Contacts of the helix formed by residues 99 - 116 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ASP* 3.0 43.7 - - + +
341F ILE* 4.4 8.3 - - + -
98O LYS* 1.3 89.5 - - + +
100O ARG* 1.3 67.4 + - - +
101O PHE* 3.3 41.5 - - + -
102O HIS* 3.0 29.2 + - + +
103O LYS* 3.2 11.6 + - - +
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Residues in contact with ARG 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D MET 3.8 0.2 - - - -
48D GLY* 2.4 49.7 - - - +
144F ALA 5.8 2.7 - - - +
145F SER 4.4 3.4 - - - -
146F GLY* 3.8 30.6 + - - -
148F THR* 4.4 0.4 - - - +
98O LYS 3.9 0.4 + - - -
99O MET* 1.3 73.7 - - - +
101O PHE* 1.3 67.1 + - + +
103O LYS* 3.0 14.9 + - - +
104O ILE* 3.0 29.4 + - + +
127O GLU* 3.9 15.8 + - - +
130O VAL* 4.3 15.9 - - + +
131O ASP* 2.6 41.0 + - - -
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Residues in contact with PHE 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLN* 5.5 1.1 - - - +
23F GLY* 5.8 2.0 - - - -
24F ASP 5.3 3.6 - - - -
25F ASP* 4.7 1.3 - - - -
143F TYR* 4.9 6.3 - - + +
144F ALA 4.9 7.2 - - - -
341F ILE* 3.8 14.6 - - + -
344F SER* 5.5 2.7 - - - -
345F ILE* 1.9 73.1 - - + -
348F SER* 5.4 0.7 - - - -
349F LEU* 4.4 4.4 - - - +
99O MET* 3.3 40.8 - - + -
100O ARG* 1.3 80.8 - - + +
102O HIS* 1.3 102.9 + + - +
104O ILE* 3.5 12.9 + - + +
105O ALA* 3.0 23.7 + - - +
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Residues in contact with HIS 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLY* 4.3 24.7 + - - -
24F ASP 6.3 0.2 - - - -
25F ASP* 4.6 3.2 + - - -
348F SER* 5.2 5.8 + - - -
95O ASP* 4.5 17.1 + - + +
96O LYS 3.4 20.0 + - - +
97O GLY* 3.5 31.1 - - - +
99O MET* 3.0 47.2 + - + +
101O PHE* 1.3 99.1 - + - +
103O LYS* 1.3 58.9 + - + +
105O ALA* 3.4 6.2 + - - +
106O ASN* 3.0 34.8 + - - +
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Residues in contact with LYS 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ARG* 3.7 47.7 - - + +
75O ASN* 3.7 31.8 - - + +
98O LYS* 3.6 26.5 + - - +
99O MET 3.5 9.4 - - - +
100O ARG* 3.0 10.9 + - - +
102O HIS* 1.3 76.0 - - + +
104O ILE* 1.3 58.9 + - - +
106O ASN* 3.2 1.3 + - - +
107O VAL* 2.8 35.5 + - - +
130O VAL* 3.8 20.3 + - + +
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Residues in contact with ILE 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY* 2.9 20.0 - - - -
49D GLN* 1.6 83.7 - - + +
50D LYS* 5.0 1.6 - - + -
349F LEU* 6.3 0.7 - - + -
100O ARG* 3.0 25.8 + - + +
101O PHE* 3.7 11.7 - - - +
102O HIS 3.4 0.2 - - - -
103O LYS* 1.3 75.0 - - - +
105O ALA* 1.3 58.8 + - - +
107O VAL 3.8 0.3 - - - -
108O ASN* 2.9 40.8 + - - +
126O ALA* 3.9 9.8 - - + +
127O GLU* 5.1 2.7 - - - -
130O VAL* 3.7 20.0 - - + -
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Residues in contact with ALA 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349F LEU* 3.1 35.2 - - + -
95O ASP* 4.2 18.2 - - - +
101O PHE 3.0 12.5 + - - +
102O HIS* 3.6 6.3 - - - +
103O LYS 3.2 0.2 - - - -
104O ILE* 1.3 77.8 - - - +
106O ASN* 1.3 62.2 + - - +
108O ASN* 3.3 7.7 + - - +
109O LYS* 3.1 29.3 + - - +
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Residues in contact with ASN 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O ASN 3.7 18.2 + - - +
76O GLY* 4.6 2.5 - - - -
77O LEU* 4.1 14.3 - - + +
80O MET* 3.5 16.6 - - - +
94O PRO* 3.2 9.3 - - - +
95O ASP* 2.7 47.2 + - - +
97O GLY 5.3 1.6 + - - -
102O HIS* 3.0 23.6 + - - +
105O ALA* 1.3 73.9 - - - +
107O VAL* 1.3 64.5 + - - +
109O LYS* 3.0 31.2 + - - +
110O ALA 3.3 7.8 + - - -
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Residues in contact with VAL 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ARG 3.8 15.3 - - - +
76O GLY* 3.7 24.2 - - - +
79O LEU* 4.7 5.2 - - + -
103O LYS 2.8 23.2 + - - +
104O ILE 4.0 2.2 - - - +
106O ASN* 1.3 73.6 - - - +
108O ASN* 1.3 58.6 + - - +
110O ALA* 3.3 6.0 + - - +
