Contacts of the helix formed by residues 106 - 111 (chain A) in PDB entry 3LQM
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 SER 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A TYR 5.8 0.4 - - - -
83A GLY 3.6 4.7 - - - -
84A ASP* 2.7 32.7 + - - +
105A PHE* 1.3 74.8 - - - +
107A PRO* 1.3 60.2 - - - +
108A VAL* 3.5 3.8 - - - -
109A ASP* 3.0 20.8 + - - -
110A ASP* 2.7 47.8 + - - +
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Residues in contact with PRO 107 (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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34A PHE* 3.7 15.9 - - + -
36A ASN* 4.3 10.8 - - - +
79A LEU* 4.9 2.2 - - + +
80A SER 3.7 14.1 - - - +
81A LYS* 3.2 21.3 - - + +
83A GLY 3.4 15.7 - - - +
85A HIS* 3.8 13.9 - - + +
105A PHE* 3.5 33.1 - - + +
106A SER* 1.3 82.3 - - - +
108A VAL* 1.3 62.9 + - - +
111A THR* 2.9 29.7 + - - +
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Residues in contact with VAL 108 (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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34A PHE* 3.9 15.0 - - + -
81A LYS* 2.9 20.5 + - + +
82A TYR* 3.2 51.4 - - + +
106A SER* 5.0 3.6 - - - +
107A PRO* 1.3 72.1 - - - +
109A ASP* 1.3 72.0 + - - +
148A VAL* 4.6 0.9 - - + -
149A TYR* 3.0 32.8 + - + +
198A ARG* 4.0 24.6 + - - +
200A LYS* 3.3 11.4 + - - +
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Residues in contact with ASP 109 (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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84A ASP* 4.8 3.3 - - - +
106A SER* 3.0 20.9 + - - +
108A VAL* 1.3 87.7 - - - +
110A ASP* 1.3 69.3 + - - +
111A THR 3.8 0.7 - - - -
198A ARG* 2.9 30.5 + - - -
200A LYS* 3.7 17.3 + - - +
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Residues in contact with ASP 110 (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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31A SER* 4.6 1.9 - - - +
104A THR 4.7 0.9 - - - +
105A PHE* 3.5 26.9 - - + -
106A SER* 2.7 44.3 + - - +
109A ASP* 1.3 82.5 - - - +
111A THR* 1.3 66.6 + - - +
112A ILE* 3.4 7.1 + - - +
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Residues in contact with THR 111 (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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31A SER* 2.8 30.2 + - - -
33A ASN* 3.3 5.5 + - - +
34A PHE* 2.9 48.5 + - + +
105A PHE* 4.3 1.6 - - - -
107A PRO* 2.9 29.1 + - - +
110A ASP* 1.3 73.8 - - - +
112A ILE* 1.3 66.8 + - - +
113A ILE* 4.8 3.8 - - + -
149A TYR* 4.1 1.1 - - - +
200A LYS* 2.9 35.9 + - - +
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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