Contacts of the helix formed by residues 99 - 116 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASP* 3.0 43.3 - - + +
341D ILE* 4.3 8.3 - - + -
98M LYS* 1.3 88.9 - - + +
100M ARG* 1.3 68.4 + - - +
101M PHE* 3.3 40.8 - - + -
102M HIS* 3.0 29.8 + - + +
103M LYS* 3.2 11.7 + - - +
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Residues in contact with ARG 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY* 2.4 50.3 - - - +
144D ALA 5.8 2.9 - - - +
145D SER 4.4 3.1 - - - -
146D GLY* 3.8 30.1 + - - -
148D THR* 4.4 0.4 - - - +
98M LYS 3.9 0.2 + - - -
99M MET* 1.3 72.9 - - - +
101M PHE* 1.3 68.4 + - + +
103M LYS* 3.0 15.1 + - - +
104M ILE* 3.0 28.0 + - + +
127M GLU* 3.9 14.6 + - - +
130M VAL* 4.3 15.2 - - + +
131M ASP* 2.6 40.6 + - - -
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Residues in contact with PHE 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 5.6 0.5 - - - +
23D GLY 5.8 1.6 - - - -
24D ASP 5.3 4.3 - - - -
25D ASP* 4.7 1.1 - - - -
143D TYR* 4.9 6.3 - - + +
144D ALA* 4.9 7.4 - - + -
341D ILE* 3.8 18.2 - - + -
344D SER* 5.5 3.1 - - - -
345D ILE* 1.9 72.5 - - + -
348D SER* 5.4 0.2 - - - -
349D LEU* 4.4 4.6 - - - +
99M MET* 3.3 37.2 - - + -
100M ARG* 1.3 80.7 - - + +
102M HIS* 1.3 102.7 + + - +
104M ILE* 3.5 12.8 + - + +
105M ALA* 3.0 23.7 + - - +
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Residues in contact with HIS 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLY* 4.3 25.0 + - - -
24D ASP 6.3 0.2 - - - -
25D ASP* 4.6 3.0 + - - -
348D SER* 5.2 6.0 + - - -
349D LEU* 6.1 0.2 - - - -
95M ASP* 4.5 17.8 + - + +
96M LYS 3.4 19.2 + - - +
97M GLY* 3.5 32.4 - - - +
98M LYS 4.6 0.2 - - - -
99M MET* 3.0 46.7 + - + +
101M PHE* 1.3 98.3 - + - +
103M LYS* 1.3 58.4 + - + +
105M ALA* 3.4 6.8 + - - +
106M ASN* 3.0 35.3 + - - +
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Residues in contact with LYS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M ARG* 3.7 48.2 - - + +
75M ASN* 3.7 32.0 - - + +
98M LYS* 3.6 25.6 + - - +
99M MET 3.5 9.6 - - - +
100M ARG* 3.0 10.5 + - - +
102M HIS* 1.3 75.6 - - + +
104M ILE* 1.3 60.0 + - - +
106M ASN* 3.2 0.9 + - - +
107M VAL* 2.8 35.2 + - - +
130M VAL* 3.8 19.2 + - + -
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Residues in contact with ILE 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY* 2.9 20.6 - - - -
49B GLN* 1.6 83.9 - - + +
50B LYS* 4.2 1.8 - - + +
349D LEU* 6.3 0.7 - - + -
100M ARG* 3.0 25.5 + - + +
101M PHE* 3.7 11.4 - - - +
102M HIS 3.4 0.2 - - - -
103M LYS* 1.3 74.9 - - - +
105M ALA* 1.3 58.9 + - - +
107M VAL 3.5 0.3 + - - -
108M ASN* 2.9 40.4 + - - +
126M ALA* 3.9 9.8 - - + +
127M GLU* 5.1 3.1 - - - -
130M VAL* 3.7 20.2 - - + -
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Residues in contact with ALA 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D LEU* 3.1 35.6 - - + +
95M ASP* 4.2 17.7 - - - +
101M PHE 3.0 13.0 + - - +
102M HIS* 3.6 6.1 - - - +
104M ILE* 1.3 79.3 - - - +
106M ASN* 1.3 63.3 + - - +
108M ASN* 3.3 7.5 + - - +
109M LYS* 3.1 28.4 + - - +
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Residues in contact with ASN 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M ASN 3.7 18.2 + - - +
76M GLY* 4.6 3.4 - - - -
77M LEU* 4.1 13.7 - - - +
80M MET* 3.5 16.7 - - - +
94M PRO* 3.2 9.9 - - - +
95M ASP* 2.7 48.4 + - - +
97M GLY 5.3 1.4 + - - -
102M HIS* 3.0 23.0 + - - +
103M LYS 3.2 0.4 + - - +
105M ALA* 1.3 74.4 - - - +
107M VAL* 1.3 64.5 + - - +
109M LYS* 3.0 31.3 + - - +
110M ALA 3.3 8.8 + - - -
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Residues in contact with VAL 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M PHE 4.0 0.4 - - - +
74M ARG 3.8 14.8 - - - +
76M GLY* 3.7 24.0 - - - +
79M LEU* 4.7 5.2 - - + -
103M LYS 2.8 23.4 + - - +
104M ILE 4.0 2.9 - - - +
106M ASN* 1.3 72.5 - - - +
108M ASN* 1.3 58.1 + - - +
110M ALA* 3.3 6.6 + - - +
111M LEU* 2.9 35.7 + - + +
126M ALA* 3.5 30.1 - - + -
