Contacts of the helix formed by residues 76 - 88 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73P PHE 3.0 18.6 + - - -
74P ARG 3.2 1.2 + - - -
75P ASN* 1.3 76.6 + - - +
77P LEU* 1.3 58.3 + - - +
78P LYS 3.6 1.8 - - - -
79P LEU* 3.4 10.7 - - - +
80P MET* 2.9 36.5 + - - +
106P ASN* 4.6 1.8 - - - -
107P VAL* 3.7 21.5 - - - -
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Residues in contact with LEU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P ASN* 2.9 40.7 + - + +
76P GLY* 1.3 69.9 - - - +
78P LYS* 1.3 63.0 + - + +
80P MET* 3.1 8.0 + - - +
81P LEU* 2.9 27.4 + - - +
94P PRO* 3.8 32.1 - - + -
95P ASP 5.1 1.6 - - - +
106P ASN* 4.1 15.5 - - + +
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Residues in contact with LYS 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P LEU* 3.6 8.3 - - + +
64P THR* 2.8 30.8 + - + +
65P GLN 2.8 29.1 + - - +
66P ILE* 3.9 13.1 - - + +
72P ASP* 4.1 16.5 + - + +
73P PHE* 3.6 17.6 - - + -
75P ASN* 4.3 2.3 + - - +
77P LEU* 1.3 76.9 - - + +
79P LEU* 1.3 59.9 + - - +
81P LEU* 3.6 12.3 - - + -
82P LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P PHE* 3.6 24.5 - - + +
76P GLY* 3.3 16.5 + - - +
77P LEU 3.1 0.4 - - - -
78P LYS* 1.3 79.6 - - - +
80P MET* 1.3 61.0 + - - +
82P LEU* 3.4 5.1 + - + +
83P LEU* 3.2 25.4 + - + +
107P VAL* 4.7 8.3 - - + -
110P ALA* 3.7 23.8 - - + -
129P ILE* 4.5 11.9 - - + -
140P MET* 3.5 42.8 - - + -
141P ILE* 4.3 9.2 - - + -
144P ILE* 3.9 22.9 - - + -
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Residues in contact with MET 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P GLY 2.9 26.0 + - - +
77P LEU* 3.5 4.9 - - - +
79P LEU* 1.3 74.5 - - - +
81P LEU* 1.3 65.0 + - - +
83P LEU* 3.2 5.1 + - - +
84P GLU* 3.1 31.7 + - - +
91P LEU* 3.9 26.0 - - + +
92P PRO 3.1 27.1 - - - +
94P PRO* 4.3 18.8 - - + -
106P ASN* 3.5 36.6 - - - +
109P LYS* 3.8 23.8 - - + -
110P ALA* 4.1 10.1 - - + -
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Residues in contact with LEU 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P LEU* 4.3 3.8 - - + -
62P ALA* 3.9 25.8 - - + +
64P THR* 3.9 29.2 - - + -
77P LEU 2.9 15.9 + - - +
78P LYS* 3.6 13.7 - - + +
80P MET* 1.3 77.2 - - - +
82P LEU* 1.3 61.9 + - - +
84P GLU* 3.3 18.8 + - - +
85P VAL* 3.0 28.0 + - + +
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Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P TRP* 4.1 14.8 - - + -
55P CYS* 3.7 38.8 - - + +
58P HIS* 3.8 27.8 - - + -
59P LEU* 3.6 13.4 - - + +
73P PHE* 4.3 9.9 - - + -
78P LYS 2.8 22.8 + - - +
79P LEU* 3.5 9.9 - - + +
81P LEU* 1.3 74.8 - - - +
83P LEU* 1.3 58.4 + - + +
85P VAL* 3.3 3.7 + - + +
86P ILE* 3.1 42.6 + - + +
141P ILE* 4.3 9.9 - - + -
144P ILE* 4.9 7.0 - - + -
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Residues in contact with LEU 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P LEU* 3.2 16.2 + - + +
80P MET 3.2 7.4 + - - +
82P LEU* 1.3 75.5 - - + +
84P GLU* 1.3 63.2 + - - +
86P ILE* 3.7 3.6 - - + +
87P SER* 2.8 31.1 + - - -
91P LEU* 4.0 14.8 - - + -
110P ALA* 3.6 39.5 - - + +
113P PHE* 4.1 11.0 - - + -
114P ILE* 4.0 14.4 - - + -
144P ILE* 3.8 30.1 - - + -
148P PHE* 3.9 28.3 - - + -
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Residues in contact with GLU 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P MET* 3.1 18.1 + - - +
81P LEU* 3.3 24.2 + - + +
83P LEU* 1.3 75.3 - - - +
85P VAL* 1.3 59.1 + - + +
87P SER* 4.0 1.3 - - - -
88P GLY* 2.8 30.8 + - - -
89P GLU 3.3 21.0 + - - +
90P ARG* 3.4 38.7 + - - +
91P LEU* 3.0 37.4 + - + +
92P PRO 5.0 0.5 - - - +
93P ARG* 3.5 13.3 + - - -
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Residues in contact with VAL 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P HIS* 3.6 42.4 - - + +
59P LEU* 5.0 1.3 - - - -
61P LYS* 4.6 14.6 - - + -
62P ALA* 3.9 28.9 - - + +
81P LEU* 3.0 19.9 + - + +
82P LEU* 3.5 10.8 - - - +
84P GLU* 1.3 81.0 - - + +
86P ILE* 1.3 63.7 + - + +
87P SER 3.5 0.2 + - - -
88P GLY* 3.7 5.7 + - - -
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Residues in contact with ILE 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P TRP* 4.1 10.3 - - + -
58P HIS* 3.5 45.5 - - + +
82P LEU* 3.1 25.3 + - + +
83P LEU* 3.7 10.8 - - + +
85P VAL* 1.3 76.4 - - - +
87P SER* 1.3 61.8 + - - +
144P ILE* 3.5 26.0 - - + -
148P PHE* 3.4 44.8 - - + +
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Residues in contact with SER 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P LEU 2.8 22.9 + - - -
84P GLU* 3.8 0.9 + - - -
86P ILE* 1.3 77.4 - - - +
88P GLY* 1.3 61.4 + - - +
89P GLU* 3.0 37.4 + - - +
113P PHE* 3.7 12.1 - - - -
148P PHE* 3.8 27.1 - - - -
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Residues in contact with GLY 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P GLU 2.8 14.1 + - - -
85P VAL 3.7 5.0 + - - -
86P ILE 3.5 1.4 - - - -
87P SER* 1.3 78.1 - - - +
89P GLU* 1.3 61.1 + - - +
90P ARG* 5.2 3.5 - - - +
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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