Contacts of the helix formed by residues 65 - 70 (chain A) in PDB entry 2L1M
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 3.7 13.7 - - - -
63A PRO* 3.1 7.8 - - - +
64A CYS* 1.3 70.4 - - - +
66A CYS* 1.3 58.8 + - - +
67A ASP* 2.9 25.0 + - + -
68A PHE* 3.0 37.4 + - + +
69A LEU* 5.4 0.3 - - - +
82A ILE* 4.3 4.0 - - + -
83A ALA* 3.7 39.3 - - + +
86A LEU* 3.4 18.2 - - + +
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Residues in contact with CYS 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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64A CYS 3.0 5.3 + - - -
65A THR* 1.3 70.5 - - - +
67A ASP* 1.3 61.3 + - - +
68A PHE 3.2 0.2 - - - -
69A LEU* 3.0 33.6 + - + +
70A HIS* 3.2 10.3 + - - -
74A THR* 5.9 1.2 - - - +
79A ALA* 5.4 1.1 - - - -
82A ILE* 4.0 34.5 - - + +
96A ILE* 4.3 17.9 - - + -
98A PHE* 4.7 4.9 - - + -
112A VAL* 4.8 2.7 - - - -
127A LEU* 6.1 0.7 - - - -
129A PHE* 3.4 40.4 - - - -
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Residues in contact with ASP 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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65A THR* 3.1 18.7 - - + +
66A CYS* 1.3 75.1 - - - +
68A PHE* 1.3 66.4 + - + +
70A HIS* 3.0 43.3 + - - -
76A ARG* 6.0 1.6 - - - -
79A ALA* 3.8 36.3 + - + +
82A ILE* 5.3 0.2 - - - +
83A ALA* 5.5 2.2 - - + -
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Residues in contact with PHE 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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62A ARG* 6.0 4.5 - - + -
63A PRO* 3.7 40.8 - - + +
65A THR* 3.0 33.3 + - + +
67A ASP* 1.3 86.4 - - + +
69A LEU* 1.3 58.4 + - + +
70A HIS 3.7 0.2 - - - -
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Residues in contact with LEU 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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48A PHE* 5.4 2.7 - - + -
52A CYS* 4.7 11.4 - - - -
54A TYR* 4.0 31.5 + - + +
59A VAL* 5.1 12.6 - - + -
65A THR 5.4 0.4 - - - +
66A CYS* 3.0 24.9 + - + +
68A PHE* 1.3 78.9 - - + +
70A HIS* 1.3 64.2 + - - +
71A GLY 3.8 0.3 + - - -
97A ALA 4.9 1.9 - - - +
98A PHE* 3.6 34.1 - - + -
99A TYR* 3.5 22.1 + - - -
129A PHE* 5.3 11.4 - - + -
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Residues in contact with HIS 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 CYS 3.2 4.9 + - - +
67A ASP* 3.0 39.2 + - - +
68A PHE 3.7 0.4 - - - -
69A LEU* 1.3 80.4 - - - +
71A GLY* 1.3 72.0 - - - +
74A THR* 3.7 23.3 - - + +
76A ARG* 3.9 34.3 + - - -
79A ALA* 5.2 2.9 - - + -
97A ALA 4.9 1.8 - - - -
99A TYR* 3.3 10.8 - - - -
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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