Contacts of the helix formed by residues 94 - 117 (chain A) in PDB entry 4LLL
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 THR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LYS* 2.8 26.7 + - + +
76A LEU 3.0 6.4 + - - -
77A ILE 3.5 29.4 - - - +
78A TYR* 3.9 15.9 - - + +
93A LEU* 1.3 73.7 - - - +
95A THR* 1.3 57.4 + - - +
96A SER* 3.4 4.4 + - - -
97A GLY 2.7 33.1 + - - -
98A ILE* 2.9 15.3 + - - +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 1.3 72.4 - - - +
96A SER* 1.3 62.8 + - - +
98A ILE* 3.3 16.9 + - + +
99A LYS* 3.2 45.9 + - + +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS 5.0 1.0 + - - -
75A LYS* 3.8 7.5 + - - +
76A LEU* 3.4 18.2 - - - +
94A THR* 3.4 8.9 + - - -
95A THR* 1.3 82.0 - - - +
97A GLY* 1.3 57.3 + - - +
99A LYS* 3.4 8.3 + - - +
100A LEU* 3.0 27.7 + - - +
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Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.8 1.7 - - - +
76A LEU* 3.4 34.5 - - - -
93A LEU* 4.4 8.7 - - - +
94A THR* 2.7 20.9 + - - -
96A SER* 1.3 73.7 - - - +
98A ILE* 1.3 54.4 - - - -
100A LEU* 3.4 3.7 + - - +
101A VAL* 3.0 31.7 + - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.5 26.0 - - + -
44A GLN* 5.1 6.3 - - - +
93A LEU* 3.9 25.5 - - + +
94A THR 3.0 17.9 - - - +
95A THR* 3.7 18.6 - - + +
96A SER 3.3 0.2 - - - -
97A GLY* 1.3 71.6 - - - +
99A LYS* 1.3 66.3 + - + +
101A VAL* 3.2 4.2 + - - +
102A GLU* 3.0 32.6 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 3.2 31.6 + - + +
96A SER* 3.7 9.2 - - - +
98A ILE* 1.3 77.2 - - + +
100A LEU* 1.3 58.7 + - - +
102A GLU* 3.1 16.6 + - - +
103A ALA* 2.8 28.6 + - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.6 42.4 - - + +
29A ILE* 3.8 19.3 - - + -
37A LEU* 4.6 5.2 - - + -
76A LEU* 3.5 38.6 - - + -
96A SER 3.0 14.0 + - - +
97A GLY* 3.5 10.5 - - - +
98A ILE 3.3 0.2 - - - -
99A LYS* 1.3 75.5 - - - +
101A VAL* 1.3 62.3 + - - +
103A ALA* 3.2 5.6 + - + +
104A PHE* 3.0 36.5 + - + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.7 39.7 - - + +
38A GLY* 4.7 5.2 - - - -
41A TYR* 3.7 37.5 - - + -
93A LEU* 4.3 4.0 - - + -
97A GLY 3.0 17.4 + - - +
98A ILE 3.6 7.6 - - - +
100A LEU* 1.3 74.2 - - - +
102A GLU* 1.3 65.6 + - - +
104A PHE* 2.9 30.4 + - + -
105A THR* 3.0 30.1 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 2.8 35.7 + - + +
98A ILE* 3.0 20.1 + - - +
99A LYS* 3.3 19.9 - - - +
101A VAL* 1.3 78.0 - - - +
103A ALA* 1.3 62.6 + - - +
105A THR* 4.3 6.6 + - - -
106A SER 5.5 0.2 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.6 26.8 - - + -
99A LYS 2.8 15.2 + - - +
100A LEU* 3.3 12.6 - - + +
101A VAL 3.0 0.6 + - - -
102A GLU* 1.3 76.7 - - - +
104A PHE* 1.3 64.5 + - - +
105A THR 3.2 1.4 + - - -
106A SER* 3.5 13.2 + - - -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.7 11.2 - - + -
27A PHE* 3.4 34.1 - - + -
29A ILE* 3.6 24.0 - - + -
34A GLY* 3.5 24.0 - - - -
37A LEU* 4.2 6.1 - - + -
38A GLY* 4.5 2.9 - - - -
100A LEU* 3.0 26.6 + - + -
101A VAL* 2.9 42.0 + - + -
103A ALA* 1.3 74.2 - - - +
105A THR* 1.3 75.7 + - - +
106A SER* 3.2 2.2 - - - -
107A ILE* 3.0 20.9 + - - +
108A PHE* 3.3 35.2 + + - -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 6.0 0.3 - - - -
101A VAL* 3.0 36.1 + - - +
102A GLU* 4.3 5.7 + - - -
103A ALA 3.2 3.0 + - - -
104A PHE* 1.3 86.1 - - - +
106A SER* 1.3 63.7 + - - +
107A ILE 3.1 1.0 + - - -
108A PHE* 3.1 11.9 + - + +
109A ASP* 3.1 38.1 + - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU 5.5 0.2 + - - -
