Contacts of the helix formed by residues 98 - 117 (chain N) in PDB entry 6CET
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 LEU 98 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5N CYS* 3.7 35.9 - - + -
7N ILE* 3.9 10.3 - - + -
69N VAL* 5.6 8.3 - - + -
87N PHE* 3.6 38.4 - - + -
89N CYS* 3.8 15.5 - - - -
95N THR* 5.5 6.1 - - - +
96N CYS 3.6 1.0 - - - -
97N ALA* 1.3 84.9 - - + +
99N GLU* 1.3 63.1 + - + +
100N PRO 3.7 1.1 - - - -
101N ILE* 3.4 19.2 + - + +
102N VAL* 3.1 29.6 + - + +
139N LEU* 5.3 8.1 - - + -
159N VAL* 5.4 6.5 - - + -
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Residues in contact with GLU 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M LEU* 3.4 31.0 - - - +
87M LYS 6.1 0.9 - - - -
88M ILE 6.1 1.0 - - - -
89M ASP* 6.1 1.4 - - - -
58N THR* 4.2 19.9 + - + +
60N MET* 4.8 6.9 - - + +
69N VAL* 5.1 15.0 - - + -
95N THR 4.7 2.5 - - - +
96N CYS* 4.1 25.9 - - - +
97N ALA 3.6 0.2 - - - -
98N LEU* 1.3 82.8 - - + +
100N PRO* 1.4 69.8 - - + +
102N VAL* 3.2 8.6 + - - +
103N LYS* 3.0 25.3 + - - +
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Residues in contact with PRO 100 (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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187D TYR* 3.4 32.5 - - + +
188D GLY* 5.0 5.0 - - - +
414D LEU* 6.1 5.2 - - + -
96N CYS 6.0 0.4 - - - +
97N ALA* 5.1 5.6 - - - +
98N LEU 4.1 1.6 - - - +
99N GLU* 1.4 91.2 - - + +
101N ILE* 1.3 58.5 + - + +
103N LYS* 3.7 10.1 - - + +
104N LYS* 2.8 31.6 + - - +
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Residues in contact with ILE 101 (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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188D GLY* 6.3 2.5 - - - -
87N PHE* 6.0 4.7 - - + -
97N ALA 3.9 17.5 - - - +
98N LEU* 3.4 14.8 + - + +
99N GLU 3.2 0.4 - - - -
100N PRO* 1.3 80.3 - - + +
102N VAL* 1.3 57.3 + - + +
104N LYS* 3.3 6.9 + - + +
105N LEU* 2.9 38.8 + - + +
139N LEU* 4.8 15.7 - - + -
157N LEU* 3.8 25.3 - - + +
158N LYS 3.4 27.6 - - - +
159N VAL* 3.8 26.2 - - + -
160N ILE 5.0 0.9 - - - +
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Residues in contact with VAL 102 (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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58N THR* 5.2 3.6 - - + -
69N VAL* 4.6 19.5 - - + -
70N CYS* 5.0 1.8 - - - +
71N ILE* 3.8 28.1 - - + +
85N LEU* 4.7 15.1 - - + +
87N PHE* 3.9 36.6 - - + -
98N LEU* 3.1 17.0 + - + +
99N GLU* 3.2 8.5 + - - +
101N ILE* 1.3 76.3 - - + +
103N LYS* 1.3 57.0 + - - +
105N LEU* 3.3 10.7 + - + +
106N ALA* 3.0 27.4 + - - +
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Residues in contact with LYS 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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411D LYS 5.5 4.4 + - - -
88M ILE* 5.8 4.4 - - - +
56N THR* 4.0 27.9 + - + -
57N VAL* 5.4 2.8 - - - +
58N THR* 4.2 17.5 - - + +
71N ILE* 4.0 17.3 - - + -
99N GLU 3.0 16.9 + - - +
100N PRO* 3.9 8.5 - - + +
102N VAL* 1.3 76.1 - - - +
104N LYS* 1.3 57.7 + - - +
106N ALA* 3.4 3.5 + - - +
107N GLY* 3.0 22.3 + - - -
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Residues in contact with LYS 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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184D PHE* 3.7 16.0 - - - -
188D GLY 3.8 15.2 - - - +
189D ASP* 3.4 35.3 - - - +
193D GLU* 3.7 12.2 + - - -
100N PRO 2.8 18.5 + - - +
101N ILE* 3.7 6.7 - - + +
102N VAL 3.2 0.2 - - - -
103N LYS* 1.3 76.3 - - - +
105N LEU* 1.3 60.4 + - - +
107N GLY* 3.2 3.7 + - - +
108N TYR* 2.9 52.5 + - + -
156N HIS* 3.0 27.1 + - - +
157N LEU* 4.1 12.7 - - + +
158N LYS 5.2 0.4 - - - +
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Residues in contact with LEU 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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10N ILE* 6.6 0.4 - - + -
85N LEU* 4.9 20.6 - - + -
87N PHE* 5.8 8.5 - - + -
101N ILE* 2.9 30.3 + - + +
102N VAL* 3.7 9.9 - - + +
104N LYS* 1.3 72.8 - - - +
106N ALA* 1.3 61.2 + - - +
108N TYR* 3.2 12.1 + - + +
109N LEU* 3.0 37.6 + - + +
135N LEU* 4.4 23.8 - - + -
139N LEU* 6.4 2.7 - - + -
155N ILE* 5.2 4.9 - - + -
157N LEU* 3.9 30.5 - - + -
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Residues in contact with ALA 106 (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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56N THR* 6.2 2.7 - - + -
71N ILE* 3.7 33.7 - - + -
72N GLU 5.6 0.7 - - - +
73N HIS* 4.0 13.7 - - - +
85N LEU* 6.0 3.2 - - - +
102N VAL 3.0 14.7 + - - +
103N LYS* 3.4 9.2 - - + +
104N LYS 3.2 0.2 - - - -
105N LEU* 1.3 76.5 - - - +
107N GLY* 1.3 53.6 + - - +
109N LEU* 3.5 7.8 + - - +
110N THR* 2.5 38.1 + - - +
