Contacts of the helix formed by residues 94 - 114 (chain N) in PDB entry 5KZ5
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 ALA 94 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N THR 3.7 2.7 + - - -
93N HIS* 1.4 78.7 + - + +
95N TYR* 1.4 68.8 + - + +
97N TRP* 3.5 5.6 + - - +
98N GLU* 3.4 29.8 + - - +
454R TRP* 4.2 27.0 + - + +
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Residues in contact with TYR 95 (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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82N ILE 3.6 23.1 + - - -
83N ASN* 3.6 38.7 - - + +
84N TYR* 4.1 1.4 - - - -
85N TYR 4.2 11.0 - - - +
86N GLY 4.4 3.4 - - - +
87N ASN* 3.8 19.1 - - - -
93N HIS* 3.4 25.3 - + + +
94N ALA* 1.4 86.7 - - + +
96N GLY* 1.3 57.6 + - - +
98N GLU* 3.6 3.0 + - - -
99N SER* 3.1 28.8 + - - -
454R TRP* 4.0 14.4 - + - -
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Residues in contact with GLY 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N GLY 4.2 11.2 + - - -
87N ASN 4.4 7.6 - - - -
88N PRO* 5.4 5.2 - - - -
93N HIS* 3.3 14.1 + - - -
94N ALA 3.2 0.6 - - - -
95N TYR* 1.3 77.0 - - - +
97N TRP* 1.4 60.0 + - - +
99N SER* 3.4 4.9 + - - -
100N GLU* 3.2 29.7 + - - +
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Residues in contact with TRP 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N THR* 5.2 11.2 - - + +
93N HIS 3.0 17.3 + - - +
94N ALA* 3.8 5.8 - - - +
96N GLY* 1.4 71.6 - - - +
98N GLU* 1.3 84.8 - - + +
100N GLU* 3.7 5.7 + - - +
101N ALA* 3.3 29.6 + - + +
451R SER* 4.3 17.3 - - - -
453R LYS 6.1 0.4 - - - -
454R TRP* 5.4 11.0 - + + -
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Residues in contact with GLU 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N ASN* 3.1 45.3 + - - +
84N TYR* 3.3 31.8 + - + -
94N ALA 3.4 16.1 + - - +
95N TYR* 3.9 0.6 - - - +
96N GLY 3.4 0.2 - - - -
97N TRP* 1.3 94.7 - - + +
99N SER* 1.3 56.9 + - - +
101N ALA* 3.5 5.1 + - - +
102N ALA* 3.1 23.2 + - - +
451R SER* 5.2 5.8 - - - +
454R TRP* 3.3 50.0 - - + +
457R HIS 3.9 0.2 - - - +
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Residues in contact with SER 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N TYR* 3.1 30.6 + - - +
85N TYR* 4.5 1.0 + - - -
86N GLY 4.6 9.0 + - - -
95N TYR 3.1 18.5 + - - -
96N GLY* 3.6 8.5 - - - -
97N TRP 3.4 0.2 - - - -
98N GLU* 1.3 73.0 - - - +
100N GLU* 1.4 64.6 + - - +
102N ALA* 3.5 3.8 + - - +
103N MET* 3.1 23.4 + - - +
298N THR* 3.4 22.7 - - - +
299N PRO* 4.8 2.9 - - - +
302N VAL* 4.2 3.9 - - - +
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Residues in contact with GLU 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N GLY 3.2 17.3 + - - +
97N TRP* 4.0 6.5 - - - +
98N GLU 3.5 0.2 - - - -
99N SER* 1.4 72.3 + - - +
101N ALA* 1.4 59.3 + - - +
103N MET* 3.4 20.9 + - - +
104N GLU* 2.9 49.4 + - - +
298N THR* 3.5 28.4 + - - +
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Residues in contact with ALA 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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97N TRP* 3.3 27.3 + - + +
98N GLU* 3.8 7.4 - - - +
99N SER 3.4 0.2 - - - -
100N GLU* 1.4 74.5 - - - +
102N ALA* 1.4 62.9 + - - +
104N GLU* 3.3 9.4 + - - +
105N ARG* 3.2 27.0 + - - +
450R LYS* 4.6 7.2 - - + -
451R SER* 5.3 7.6 - - - +
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Residues in contact with ALA 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N TYR* 4.6 0.2 - - + -
84N TYR* 3.9 14.6 - - + -
98N GLU 3.1 17.7 + - - +
99N SER* 3.7 5.2 - - - +
100N GLU 3.4 0.2 - - - -
101N ALA* 1.4 71.4 - - - +
103N MET* 1.3 60.4 + - - +
105N ARG* 3.5 4.0 + - - +
106N ALA* 3.0 29.5 + - - +
302N VAL* 3.7 24.1 - - + +
450R LYS* 3.7 28.9 - - + +
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Residues in contact with MET 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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99N SER 3.1 10.9 + - - +
100N GLU* 3.4 41.3 - - - +
102N ALA* 1.3 78.9 - - - +
104N GLU* 1.3 68.5 + - - +
106N ALA* 3.8 3.3 - - - +
107N ARG* 2.8 43.4 + - + +
298N THR* 3.7 20.0 - - + +
301N VAL* 3.8 37.0 - - + +
302N VAL* 3.7 14.5 - - + +
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Residues in contact with GLU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N GLU* 2.9 38.0 + - - +
101N ALA* 3.3 12.0 + - - +
103N MET* 1.3 94.6 - - - +
105N ARG* 1.4 60.6 + - + +
107N ARG* 3.7 8.7 + - - +