111O LEU* 2.9 35.2 + - + +
126O ALA* 3.5 29.6 - - + -
129O ILE* 3.7 29.6 - - + -
130O VAL* 4.1 5.4 - - + -
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Residues in contact with ASN 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN* 4.1 12.0 + - - +
51D ASP* 4.4 16.0 + - - +
52D SER* 5.4 2.4 - - - +
104O ILE* 2.9 31.5 + - - +
105O ALA* 3.6 8.4 - - - +
106O ASN 3.1 0.2 - - - -
107O VAL* 1.3 76.5 - - - +
109O LYS* 1.3 60.0 + - - +
111O LEU* 3.8 13.2 - - - +
112O ASP* 2.9 45.0 + - - +
126O ALA* 3.0 24.7 - - - +
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Residues in contact with LYS 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F SER* 4.9 17.6 + - - +
80O MET* 3.8 20.4 - - + -
91O LEU* 4.4 3.2 - - - +
92O PRO* 4.4 28.8 - - + +
93O ARG 3.4 21.8 + - - +
95O ASP* 3.2 24.2 + - - -
105O ALA* 3.1 16.6 + - - +
106O ASN* 3.0 35.3 + - - +
108O ASN* 1.3 76.8 - - - +
110O ALA* 1.3 58.0 + - - +
112O ASP* 3.9 4.8 - - - +
113O PHE* 3.0 28.6 + - - +
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Residues in contact with ALA 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O LEU* 3.7 26.5 - - + -
80O MET* 4.1 14.1 - - + +
83O LEU* 3.6 25.5 - - + +
91O LEU* 4.2 5.2 - - - -
106O ASN 3.3 3.5 + - - +
107O VAL* 3.5 7.9 - - - +
109O LYS* 1.3 77.2 - - - +
111O LEU* 1.3 66.1 + - - +
113O PHE* 3.1 4.0 + - - +
114O ILE* 3.0 27.1 + - + +
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Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D SER* 4.2 3.1 - - - +
79O LEU* 5.4 0.2 - - + -
107O VAL* 2.9 26.6 + - + +
108O ASN* 3.8 15.3 - - - +
110O ALA* 1.3 73.1 - - - +
112O ASP* 1.3 59.4 + - - +
114O ILE* 3.4 8.1 + - + +
115O ALA* 2.9 28.6 + - - +
121O LEU* 3.7 20.8 - - + +
124O ILE* 4.1 21.5 - - + +
125O GLY 3.8 6.5 - - - -
126O ALA* 3.4 37.2 - - - +
129O ILE* 4.7 1.1 - - + -
140O MET* 3.8 30.1 - - + -
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Residues in contact with ASP 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ASN* 2.9 33.4 + - - +
109O LYS* 3.9 6.0 - - - +
111O LEU* 1.3 76.2 - - - +
113O PHE* 1.3 61.3 + - - +
115O ALA* 3.2 7.7 + - - +
116O SER* 2.8 31.5 + - - -
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Residues in contact with PHE 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O LEU* 4.1 22.7 - - + -
87O SER* 3.7 21.1 - - - -
89O GLU* 3.8 21.8 - - + -
90O ARG 5.1 2.9 - - - -
91O LEU* 3.6 40.4 - - + -
92O PRO* 5.7 3.1 - - + -
109O LYS 3.0 15.6 + - - +
110O ALA 3.1 7.8 + - - +
112O ASP* 1.3 77.0 - - - +
114O ILE* 1.3 62.5 + - - +
116O SER* 2.5 28.1 + - - -
117O LYS* 3.4 28.5 + - - +
148O PHE* 3.7 23.8 - + - -
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Residues in contact with ILE 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O LEU* 4.0 23.1 - - + -
110O ALA* 3.0 22.2 + - + +
111O LEU* 3.5 13.7 - - + +
113O PHE* 1.3 75.4 - - - +
115O ALA* 1.3 61.1 + - - +
117O LYS* 2.9 25.9 + - - +
119O VAL* 3.2 45.4 - - + +
121O LEU* 4.0 9.6 - - + -
140O MET* 4.5 14.1 - - + +
143O THR* 4.4 6.5 - - + +
144O ILE* 3.4 34.5 - - + -
148O PHE* 4.6 6.5 - - + -
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Residues in contact with ALA 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 5.2 10.3 - - + -
111O LEU 2.9 13.8 + - - +
112O ASP* 3.6 9.2 - - - +
114O ILE* 1.3 76.6 - - - +
116O SER* 1.3 61.0 + - - +
117O LYS 3.1 1.4 + - - -
118O GLY* 3.1 12.1 + - - -
119O VAL 3.2 20.3 + - - +
121O LEU* 3.4 20.2 - - + -
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Residues in contact with SER 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ASP 2.8 14.7 + - - -
113O PHE* 2.5 30.5 + - - -
115O ALA* 1.3 76.0 - - - +
117O LYS* 1.3 64.2 + - - +
118O GLY 3.1 4.1 + - - -
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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