Contacts of the helix formed by residues 99 - 116 (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 MET 99 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98R LYS* 1.3 89.1 - - + +
100R ARG* 1.3 65.9 + - - +
101R PHE* 3.3 43.3 - - + -
102R HIS* 3.0 32.5 + - + +
103R LYS* 3.2 12.4 + - - +
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Residues in contact with ARG 100 (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* 3.8 1.1 - - - -
48I GLY* 2.4 50.9 - - - +
99R MET* 1.3 72.0 - - - +
101R PHE* 1.3 67.0 + - + +
103R LYS* 3.0 15.2 + - - +
104R ILE* 3.0 29.2 + - + +
127R GLU* 3.9 15.5 + - - +
130R VAL* 4.3 16.7 - - + +
131R ASP* 2.6 41.4 + - - -
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Residues in contact with PHE 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLN* 5.4 9.2 - - + +
99R MET* 3.3 40.6 - - + -
100R ARG* 1.3 80.7 - - + +
102R HIS* 1.3 102.0 + + - +
104R ILE* 3.5 14.4 + - + +
105R ALA* 3.0 23.2 + - - +
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Residues in contact with HIS 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ASP* 4.5 17.3 + - + +
96R LYS 3.4 20.2 + - - +
97R GLY* 3.5 30.2 - - - +
98R LYS* 4.6 0.4 - - - -
99R MET* 3.0 47.4 + - + +
101R PHE* 1.3 100.0 - + - +
103R LYS* 1.3 58.1 + - + +
105R ALA* 3.4 6.8 + - - +
106R ASN* 3.0 34.0 + - - +
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Residues in contact with LYS 103 (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* 3.7 48.4 - - + +
75R ASN* 3.7 31.1 - - + +
98R LYS* 3.6 26.1 + - - +
99R MET 3.5 9.0 - - - +
100R ARG* 3.0 11.3 + - - +
102R HIS* 1.3 76.7 - - + +
104R ILE* 1.3 59.5 + - - +
106R ASN* 3.2 0.7 + - - +
107R VAL* 2.8 35.3 + - - +
130R VAL* 3.8 20.3 + - + +
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Residues in contact with ILE 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLY* 2.9 20.0 - - - -
49I GLN* 1.6 82.6 - - + +
50I LYS* 4.1 1.8 - - + +
100R ARG* 3.0 25.7 + - + +
101R PHE* 3.7 11.2 - - - +
103R LYS* 1.3 75.0 - - - +
105R ALA* 1.3 59.2 + - - +
107R VAL 3.8 0.2 - - - -
108R ASN* 2.9 41.2 + - - +
126R ALA* 3.9 10.5 - - + +
127R GLU* 5.1 2.7 - - - -
130R VAL* 3.7 20.6 - - + -
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Residues in contact with ALA 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ASP* 4.2 23.3 - - - +
101R PHE 3.0 17.5 + - - +
102R HIS* 3.6 6.1 - - - +
103R LYS 3.2 0.2 - - - -
104R ILE* 1.3 78.9 - - - +
106R ASN* 1.3 63.5 + - - +
108R ASN* 3.3 7.3 + - - +
109R LYS* 3.1 28.0 + - - +
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Residues in contact with ASN 106 (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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75R ASN 3.7 17.9 + - - +
76R GLY* 4.6 3.1 - - - -
77R LEU* 4.1 13.3 - - + +
80R MET* 3.5 16.5 - - - +
94R PRO* 3.2 9.7 - - - +
95R ASP* 2.7 47.1 + - - +
97R GLY 5.3 1.4 + - - -
102R HIS* 3.0 23.6 + - - +
103R LYS 4.0 0.2 - - - +
105R ALA* 1.3 74.0 - - - +
107R VAL* 1.3 65.0 + - - +
109R LYS* 3.0 31.4 + - - +
110R ALA 3.3 8.3 + - - -
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Residues in contact with VAL 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R ARG 3.8 15.5 - - - +
76R GLY* 3.7 23.5 - - - +
79R LEU* 4.7 4.9 - - + -
103R LYS 2.8 23.6 + - - +
104R ILE 4.0 2.2 - - - +
106R ASN* 1.3 72.6 - - - +
108R ASN* 1.3 58.5 + - - +
110R ALA* 3.3 6.4 + - - +
111R LEU* 2.9 34.8 + - + +
126R ALA* 3.5 29.8 - - + -
129R ILE* 3.7 29.4 - - + -
130R VAL* 4.1 5.4 - - + -
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Residues in contact with ASN 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLN* 4.2 12.1 + - - +
51I ASP* 4.4 16.1 + - - +
52I SER* 5.4 2.6 - - - +
104R ILE* 2.9 33.0 + - - +
105R ALA* 3.6 7.9 - - - +
106R ASN 3.1 0.2 - - - -
107R VAL* 1.3 76.9 - - - +
