Contacts of the helix formed by residues 125 - 131 (chain R) in PDB entry 3LUE
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 125 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50I LYS* 3.5 2.2 - - - -
52I SER* 1.3 52.0 - - - -
54I VAL* 3.0 7.7 - - - +
111R LEU* 3.8 4.3 - - - -
124R ILE* 1.3 64.7 - - - +
126R ALA* 1.3 64.7 + - - -
127R GLU 3.1 3.7 + - - -
128R GLU* 3.2 17.6 + - - +
129R ILE* 3.4 12.8 + - - +
136R MET* 4.8 0.2 - - - +
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Residues in contact with ALA 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I GLN 4.7 0.4 - - - +
50I LYS* 4.1 3.0 - - + +
52I SER* 3.1 4.8 + - - +
104R ILE* 3.9 17.5 - - + +
107R VAL* 3.5 26.0 - - + -
108R ASN* 3.0 35.1 - - - +
111R LEU* 3.4 4.6 - - - +
125R GLY* 1.3 71.7 - - - -
127R GLU* 1.3 58.6 + - - +
129R ILE* 3.1 2.9 + - - +
130R VAL* 2.8 34.5 + - - +
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Residues in contact with GLU 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I MET* 3.1 32.0 - - - +
48I GLY 3.7 2.1 + - - -
50I LYS* 1.3 111.5 - - + +
53I TYR* 3.4 12.5 - - - -
57I GLU* 4.5 3.3 - - - +
100R ARG* 3.9 10.6 + - - +
104R ILE* 5.1 2.4 - - - +
126R ALA* 1.3 71.4 - - - +
128R GLU* 1.3 58.6 + - + +
130R VAL* 3.2 6.8 + - - +
131R ASP* 2.8 49.4 + - - +
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Residues in contact with GLU 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I LYS* 1.9 43.8 + - - -
54I VAL* 3.3 8.7 - - - +
57I GLU* 2.7 21.4 - - - +
125R GLY 3.2 17.2 + - - +
127R GLU* 1.3 81.3 - - + +
129R ILE* 1.3 60.9 + - - +
131R ASP* 3.3 8.1 + - - -
132R GLY 3.2 3.3 + - - -
133R ASN* 2.9 39.9 + - + +
136R MET* 3.0 48.3 - - + +
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Residues in contact with ILE 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R PHE* 3.9 21.3 - - + +
74R ARG* 3.5 13.2 + - - +
79R LEU* 4.5 0.9 - - + -
107R VAL* 3.7 27.4 - - + -
111R LEU* 4.7 3.4 - - + -
124R ILE* 4.3 10.8 - - + -
125R GLY 3.4 16.2 - - - +
126R ALA* 3.1 6.0 + - - +
128R GLU* 1.3 74.0 - - - +
130R VAL* 1.3 66.6 + - - +
132R GLY* 3.1 11.6 + - - -
136R MET* 4.1 23.1 - - + +
137R THR* 4.2 15.4 + - - +
140R MET* 3.8 36.6 - - + -
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Residues in contact with VAL 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R ARG* 3.1 35.4 + - - +
100R ARG* 4.3 30.3 - - + +
103R LYS* 3.8 28.9 + - + +
104R ILE* 3.7 35.9 - - + +
107R VAL* 4.1 4.5 - - + -
126R ALA 2.8 23.6 + - - +
127R GLU* 3.6 6.5 - - - +
129R ILE* 1.3 72.3 - - - +
131R ASP* 1.3 57.9 - - - +
132R GLY 3.1 0.4 - - - -
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Residues in contact with ASP 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R ARG* 4.4 4.0 - - - -
100R ARG* 2.6 31.0 + - - -
127R GLU* 2.8 33.8 + - - +
128R GLU* 3.6 8.0 + - - +
129R ILE 3.2 0.4 - - - -
130R VAL* 1.3 76.8 - - - +
132R GLY* 1.3 60.3 + - - +
133R ASN* 3.5 4.7 + - + +
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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