103A ALA 3.5 16.3 + - - -
104A PHE 3.9 1.0 + - - -
105A THR* 1.3 72.6 - - - +
107A ILE* 1.3 54.1 + - - +
109A ASP* 3.2 11.9 + - - +
110A GLU* 2.5 38.0 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 4.9 3.4 - - - +
23A LYS* 3.5 65.1 - - + +
24A LEU* 3.6 26.5 - - + -
26A GLN* 5.9 0.9 - - - +
27A PHE* 4.2 11.7 - - + -
104A PHE 3.0 12.4 + - - +
106A SER* 1.3 75.2 - - - +
108A PHE* 1.3 71.3 + - + +
110A GLU* 2.9 7.2 + - - +
111A MET* 2.9 33.5 + - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 4.6 9.6 - - + -
24A LEU* 4.1 16.6 - - + -
31A ASN* 3.7 17.3 - - - -
34A GLY* 3.8 15.0 - - - -
35A HIS* 3.1 48.2 - + + -
104A PHE* 3.3 41.7 - + - -
105A THR* 3.1 13.4 + - + +
107A ILE* 1.3 81.8 - - + +
109A ASP* 1.3 65.2 + - - +
111A MET* 3.5 6.8 + - - +
112A GLU* 3.1 23.0 + - - +
4B THR* 5.8 0.9 - - - +
6B SER* 5.7 2.4 - - - -
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 3.1 33.3 + - - +
106A SER* 3.4 9.3 - - - +
107A ILE 3.1 0.4 - - - -
108A PHE* 1.3 75.5 - - - +
110A GLU* 1.3 67.8 + - - +
112A GLU* 3.7 6.0 - - - +
113A GLN* 3.0 29.8 + - + +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.4 33.8 - - - +
106A SER* 2.5 20.5 + - - +
107A ILE* 2.9 9.2 + - - +
109A ASP* 1.3 74.6 - - - +
111A MET* 1.3 68.5 + - - +
113A GLN* 3.4 4.8 + - - +
114A THR* 3.0 50.2 + - - +
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Residues in contact with MET 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.6 52.7 - - + +
19A LYS* 3.9 18.8 - - + -
20A ALA* 3.6 29.6 - - + -
23A LYS* 4.4 7.9 - - + -
107A ILE* 2.9 23.6 + - + +
108A PHE* 3.9 9.2 - - + +
110A GLU* 1.3 89.3 - - - +
112A GLU* 1.3 64.3 + - - +
114A THR* 3.9 5.3 - - - -
115A LEU* 3.0 29.9 + - - +
138B LEU* 4.7 8.9 - - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 5.5 1.5 - - - +
108A PHE 3.1 18.2 + - - +
109A ASP* 3.7 7.0 - - - +
111A MET* 1.3 76.6 - - - +
113A GLN* 1.3 64.0 + - + +
115A LEU* 3.4 6.7 + - - +
116A VAL* 2.8 53.2 + - + +
3B PHE 4.9 2.4 - - - +
4B THR* 3.2 20.4 - - + +
5B TYR* 2.9 40.3 + - - +
6B SER 4.2 0.7 + - - -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 3.0 20.0 + - + +
110A GLU* 3.6 4.7 - - - +
112A GLU* 1.3 79.4 - - + +
114A THR* 1.3 56.6 + - - +
116A VAL* 2.7 24.1 + - - +
117A SER* 2.5 43.5 + - - -
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 3.0 34.1 + - - +
111A MET* 3.9 7.4 - - - -
113A GLN* 1.3 77.7 - - - +
115A LEU* 1.3 59.2 + - + +
117A SER* 3.1 14.8 + - - +
118A GLN* 3.1 29.1 + - - +
137B SER* 5.3 8.1 - - - +
138B LEU* 6.2 2.9 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 6.2 0.2 - - + -
16A MET* 3.9 23.8 - - + -
111A MET 3.0 15.9 + - - +
112A GLU* 3.4 9.2 - - - +
113A GLN 3.0 0.6 - - - -
114A THR* 1.3 76.4 - - + +
116A VAL* 1.3 56.3 + - - +
118A GLN* 2.7 36.9 + - + +
5B TYR* 3.5 38.8 - - + -
9B PHE* 4.0 12.6 - - + -
134B MET* 4.0 29.9 - - + +
137B SER* 4.2 18.8 - - - +
138B LEU* 4.2 19.7 - - + -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.8 43.8 + - + +
113A GLN* 2.7 27.2 + - - +
115A LEU* 1.3 71.5 - - - +
117A SER* 1.3 56.0 + - - +
118A GLN 2.8 6.4 + - - -
119A LEU 3.1 14.0 + - - +
124A ASN* 3.3 32.5 + - + +
5B TYR* 4.1 12.1 - - + -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLN* 2.5 24.4 + - - -
114A THR* 3.1 21.4 + - - +
115A LEU 3.0 0.2 + - - -
116A VAL* 1.3 72.0 - - - +
118A GLN* 1.3 61.9 + - - +
119A LEU 3.5 2.4 - - - +
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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