Contacts of the helix formed by residues 119 - 124 (chain D) in PDB entry 3LEE
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 ARG 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D THR* 4.3 8.2 - - - +
114D SER* 3.3 43.5 - - - +
115D LYS* 4.3 5.5 + - - +
116D GLU 3.1 31.5 + - - +
117D LYS* 3.3 7.1 + - - +
118D ASP* 1.3 76.2 - - - +
120D GLN* 1.3 61.8 + - + +
121D VAL* 2.9 1.8 - - - -
122D LEU* 2.8 24.0 + - - +
123D GLU* 2.9 33.3 + - + +
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Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 3.3 38.1 + - + -
49D GLN* 4.5 15.3 - - - +
117D LYS 5.0 0.6 + - - -
118D ASP 2.7 5.9 + - - +
119D ARG* 1.3 79.9 - - + +
121D VAL* 1.3 57.5 + - - +
122D LEU 3.2 0.2 - - - -
123D GLU* 2.9 28.9 + - - +
124D ASP* 3.1 34.8 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D TYR* 4.5 27.3 - - + -
49D GLN* 5.9 0.4 - - - +
50D THR* 5.1 5.6 - - + -
74D LEU* 4.3 15.7 - - + +
77D ARG* 4.3 14.1 - - + -
78D ALA* 3.5 28.5 - - - +
81D THR* 4.3 3.4 - - - +
118D ASP 2.9 15.7 + - - +
120D GLN* 1.3 79.4 - - - +
122D LEU* 1.3 64.1 + - + +
125D PHE* 3.5 13.7 - - - -
128D ILE* 3.3 41.1 - - + +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 2.9 47.8 - - + +
81D THR* 3.9 19.1 - - + -
82D LEU* 4.3 8.5 - - + -
100D PHE* 4.2 5.6 - - + -
109D TRP* 3.8 22.2 - - + -
111D PHE* 3.3 59.6 + - + +
114D SER* 4.9 5.6 - - - +
119D ARG* 2.8 11.8 + - - +
121D VAL* 1.3 80.9 - - + +
123D GLU* 1.3 66.4 + - - +
124D ASP 3.3 1.1 - - - -
125D PHE* 3.3 13.2 + - + +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG* 3.5 24.1 - - - +
111D PHE 3.4 10.3 + - - +
112D MET* 3.9 37.0 - - + +
114D SER* 6.6 0.2 - - - -
119D ARG* 2.9 31.8 + - + +
120D GLN* 2.9 35.7 + - - +
122D LEU* 1.3 79.7 - - - +
124D ASP* 1.3 56.5 + - + +
125D PHE 3.4 2.4 + - - -
126D PRO* 3.9 1.7 - - - +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D THR* 3.8 6.1 - - - +
46D TYR* 2.6 44.2 + - + +
120D GLN* 3.1 16.8 + - - +
121D VAL 4.2 4.2 - - - +
123D GLU* 1.3 76.7 - - + +
125D PHE* 1.3 63.2 + - - +
126D PRO* 3.3 7.1 - - - +
127D THR* 2.7 37.5 + - - -
128D ILE* 3.9 3.1 + - - +
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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