Contacts of the helix formed by residues 76 - 88 (chain T) 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 76 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73T PHE 3.0 18.0 + - - -
74T ARG 3.2 1.4 + - - -
75T ASN* 1.3 77.5 + - - +
77T LEU* 1.3 58.9 + - - +
78T LYS 3.6 1.6 - - - -
79T LEU* 3.4 10.3 - - - +
80T MET* 2.9 37.5 + - - +
106T ASN* 4.6 1.6 - - - -
107T VAL* 3.7 21.5 - - - +
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Residues in contact with LEU 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T ASN* 2.9 42.3 + - + +
76T GLY* 1.3 70.2 - - - +
78T LYS* 1.3 62.1 + - + +
80T MET* 3.1 8.0 + - - +
81T LEU* 2.9 27.1 + - - +
94T PRO* 3.8 32.1 - - + -
95T ASP 5.1 1.6 - - - +
106T ASN* 4.1 15.0 - - - +
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Residues in contact with LYS 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T LEU* 3.6 9.5 - - + +
64T THR* 2.8 31.3 + - + +
65T GLN 2.8 28.8 + - - +
66T ILE* 3.9 13.8 - - + +
72T ASP* 4.1 15.3 + - + +
73T PHE* 3.6 17.0 - - + -
75T ASN* 4.3 2.7 + - - +
77T LEU* 1.3 78.4 - - + +
79T LEU* 1.3 59.9 + - - +
80T MET 3.3 0.2 - - - -
81T LEU* 3.6 11.9 - - + -
82T LEU* 2.8 29.8 + - - +
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Residues in contact with LEU 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73T PHE* 3.6 23.4 - - + +
76T GLY* 3.3 16.3 + - - +
77T LEU 3.1 0.6 - - - -
78T LYS* 1.3 79.2 - - - +
80T MET* 1.3 62.1 + - - +
82T LEU* 3.4 6.1 + - + +
83T LEU* 3.2 25.7 + - + +
107T VAL* 4.7 8.5 - - + +
110T ALA* 3.7 23.6 - - + -
129T ILE* 4.5 11.9 - - + -
140T MET* 3.5 43.5 - - + -
141T ILE* 4.3 9.4 - - + -
144T ILE* 3.9 22.4 - - + -
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Residues in contact with MET 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T GLY 2.9 26.3 + - - +
77T LEU* 3.5 6.5 - - - +
79T LEU* 1.3 73.1 - - - +
81T LEU* 1.3 65.0 + - - +
83T LEU* 3.2 5.5 + - - +
84T GLU* 3.1 30.9 + - - +
91T LEU* 4.0 24.8 - - + +
92T PRO 3.1 27.8 - - - +
94T PRO* 4.3 17.5 - - + -
106T ASN* 3.5 37.7 - - - +
109T LYS* 3.8 23.3 - - + -
110T ALA* 4.1 10.3 - - + -
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Residues in contact with LEU 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T LEU* 4.3 3.4 - - + -
62T ALA* 3.9 26.0 - - + +
64T THR* 3.9 29.8 - - + -
77T LEU 2.9 15.3 + - - +
78T LYS* 3.6 13.2 - - + +
80T MET* 1.3 76.7 - - - +
82T LEU* 1.3 60.8 + - - +
84T GLU* 3.3 18.8 + - + +
85T VAL* 3.0 28.5 + - + +
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Residues in contact with LEU 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T TRP* 4.1 14.8 - - + -
55T CYS* 3.7 38.6 - - + +
58T HIS* 3.8 28.9 - - + -
59T LEU* 3.6 13.6 - - + +
73T PHE* 4.3 9.2 - - + -
78T LYS 2.8 22.1 + - - +
79T LEU* 3.5 9.6 - - + +
80T MET 3.2 0.2 - - - -
81T LEU* 1.3 74.2 - - - +
83T LEU* 1.3 57.7 + - + +
85T VAL* 3.3 3.9 + - + +
86T ILE* 3.1 42.3 + - + +
141T ILE* 4.3 10.3 - - + -
144T ILE* 4.9 7.0 - - + -
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Residues in contact with LEU 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T LEU* 3.2 16.2 + - + +
80T MET 3.2 6.9 + - - +
82T LEU* 1.3 75.4 - - + +
84T GLU* 1.3 63.7 + - - +
86T ILE* 3.7 4.6 - - + +
87T SER* 2.8 30.6 + - - -
91T LEU* 4.0 14.8 - - + -
110T ALA* 3.6 40.8 - - + +
113T PHE* 4.1 10.9 - - + -
114T ILE* 4.0 12.3 - - + -
144T ILE* 3.8 30.5 - - + -
148T PHE* 3.9 28.5 - - + -
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Residues in contact with GLU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T MET* 3.1 20.0 + - - +
81T LEU* 3.8 23.7 - - + +
83T LEU* 1.3 74.9 - - - +
85T VAL* 1.3 59.1 + - + +
87T SER* 4.0 1.1 - - - -
88T GLY* 2.8 30.3 + - - -
89T GLU 3.3 20.6 + - - +
90T ARG* 3.4 37.0 + - - +
91T LEU* 3.0 37.1 + - + +
92T PRO 5.0 0.5 - - - +
93T ARG* 3.5 13.3 + - - -
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Residues in contact with VAL 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T HIS* 3.6 42.2 - - + +
59T LEU* 5.0 1.6 - - - -
61T LYS* 4.6 13.7 - - + +
62T ALA* 3.9 29.2 - - + +
81T LEU* 3.0 20.5 + - + +
82T LEU* 3.5 10.3 - - - +
83T LEU 3.3 0.2 - - - -
84T GLU* 1.3 79.3 - - - +
86T ILE* 1.3 63.8 + - + +
88T GLY* 3.7 5.5 + - - -
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Residues in contact with ILE 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T TRP* 4.1 10.1 - - + -
58T HIS* 3.5 46.0 - - + +
82T LEU* 3.1 23.8 + - + +
83T LEU* 3.7 10.8 - - + +
85T VAL* 1.3 76.9 - - - +
87T SER* 1.3 61.9 + - - +
144T ILE* 3.5 27.4 - - + -
148T PHE* 3.4 43.9 - - + +
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Residues in contact with SER 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83T LEU 2.8 22.4 + - - -
84T GLU* 3.8 0.7 + - - -
86T ILE* 1.3 79.2 - - - +
88T GLY* 1.3 61.4 + - - +
89T GLU* 3.0 38.2 + - - +
113T PHE* 3.7 12.0 - - - -
148T PHE* 3.8 26.9 - - - -
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Residues in contact with GLY 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T GLU 2.8 13.9 + - - -
85T VAL 3.7 4.8 + - - -
86T ILE 3.5 2.0 - - - -
87T SER* 1.3 79.4 - - - +
89T GLU* 1.3 61.4 + - - +
90T ARG* 5.2 3.9 - - - +
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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