Contacts of the helix formed by residues 76 - 88 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73Q PHE 3.0 18.2 + - - -
74Q ARG 3.2 1.6 + - - -
75Q ASN* 1.3 77.7 + - - +
77Q LEU* 1.3 58.8 + - - +
78Q LYS 3.6 1.8 - - - -
79Q LEU* 3.4 10.7 - - - +
80Q MET* 2.9 37.1 + - - +
106Q ASN* 4.6 2.0 - - - -
107Q VAL* 3.7 21.5 - - - +
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Residues in contact with LEU 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Q ASN* 2.9 42.2 + - + +
76Q GLY* 1.3 70.8 - - - +
78Q LYS* 1.3 62.8 + - + +
80Q MET* 3.1 8.0 + - - +
81Q LEU* 2.9 27.2 + - - +
94Q PRO* 3.8 31.9 - - + -
95Q ASP 5.1 1.8 - - - +
106Q ASN* 4.1 15.7 - - - +
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Residues in contact with LYS 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q LEU* 3.6 9.7 - - + +
64Q THR* 2.8 31.1 + - + +
65Q GLN 2.8 29.2 + - - +
66Q ILE* 3.9 13.4 - - + +
72Q ASP* 4.1 15.0 + - + +
73Q PHE* 3.6 17.6 - - + -
75Q ASN* 4.3 2.7 + - - +
77Q LEU* 1.3 78.6 - - + +
79Q LEU* 1.3 59.7 + - - +
80Q MET 3.3 0.2 - - - -
81Q LEU* 3.6 11.7 - - + -
82Q LEU* 2.8 29.3 + - - +
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Residues in contact with LEU 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q PHE* 3.6 24.3 - - + +
76Q GLY* 3.3 16.1 + - - +
77Q LEU 3.1 0.6 - - - -
78Q LYS* 1.3 78.6 - - - +
80Q MET* 1.3 62.1 + - - +
82Q LEU* 3.4 5.6 + - + +
83Q LEU* 3.2 25.2 + - + +
107Q VAL* 4.7 8.7 - - + +
110Q ALA* 3.7 23.6 - - + -
129Q ILE* 4.5 11.7 - - + -
140Q MET* 3.5 42.8 - - + -
141Q ILE* 4.3 9.2 - - + -
144Q ILE* 3.9 22.7 - - + -
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Residues in contact with MET 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q GLY 2.9 26.7 + - - +
77Q LEU* 3.5 5.6 - - - +
79Q LEU* 1.3 75.2 - - - +
81Q LEU* 1.3 65.3 + - - +
83Q LEU* 3.2 4.6 + - - +
84Q GLU* 3.1 32.0 + - - +
91Q LEU* 3.9 26.0 - - + +
92Q PRO 3.1 27.4 - - - +
94Q PRO* 4.3 18.2 - - + -
106Q ASN* 3.5 37.2 - - - +
109Q LYS* 3.8 23.3 - - + -
110Q ALA* 4.1 10.3 - - + -
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Residues in contact with LEU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q LEU* 4.3 3.4 - - + -
62Q ALA* 3.9 25.4 - - + +
64Q THR* 3.9 29.8 - - + -
77Q LEU 2.9 16.5 + - - +
78Q LYS* 3.6 13.5 - - + +
80Q MET* 1.3 76.8 - - - +
82Q LEU* 1.3 61.3 + - - +
84Q GLU* 3.3 19.6 + - + +
85Q VAL* 3.0 28.4 + - + +
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Residues in contact with LEU 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q TRP* 4.1 14.8 - - + -
55Q CYS* 3.7 38.1 - - + +
58Q HIS* 3.8 28.7 - - + -
59Q LEU* 3.6 13.4 - - + +
73Q PHE* 4.3 9.4 - - + -
78Q LYS 2.8 22.4 + - - +
79Q LEU* 3.5 9.4 - - + +
81Q LEU* 1.3 74.2 - - - +
83Q LEU* 1.3 58.4 + - + +
85Q VAL* 3.3 3.9 + - + +
86Q ILE* 3.1 42.0 + - + +
141Q ILE* 4.3 10.5 - - + -
144Q ILE* 4.9 6.3 - - + -
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Residues in contact with LEU 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q LEU* 3.2 15.7 + - + +
80Q MET 3.2 6.3 + - - +
82Q LEU* 1.3 74.9 - - + +
84Q GLU* 1.3 63.7 + - - +
86Q ILE* 3.7 4.2 - - + +
87Q SER* 2.8 30.9 + - - -
91Q LEU* 4.0 15.0 - - + -
110Q ALA* 3.6 40.8 - - + +
113Q PHE* 4.1 11.6 - - + -
114Q ILE* 4.0 12.8 - - + -
144Q ILE* 3.8 30.7 - - + -
148Q PHE* 3.9 28.7 - - + -
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Residues in contact with GLU 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q MET* 3.1 19.4 + - - +
81Q LEU* 3.8 23.4 - - + +
83Q LEU* 1.3 74.9 - - - +
85Q VAL* 1.3 59.8 + - + +
87Q SER* 4.0 1.3 - - - -
88Q GLY* 2.8 30.1 + - - -
89Q GLU 3.3 20.8 + - - +
90Q ARG* 3.4 36.6 + - - +
91Q LEU* 3.0 37.8 + - + +
92Q PRO 5.0 0.5 - - - +
93Q ARG* 3.5 13.4 + - - -
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Residues in contact with VAL 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Q HIS* 3.6 42.0 - - + +
59Q LEU* 5.0 1.3 - - - -
61Q LYS* 4.6 14.1 - - + +
62Q ALA* 3.9 29.8 - - + +
81Q LEU* 3.0 19.9 + - + +
82Q LEU* 3.5 10.5 - - - +
83Q LEU 3.3 0.2 - - - -
84Q GLU* 1.3 80.2 - - - +
86Q ILE* 1.3 63.2 + - + +
88Q GLY* 3.7 5.5 + - - -
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Residues in contact with ILE 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q TRP* 4.1 9.9 - - + -
58Q HIS* 3.5 46.4 - - + +
82Q LEU* 3.1 23.5 + - + +
83Q LEU* 3.7 10.8 - - + +
85Q VAL* 1.3 76.3 - - - +
87Q SER* 1.3 62.2 + - - +
144Q ILE* 3.5 26.5 - - + -
148Q PHE* 3.4 43.7 - - + +
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Residues in contact with SER 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Q LEU 2.8 22.0 + - - -
84Q GLU* 3.8 0.9 + - - -
86Q ILE* 1.3 78.1 - - - +
88Q GLY* 1.3 61.4 + - - +
89Q GLU* 3.0 37.8 + - - +
113Q PHE* 3.7 11.7 - - - -
148Q PHE* 3.8 26.9 - - - -
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Residues in contact with GLY 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Q GLU 2.8 13.7 + - - -
85Q VAL 3.7 5.0 + - - -
86Q ILE 3.5 1.8 - - - -
87Q SER* 1.3 79.2 - - - +
89Q GLU* 1.3 61.2 + - - +
90Q ARG* 5.2 3.4 - - - -
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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