108N GLN* 3.6 19.9 + - - +
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Residues in contact with ARG 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 ALA 3.2 16.5 + - - +
102N ALA 3.8 6.7 - - - +
104N GLU* 1.4 76.0 - - + +
106N ALA* 1.3 59.0 + - - +
108N GLN* 3.9 15.0 + - - +
109N GLN* 3.1 24.5 + - - +
309N GLU* 3.8 3.8 - - - +
447R ILE 3.2 28.7 + - - -
448R ASP* 3.8 30.4 - - - +
450R LYS* 3.9 29.0 - - + +
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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
----------------------------------------------------------
102N ALA 3.0 18.3 + - - +
103N MET 3.8 3.4 - - - +
105N ARG* 1.3 75.4 - - - +
107N ARG* 1.4 62.9 + - - +
109N GLN* 3.1 22.2 + - - +
110N VAL* 4.0 0.9 - - - +
301N VAL 3.9 2.5 - - - +
302N VAL* 3.8 23.6 - - + +
305N GLY* 3.3 21.2 - - - +
306N ALA* 3.7 23.1 - - + +
309N GLU* 5.4 1.3 - - - -
450R LYS* 5.3 1.3 - - - +
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Residues in contact with ARG 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N MET* 2.8 27.7 + - - +
104N GLU* 4.0 8.7 - - - +
106N ALA* 1.4 74.3 - - - +
108N GLN* 1.3 58.2 + - - +
110N VAL* 3.1 18.8 - - + +
111N ALA* 2.8 35.6 + - + +
121N ILE* 4.1 34.4 - - - +
288N GLU* 5.6 3.8 + - - -
301N VAL* 3.6 33.3 - - + +
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Residues in contact with GLN 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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104N GLU 3.6 10.4 + - - +
105N ARG* 4.0 20.8 + - - +
106N ALA 3.4 0.8 - - - -
107N ARG* 1.3 77.6 - - - +
109N GLN* 1.4 68.3 + - - +
111N ALA* 3.5 8.1 + - + +
112N SER* 3.3 20.6 + - - -
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Residues in contact with GLN 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 ARG 3.1 15.9 + - - +
106N ALA* 3.1 20.2 - - - +
107N ARG 3.3 0.6 - - - -
108N GLN* 1.4 84.4 + - - +
110N VAL* 1.3 62.5 + - - +
112N SER* 3.5 16.1 + - - -
113N LEU* 4.1 2.8 + - - +
305N GLY 3.6 14.9 - - - +
308N CYS* 4.5 9.6 - - + -
309N GLU* 3.0 48.6 + - + +
312N GLN* 4.8 13.7 - - + -
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Residues in contact with VAL 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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106N ALA 4.0 2.5 - - - +
107N ARG* 3.1 36.6 - - + +
109N GLN* 1.3 78.8 - - - +
111N ALA* 1.3 55.4 + - - +
113N LEU* 3.0 29.0 + - + +
114N ILE* 3.1 19.4 - - + +
269N TYR* 5.7 2.0 - - - +
301N VAL* 5.4 5.6 - - + +
304N LEU* 4.4 9.2 - - + +
305N GLY* 4.1 22.9 - - - +
308N CYS* 4.1 20.6 - - + -
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Residues in contact with ALA 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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107N ARG* 2.8 25.7 + - + +
108N GLN* 3.5 11.9 - - + +
110N VAL* 1.3 72.0 - - - +
112N SER* 1.4 65.1 + - - +
114N ILE* 3.1 23.9 + - - +
115N GLY 3.3 8.1 + - - -
116N ALA* 4.0 6.1 + - - -
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Residues in contact with SER 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 GLN 3.3 9.1 + - - -
109N GLN* 3.6 12.1 - - - -
110N VAL 3.2 0.8 - - - -
111N ALA* 1.4 78.4 - - - +
113N LEU* 1.4 59.9 + - - +
115N GLY* 3.3 11.4 + - - -
245N ASN* 3.3 12.5 + - - +
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Residues in contact with LEU 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 GLN 4.1 1.7 + - - +
110N VAL* 3.0 19.7 + - + +
112N SER* 1.4 77.0 - - - +
114N ILE* 1.3 63.0 + - - +
242N LEU* 3.5 46.4 - - + +
243N ASP* 3.6 14.8 - - - +
244N VAL* 4.0 15.4 - - + +
245N ASN* 3.4 14.0 + - - +
252N MET* 4.4 3.1 - - - -
254N ILE* 3.9 27.8 - - + -
269N TYR* 4.1 19.1 - - + +
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Residues in contact with ILE 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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110N VAL* 3.1 35.2 - - + +
111N ALA* 3.1 13.9 + - - +
113N LEU* 1.3 75.8 - - + +
115N GLY* 1.4 58.1 + - - +
116N ALA* 3.4 23.1 - - - +
117N ASP 4.9 1.1 - - - +
120N GLU* 3.0 44.0 - - + +
121N ILE* 3.9 21.5 - - + -
244N VAL* 4.8 3.1 - - - +
269N TYR* 3.4 48.9 - - + +
271N ARG* 4.7 8.1 - - - -
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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
------------------------------------------------------------
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