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Residues in contact with GLY 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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103N LYS 3.0 14.6 + - - -
104N LYS* 3.2 5.3 + - - -
106N ALA* 1.3 74.6 - - - +
108N TYR* 1.3 57.9 + - - +
110N THR* 3.7 5.7 - - - -
111N THR* 3.0 38.5 + - - +
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Residues in contact with TYR 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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193D GLU* 3.6 22.5 + - + -
104N LYS* 2.9 50.7 + - + -
105N LEU* 3.5 17.5 - - + +
107N GLY* 1.3 75.2 - - - +
109N LEU* 1.3 60.6 + - + +
111N THR* 3.1 7.6 + - - -
112N LEU* 2.9 30.6 + - - +
153N ASN* 4.6 20.4 + - - -
154N THR 4.1 7.2 + - - -
155N ILE* 3.6 33.4 - - + -
156N HIS* 3.1 37.3 + - - +
157N LEU* 4.5 4.0 - - + -
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Residues in contact with LEU 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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12N PHE* 5.2 7.6 - - + -
73N HIS* 4.3 12.9 + - + +
83N PHE* 4.8 17.0 - - + -
85N LEU* 4.8 26.7 - - + -
105N LEU* 3.0 26.1 + - + +
106N ALA* 3.9 5.4 - - - +
108N TYR* 1.3 76.3 - - + +
110N THR* 1.3 57.3 + - - +
112N LEU* 3.6 17.6 - - + +
113N GLU* 3.0 30.1 + - - +
118N PHE* 6.0 2.7 - - + -
128N LEU* 4.6 21.5 - - + -
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Residues in contact with THR 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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73N HIS* 3.1 36.1 + - + -
106N ALA* 2.5 24.2 + - - +
107N GLY* 3.7 7.6 - - - -
108N TYR 3.2 0.2 - - - -
109N LEU* 1.3 76.6 - - - +
111N THR* 1.3 60.7 + - + +
113N GLU* 3.3 4.3 + - - +
114N LEU* 2.9 50.7 + - + +
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Residues in contact with THR 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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197D ASN* 4.6 17.5 - - - +
275D LYS* 4.3 19.5 + - - +
107N GLY* 3.0 19.7 + - - +
108N TYR* 3.1 12.3 + - - -
110N THR* 1.3 74.9 - - + +
112N LEU* 1.3 65.0 + - - +
114N LEU* 4.3 6.5 - - + -
115N GLU* 2.9 38.1 + - - +
153N ASN* 4.6 9.1 + - - -
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Residues in contact with LEU 112 (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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108N TYR 2.9 20.3 + - - +
109N LEU* 3.6 17.5 - - + +
110N THR 3.3 0.2 - - - -
111N THR* 1.3 76.9 + - - +
113N GLU* 1.3 55.2 + - - +
115N GLU* 5.7 0.2 - - - -
116N SER* 2.4 50.1 + - - +
118N PHE* 3.7 38.4 - - + -
149N ILE* 3.8 24.5 - - + -
150N ASP* 3.8 20.4 - - + +
152N SER* 5.1 1.3 - - - +
153N ASN* 3.5 24.7 - - - +
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Residues in contact with GLU 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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73N HIS* 5.7 1.1 - - + +
75N LYS* 5.4 12.3 - - + -
76N TYR* 3.2 41.1 + - + +
81N LEU* 5.6 2.5 - - + -
83N PHE* 5.5 10.1 - - + -
109N LEU 3.0 18.2 + - - +
110N THR* 3.3 5.1 + - - +
112N LEU* 1.3 77.3 - - - +
114N LEU* 1.3 63.8 + - + +
117N SER* 3.1 21.7 + - - -
118N PHE* 2.8 22.7 + - + +
119N VAL* 2.6 47.9 + - + +
120N SER* 4.0 1.2 + - - -
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Residues in contact with LEU 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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75N LYS* 4.0 36.8 - - + +
110N THR* 2.9 40.5 + - + +
111N THR* 3.3 6.2 + - + +
113N GLU* 1.3 78.6 - - + +
115N GLU* 1.3 76.6 + - - +
117N SER 5.0 0.2 - - - -
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Residues in contact with GLU 115 (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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268D THR* 5.6 1.6 - - - +
272D VAL* 3.7 36.1 - - + +
275D LYS* 5.6 4.2 + - - -
111N THR* 2.9 26.3 + - - +
112N LEU* 5.7 0.2 - - - -
114N LEU* 1.3 95.3 - - - +
116N SER* 1.3 58.4 + - - +
117N SER 3.8 0.4 - - - -
152N SER* 6.1 0.9 - - - +
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Residues in contact with SER 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 LEU* 2.4 37.8 + - - +
115N GLU* 1.3 78.2 - - - +
117N SER* 1.3 69.5 + - - +
118N PHE* 3.3 21.2 - - - +
150N ASP* 4.5 9.6 - - - -
152N SER* 6.1 0.4 - - - -
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Residues in contact with SER 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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76N TYR* 3.0 18.6 + - - -
113N GLU* 3.1 24.0 + - - -
115N GLU 3.8 0.6 - - - -
116N SER* 1.3 80.4 - - - +
118N PHE* 1.3 65.1 + - - +
120N SER* 3.3 19.7 + - - -
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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