Contacts of the helix formed by residues 100 - 121 (chain N) in PDB entry 6L49
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 PRO 100 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92M GLU* 3.8 38.6 - - + +
95M LYS* 4.0 36.1 - - + +
96M LEU* 5.4 4.0 - - + +
98N LEU 4.1 4.5 - - - +
99N LEU* 1.3 88.5 - - + +
101N GLY* 1.3 56.0 - - - +
102N GLU 3.6 1.1 - - - -
103N LEU* 3.1 20.9 + - + +
104N ALA* 2.5 33.5 + - - -
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Residues in contact with GLY 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M GLU* 4.3 0.8 + - - -
99N LEU 3.9 0.4 + - - -
100N PRO* 1.3 72.1 - - - +
102N GLU* 1.3 57.1 + - - +
104N ALA* 3.4 5.3 + - - +
105N LYS* 2.9 31.8 + - - +
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Residues in contact with GLU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M GLU* 3.5 15.3 + - - +
101N GLY* 1.3 71.7 - - - +
103N LEU* 1.3 60.4 + - - +
105N LYS* 3.3 27.1 + - - +
106N HIS* 3.0 66.7 + - + -
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Residues in contact with LEU 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M TYR* 3.4 35.2 - - + +
58M LEU* 3.8 17.9 - - + -
61M GLU* 5.2 9.2 - - + -
92M GLU* 3.1 36.3 + - + +
93M LEU* 4.7 15.9 - - + -
96M LEU* 5.2 1.8 - - + -
99N LEU* 3.8 30.7 - - + -
100N PRO* 3.1 17.8 + - + +
102N GLU* 1.3 76.6 - - - +
104N ALA* 1.3 55.6 + - - +
106N HIS* 3.5 0.7 + - - -
107N ALA* 2.9 30.2 + - - +
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Residues in contact with ALA 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N VAL* 3.8 10.5 - - - +
96N ARG* 4.1 14.4 - - + +
99N LEU* 3.4 29.1 - - + +
100N PRO 2.5 21.2 + - - +
101N GLY* 3.8 6.3 - - - +
103N LEU* 1.3 73.4 - - - +
105N LYS* 1.3 57.9 + - - +
107N ALA* 3.7 3.5 - - - +
108N VAL* 2.9 35.4 + - - +
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Residues in contact with LYS 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N GLY 2.9 19.2 + - - +
102N GLU* 3.6 31.2 + - - +
103N LEU 3.3 0.2 - - - -
104N ALA* 1.3 73.7 - - - +
106N HIS* 1.3 64.4 + - + +
108N VAL* 3.3 12.0 - - + +
109N SER* 3.0 29.9 + - - -
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Residues in contact with HIS 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 3.3 36.9 + + + +
102N GLU* 3.0 52.7 + - + +
103N LEU 3.9 0.4 - - - +
105N LYS* 1.3 80.7 - - + +
107N ALA* 1.3 57.7 + - - +
109N SER* 2.7 21.3 + - - -
110N GLU* 3.0 22.8 + - + +
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Residues in contact with ALA 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M VAL* 3.9 20.2 - - + +
57M TYR* 4.1 18.3 - - + -
95N VAL* 3.8 18.6 - - + -
99N LEU* 3.8 11.9 - - + -
103N LEU 2.9 18.0 + - - +
104N ALA 3.7 4.3 - - - +
106N HIS* 1.3 78.3 - - - +
108N VAL* 1.3 57.4 + - - +
110N GLU* 3.5 3.6 + - - +
111N GLY* 2.8 25.8 + - - -
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Residues in contact with VAL 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 3.3 21.3 + - - +
92N GLN* 4.0 14.6 - - + +
95N VAL* 3.8 18.2 - - + -
96N ARG* 3.9 25.6 - - + -
104N ALA 2.9 24.4 + - - +
105N LYS* 3.3 18.8 - - + +
107N ALA* 1.3 73.5 - - - +
109N SER* 1.3 53.8 + - - +
112N THR* 2.6 41.5 + - + +
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Residues in contact with SER 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N LYS* 3.0 16.6 + - - -
106N HIS* 2.7 28.9 + - - -
108N VAL* 1.3 78.1 - - - +
110N GLU* 1.3 56.3 + - - +
112N THR* 2.9 18.4 + - - -
113N LYS* 3.0 19.3 + - - +
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Residues in contact with GLU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M LEU* 5.7 4.5 - - - +
53M ALA* 3.8 10.3 - - + +
56M GLU* 6.1 1.2 - - - +
57M TYR* 4.4 32.2 + - + +
106N HIS* 3.0 20.8 + - + +
107N ALA 3.9 2.9 - - - +
109N SER* 1.3 76.6 + - - +
111N GLY* 1.3 58.4 + - - +
113N LYS* 2.9 41.2 + - - +
114N ALA* 3.0 29.6 + - - +