109R LYS* 1.3 60.2 + - - +
111R LEU* 3.8 13.2 - - - +
112R ASP* 2.9 45.2 + - - +
126R ALA* 3.0 24.7 - - - +
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Residues in contact with LYS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R MET* 3.8 19.7 - - + -
91R LEU* 4.4 3.1 - - - +
92R PRO* 4.4 28.6 - - + +
93R ARG 3.4 21.8 + - - +
95R ASP* 3.2 23.7 + - - -
105R ALA* 3.1 15.8 + - - +
106R ASN* 3.0 35.5 + - - +
108R ASN* 1.3 76.4 - - - +
110R ALA* 1.3 57.9 + - - +
112R ASP* 3.9 4.7 - - - +
113R PHE* 3.0 28.6 + - - +
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Residues in contact with ALA 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R LEU* 3.7 26.5 - - + -
80R MET* 4.1 13.8 - - + +
83R LEU* 3.6 25.3 - - + +
91R LEU* 4.2 6.1 - - - -
106R ASN 3.3 3.7 + - - +
107R VAL* 3.5 7.2 - - - +
109R LYS* 1.3 77.2 - - - +
111R LEU* 1.3 67.0 + - - +
113R PHE* 3.0 4.3 + - - +
114R ILE* 3.0 27.5 + - + +
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Residues in contact with LEU 111 (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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52I SER* 4.2 2.9 - - - +
79R LEU* 5.4 0.2 - - + -
107R VAL* 2.9 26.6 + - + +
108R ASN* 3.8 15.9 - - - +
110R ALA* 1.3 73.9 - - - +
112R ASP* 1.3 59.8 + - - +
114R ILE* 3.4 8.0 + - + +
115R ALA* 2.9 28.1 + - - +
121R LEU* 3.7 21.4 - - + +
124R ILE* 4.1 23.1 - - + +
125R GLY 3.8 4.9 - - - +
126R ALA* 3.4 37.9 - - - +
129R ILE* 4.7 0.9 - - + -
140R MET* 3.8 29.8 - - + -
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Residues in contact with ASP 112 (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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108R ASN* 2.9 34.9 + - - +
109R LYS* 3.9 5.1 - - - +
111R LEU* 1.3 75.3 - - - +
113R PHE* 1.3 62.0 + - - +
115R ALA* 3.2 8.3 + - - +
116R SER* 2.8 31.8 + - - -
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Residues in contact with PHE 113 (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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83R LEU* 4.1 22.2 - - + -
87R SER* 3.7 22.4 - - - -
89R GLU* 3.8 21.1 - - + -
90R ARG 5.1 2.5 - - - -
91R LEU* 3.6 40.6 - - + -
92R PRO* 5.7 2.9 - - + -
109R LYS 3.0 15.1 + - - +
110R ALA 3.4 7.6 - - - +
112R ASP* 1.3 77.2 - - - +
114R ILE* 1.3 61.8 + - - +
116R SER* 2.5 28.1 + - - -
117R LYS* 3.4 29.1 + - - +
148R PHE* 3.7 24.0 - + - -
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Residues in contact with ILE 114 (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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83R LEU* 4.0 22.4 - - + -
110R ALA* 3.0 23.5 + - + +
111R LEU* 3.5 14.1 - - + +
113R PHE* 1.3 75.2 - - - +
115R ALA* 1.3 60.3 + - - +
117R LYS* 2.9 25.5 + - - +
119R VAL* 3.2 45.9 - - + +
121R LEU* 4.0 9.4 - - + -
140R MET* 4.5 14.8 - - + +
143R THR* 4.4 6.5 - - + +
144R ILE* 3.4 35.4 - - + -
148R PHE* 4.6 6.1 - - + -
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Residues in contact with ALA 115 (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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68I LYS* 5.1 10.1 - - - -
111R LEU 2.9 12.9 + - - +
112R ASP* 3.6 9.2 - - - +
114R ILE* 1.3 76.9 - - - +
116R SER* 1.3 61.9 + - - +
117R LYS 3.0 1.6 + - - -
118R GLY* 3.1 11.8 + - - -
119R VAL 3.2 20.6 + - - +
121R LEU* 3.4 20.6 - - + -
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Residues in contact with SER 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R ASP 2.8 13.9 + - - -
113R PHE* 2.5 30.2 + - - -
115R ALA* 1.3 75.5 - - - +
117R LYS* 1.3 63.2 + - - +
118R GLY 3.1 4.0 + - - -
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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
------------------------------------------------------------
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