129M ILE* 3.7 28.3 - - + -
130M VAL* 4.1 5.2 - - + -
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Residues in contact with ASN 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 4.1 12.8 + - - +
51B ASP* 4.4 15.9 + - - +
52B SER* 5.4 2.4 + - - +
104M ILE* 2.9 33.3 + - - +
105M ALA* 3.6 7.2 - - - +
106M ASN 3.1 0.2 - - - -
107M VAL* 1.3 74.5 - - - +
109M LYS* 1.3 59.3 + - - +
111M LEU* 3.8 13.8 - - - +
112M ASP* 2.9 45.1 + - - +
126M ALA* 3.0 24.8 - - - +
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Residues in contact with LYS 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D SER* 4.9 17.2 + - - +
80M MET* 3.8 20.0 - - + -
91M LEU* 4.4 3.3 - - - +
92M PRO* 4.4 27.1 - - + +
93M ARG 3.4 21.9 + - - +
95M ASP* 3.2 24.4 + - - -
105M ALA* 3.1 16.5 + - - +
106M ASN* 3.0 35.7 + - - +
108M ASN* 1.3 76.6 - - - +
110M ALA* 1.3 58.2 + - - +
112M ASP* 3.9 4.9 - - - +
113M PHE* 3.0 28.3 + - - +
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Residues in contact with ALA 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU* 3.7 26.2 - - + -
80M MET* 4.1 14.0 - - + +
83M LEU* 3.6 24.4 - - + +
91M LEU* 4.2 5.6 - - - -
106M ASN 3.3 3.3 + - - +
107M VAL* 3.5 8.3 - - - +
108M ASN 3.2 0.2 - - - -
109M LYS* 1.3 77.3 - - - +
111M LEU* 1.3 66.8 + - - +
113M PHE* 3.1 4.0 + - - +
114M ILE* 3.0 27.8 + - + +
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Residues in contact with LEU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER* 4.2 2.9 - - - +
79M LEU* 5.4 0.4 - - + -
107M VAL* 2.9 24.8 + - + +
108M ASN* 3.8 16.2 - - - +
110M ALA* 1.3 72.1 - - - +
112M ASP* 1.3 61.5 + - - +
114M ILE* 3.4 8.6 + - + +
115M ALA* 2.9 28.5 + - - +
121M LEU* 3.7 21.3 - - + +
124M ILE* 4.1 21.8 - - + +
125M GLY 3.8 5.8 - - - -
126M ALA* 3.4 37.7 - - - +
129M ILE* 4.7 1.3 - - + -
140M MET* 3.8 29.8 - - + -
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Residues in contact with ASP 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M ASN* 2.9 33.9 + - - +
109M LYS* 3.9 4.8 - - - +
111M LEU* 1.3 74.9 - - - +
113M PHE* 1.3 60.9 + - - +
115M ALA* 3.2 8.9 + - - +
116M SER* 2.8 31.4 + - - -
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Residues in contact with PHE 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M LEU* 4.1 22.2 - - + -
87M SER* 3.7 22.0 - - - -
89M GLU* 3.8 22.0 - - + -
90M ARG 5.1 3.4 - - - -
91M LEU* 3.6 41.3 - - + -
92M PRO* 5.7 3.1 - - + -
109M LYS 3.0 15.5 + - - +
110M ALA 3.1 7.4 + - - +
112M ASP* 1.3 76.9 - - - +
114M ILE* 1.3 63.0 + - - +
116M SER* 2.5 27.6 + - - -
117M LYS* 3.4 28.4 + - - +
148M PHE* 3.7 23.3 - + - -
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Residues in contact with ILE 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU* 5.6 0.2 - - + -
83M LEU* 4.0 23.6 - - + -
110M ALA* 3.0 22.4 + - + +
111M LEU* 3.5 13.2 - - + +
113M PHE* 1.3 75.2 - - - +
115M ALA* 1.3 61.3 + - - +
117M LYS* 2.9 25.1 + - - +
119M VAL* 3.2 45.6 - - + +
121M LEU* 4.0 9.6 - - + -
140M MET* 4.5 13.9 - - + +
143M THR* 4.4 6.3 - - + +
144M ILE* 3.4 34.8 - - + -
148M PHE* 4.6 6.1 - - + -
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Residues in contact with ALA 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LYS* 5.2 10.1 - - + -
111M LEU 2.9 13.3 + - - +
112M ASP* 3.6 9.9 - - - +
114M ILE* 1.3 75.2 - - - +
116M SER* 1.3 61.4 + - - +
117M LYS 3.1 0.7 + - - -
118M GLY* 3.1 12.5 + - - -
119M VAL 3.2 20.6 + - - +
121M LEU* 3.4 20.6 - - + +
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Residues in contact with SER 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M ASP 2.8 13.4 + - - -
113M PHE* 2.5 30.9 + - - -
115M ALA* 1.3 76.0 - - - +
117M LYS* 1.3 64.2 + - - +
118M GLY 3.1 5.0 + - - -
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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
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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