Contacts of the helix formed by residues 125 - 131 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E LYS* 3.5 2.5 - - - -
52E SER* 1.3 52.0 - - - -
54E VAL* 3.0 7.5 - - - +
111N LEU* 3.8 4.0 - - - -
124N ILE* 1.3 64.4 - - - +
126N ALA* 1.3 65.5 + - - -
127N GLU 3.1 3.4 + - - -
128N GLU* 3.2 17.4 + - - +
129N ILE* 3.4 12.8 + - - +
136N MET* 4.8 0.2 - - - +
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Residues in contact with ALA 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLN 4.7 0.7 - - - +
50E LYS* 4.1 3.4 - - + +
52E SER* 3.1 4.4 + - - +
104N ILE* 3.9 16.8 - - + +
107N VAL* 3.5 26.9 - - + -
108N ASN* 3.0 35.5 - - - +
111N LEU* 3.4 4.6 - - - +
125N GLY* 1.3 71.9 - - - -
127N GLU* 1.3 58.6 + - - +
129N ILE* 3.1 2.6 + - - +
130N VAL* 2.8 34.5 + - - +
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Residues in contact with GLU 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E MET* 3.1 6.4 - - - +
48E GLY 3.7 1.6 + - - -
50E LYS* 1.3 100.6 - - + +
53E TYR* 3.4 4.5 - - - -
57E GLU* 4.5 2.8 - - - +
146G GLY 4.6 0.9 - - - +
147G ARG* 4.0 2.9 - - - -
148G THR* 1.4 48.6 + - + +
149G THR* 4.5 1.2 + - - -
167G GLU* 4.3 0.7 - - - +
100N ARG* 3.9 10.0 + - - +
104N ILE* 5.1 2.7 - - - +
126N ALA* 1.3 71.6 - - - +
128N GLU* 1.3 58.0 + - + +
130N VAL* 3.2 6.7 + - - +
131N ASP* 2.8 49.9 + - - +
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Residues in contact with GLU 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LYS* 1.9 44.1 + - - -
54E VAL* 3.3 8.7 - - - +
57E GLU* 2.7 22.1 - - - +
125N GLY 3.2 16.4 + - - +
127N GLU* 1.3 82.5 - - + +
129N ILE* 1.3 61.2 + - - +
131N ASP* 3.3 8.1 + - - -
132N GLY 3.2 3.6 + - - -
133N ASN* 2.9 39.6 + - + +
136N MET* 3.0 48.2 - - + +
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Residues in contact with ILE 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N PHE* 3.9 22.2 - - + +
74N ARG* 3.5 13.2 + - - +
79N LEU* 4.5 0.9 - - + -
107N VAL* 3.7 26.5 - - + -
111N LEU* 4.7 3.1 - - + -
124N ILE* 4.3 10.1 - - + -
125N GLY 3.4 16.2 - - - +
126N ALA* 3.1 6.2 + - - +
128N GLU* 1.3 73.8 - - - +
130N VAL* 1.3 65.7 + - - +
132N GLY* 3.1 11.8 + - - -
136N MET* 4.1 23.1 - - + +
137N THR* 4.2 15.6 + - - +
140N MET* 3.8 38.1 - - + -
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Residues in contact with VAL 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ARG* 3.1 35.4 + - - +
100N ARG* 4.3 30.5 - - + +
103N LYS* 3.8 29.3 + - + +
104N ILE* 3.7 35.9 - - + +
107N VAL* 4.1 4.5 - - + -
126N ALA 2.8 24.2 + - - +
127N GLU* 3.6 6.3 - - - +
129N ILE* 1.3 72.3 - - - +
131N ASP* 1.3 58.5 + - - +
132N GLY 3.1 0.4 - - - -
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Residues in contact with ASP 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ARG* 4.4 3.7 - - - -
100N ARG* 2.6 31.2 + - - -
127N GLU* 2.8 33.5 + - - +
128N GLU* 3.6 9.4 + - - +
129N ILE 3.2 0.2 - - - -
130N VAL* 1.3 77.0 - - - +
132N GLY* 1.3 60.6 + - - +
133N ASN* 3.5 4.5 + - + +
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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