILE* 1.3 78.0 - - - +
70A SER* 1.3 62.3 + - - +
73A ALA* 3.7 16.0 - - - +
74A PRO* 4.0 2.6 - - - +
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Residues in contact with SER 70 (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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66A ASP* 2.9 26.0 + - - +
69A ASN* 1.3 80.5 - - - +
71A THR* 1.3 64.9 + - - +
74A PRO* 3.6 14.6 - - - +
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Residues in contact with THR 71 (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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67A HIS* 3.0 19.3 + - - -
69A ASN 3.7 0.4 - - - -
70A SER* 1.3 86.8 + - - +
72A ILE* 1.3 67.8 + - - +
73A ALA 3.4 0.9 - - - -
74A PRO* 3.1 14.9 - - - +
75A ALA* 3.6 11.3 + - + +
96A LEU* 6.1 3.8 - - + -
105A PHE* 3.6 32.3 - - + -
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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