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Residues in contact with GLY 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 3.6 24.4 - - - -
53M ALA* 3.7 15.6 - - - +
107N ALA 2.8 17.9 + - - -
108N VAL 3.9 0.9 - - - -
109N SER 3.3 0.2 - - - -
110N GLU* 1.3 74.8 - - - +
112N THR* 1.3 59.5 + - - +
114N ALA* 3.3 2.1 + - - +
115N VAL* 2.9 33.3 + - - +
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Residues in contact with THR 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 4.1 7.6 - - + +
92N GLN* 3.9 24.0 - - - +
108N VAL* 2.6 25.2 + - + +
109N SER* 2.9 16.6 + - - -
111N GLY* 1.3 71.6 - - - +
113N LYS* 1.3 58.1 + - - +
115N VAL* 3.9 5.0 - - - +
116N THR* 3.0 38.8 + - - +
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Residues in contact with LYS 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N SER 3.0 16.7 + - - +
110N GLU* 2.9 45.5 + - - +
111N GLY 3.3 0.2 - - - -
112N THR* 1.3 76.6 + - - +
114N ALA* 1.3 56.2 + - - +
116N THR* 2.8 21.2 + - - +
117N LYS* 2.9 42.6 + - + +
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Residues in contact with ALA 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ALA 4.1 6.4 - - - +
23M LEU* 3.9 14.1 - - + -
49M VAL* 3.3 22.7 - - + +
53M ALA* 3.7 22.2 - - + -
110N GLU 3.0 16.1 + - - +
111N GLY 3.3 1.5 + - - +
113N LYS* 1.3 74.4 - - - +
115N VAL* 1.3 61.1 + - - +
117N LYS* 3.3 12.8 + - - +
118N TYR* 2.9 23.6 + - - +
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Residues in contact with VAL 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M GLY* 3.4 24.5 - - - +
49M VAL* 4.4 4.5 - - + -
50M TYR* 3.5 17.5 - - + +
88N SER* 3.3 30.7 - - - +
111N GLY 2.9 21.4 + - - +
112N THR* 4.0 6.1 - - - +
114N ALA* 1.3 74.2 - - - +
116N THR* 1.3 58.1 + - + +
118N TYR* 3.3 3.1 + - + +
119N THR* 2.4 46.2 + - - +
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Residues in contact with THR 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N THR* 3.0 20.7 + - - +
113N LYS* 2.8 24.3 + - - +
115N VAL* 1.3 77.4 - - + +
117N LYS* 1.3 57.5 + - - +
119N THR* 3.8 5.5 - - - -
120N SER* 2.9 30.8 + - - -
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Residues in contact with LYS 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ARG 3.0 14.0 - - - +
21M ALA 3.4 19.3 + - - +
22M GLY* 3.5 29.5 + - - -
23M LEU* 5.1 2.4 - - - +
113N LYS* 2.9 49.8 + - + +
114N ALA* 3.3 12.9 + - - +
116N THR* 1.3 78.1 + - - +
118N TYR* 1.3 59.2 + - - +
120N SER* 2.8 18.0 + - - +
121N ALA* 3.6 5.2 + - - +
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Residues in contact with TYR 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ARG* 3.1 53.7 + - + -
20M ARG* 3.5 16.2 - - + -
21M ALA* 4.1 13.9 - - + +
27M VAL* 4.5 3.8 - - + -
45M ALA* 3.4 40.4 - - + +
46M GLY* 4.7 3.4 - - - -
49M VAL* 3.6 30.3 - - + -
114N ALA 2.9 17.0 + - - +
115N VAL* 3.9 3.1 - - - +
116N THR 3.3 0.2 - - - -
117N LYS* 1.3 74.4 - - - +
119N THR* 1.3 66.1 + - - +
121N ALA* 2.9 23.8 + - + +
122N LYS* 4.8 11.5 + - - -
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Residues in contact with THR 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLY* 6.0 0.3 - - - -
115N VAL* 2.4 36.0 + - - +
116N THR* 3.4 5.3 + - - -
118N TYR* 1.3 79.9 - - - +
120N SER* 1.3 63.7 + - - +
121N ALA 3.2 7.0 - - - +
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Residues in contact with SER 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N THR 2.9 16.0 + - - -
117N LYS* 2.8 23.9 + - - +
119N THR* 1.3 78.4 - - - +
121N ALA* 1.3 56.7 + - - +
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Residues in contact with ALA 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ARG* 3.6 45.1 - - + +
117N LYS 3.6 3.1 + - - +
118N TYR* 2.9 17.0 + - + +
119N THR* 3.2 12.0 - - - +
120N SER* 1.3 79.1 + - - +
122N LYS* 1.3 64.9 + - - +
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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
------------------------------------------------------------
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