Contacts of the helix formed by residues 103 - 123 (chain N) in PDB entry 5GSE
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 103 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M GLU* 2.7 52.8 - - + +
95M LYS* 4.3 19.3 - - + -
96M LEU* 4.1 22.7 - - + +
101N LEU 3.9 4.9 - - - +
102N LEU* 1.3 89.1 - - + +
104N GLY* 1.3 62.1 + - - +
106N LEU* 3.4 14.7 + - + +
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Residues in contact with GLY 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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92M GLU* 3.5 5.6 - - - -
102N LEU 3.8 3.4 + - - -
103N PRO* 1.3 70.0 - - - +
105N GLU* 1.3 68.2 + - - -
107N ALA* 2.9 23.4 + - - +
108N LYS* 3.5 6.1 + - - +
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Residues in contact with GLU 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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92M GLU* 3.0 17.1 + - + +
104N GLY* 1.3 73.1 - - - -
106N LEU* 1.3 66.3 + - + +
108N LYS* 2.9 29.3 + - - +
109N HIS* 3.2 28.7 + - + +
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Residues in contact with LEU 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 4.1 16.0 - - + +
58M LEU* 4.1 21.8 - - + -
61M GLU* 4.6 13.7 - - + +
90M ASP* 5.1 1.1 - - - +
92M GLU* 3.8 29.4 - - + -
93M LEU* 3.5 32.1 - - + -
96M LEU* 4.2 9.4 - - + -
102N LEU* 3.9 11.9 - - + -
103N PRO* 3.4 21.7 + - + +
104N GLY 3.2 0.2 + - - -
105N GLU* 1.3 77.9 - - + +
107N ALA* 1.3 54.1 + - - +
109N HIS* 3.0 4.0 + - - +
110N ALA* 2.7 34.1 + - - +
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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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98N VAL* 4.1 11.8 - - - +
99N ARG* 4.4 14.0 - - + +
102N LEU* 3.7 36.3 - - + +
103N PRO 3.9 0.6 + - - -
104N GLY* 2.9 15.4 + - - +
106N LEU* 1.3 78.0 - - - +
108N LYS* 1.3 59.6 + - + +
110N ALA* 4.1 2.4 - - - +
111N VAL* 3.0 29.7 + - - +
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Residues in contact with LYS 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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99N ARG* 6.0 3.7 - - - +
104N GLY 3.5 6.4 + - - +
105N GLU* 2.9 26.7 + - - +
107N ALA* 1.3 77.6 - - + +
109N HIS* 1.3 66.3 + - + +
111N VAL* 3.0 32.0 + - + +
112N SER* 2.7 29.5 + - - -
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Residues in contact with HIS 109 (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 41.4 + + + +
105N GLU* 3.3 26.8 + - + +
106N LEU 3.0 2.9 + - - +
108N LYS* 1.3 76.5 - - + +
110N ALA* 1.3 58.8 + - - +
112N SER* 3.0 7.3 + - - -
113N GLU* 2.8 41.9 + - + +
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Residues in contact with ALA 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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50M TYR* 4.1 0.2 - - - -
54M VAL* 3.7 24.2 - - + +
57M TYR* 4.0 14.4 - - + -
58M LEU* 5.4 0.4 - - + -
98N VAL* 3.9 14.6 - - + -
102N LEU* 3.6 24.0 - - + -
106N LEU 2.7 20.0 + - - +
107N ALA 4.1 0.7 - - - +
109N HIS* 1.3 73.0 - - - +
111N VAL* 1.3 60.8 + - - +
113N GLU* 4.2 2.1 - - - +
114N GLY* 3.0 23.0 + - - -
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Residues in contact with VAL 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* 3.1 26.8 + - - +
95N GLN* 3.6 24.7 - - + +
98N VAL* 4.6 4.4 - - + +
99N ARG* 4.8 17.0 - - + -
107N ALA 3.0 18.1 + - - +
108N LYS* 3.0 47.4 + - - +
110N ALA* 1.3 76.6 - - - +
112N SER* 1.3 63.1 + - - +
115N THR* 3.2 24.1 + - - +
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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 LYS 2.7 13.6 + - - -
109N HIS* 3.0 11.6 + - - -
111N VAL* 1.3 76.0 - - - +
113N GLU* 1.3 70.5 + - - +
115N THR* 3.0 11.7 + - - +
116N LYS* 2.8 39.1 + - - +
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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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53M ALA* 4.1 18.4 - - + +
57M TYR* 4.1 29.3 - - + -
109N HIS* 2.8 25.6 + - - +
110N ALA 4.2 2.2 - - - +
112N SER* 1.3 73.7 + - - +
114N GLY* 1.3 63.4 + - - +
116N LYS* 3.0 31.7 + - - +
117N ALA* 2.8 27.5 + - - +
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Residues in contact with GLY 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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50M TYR* 3.5 42.8 - - - -
53M ALA* 3.6 17.2 - - - +
54M VAL* 4.4 0.9 - - - +
110N ALA 3.0 11.2 + - - -
113N GLU* 1.3 77.7 - - - +
115N THR* 1.3 61.3 + - - +
117N ALA* 3.9 2.1 - - - +
118N VAL* 3.2 17.3 + - - +
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Residues in contact with THR 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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50M TYR* 3.6 11.7 - - - -
95N GLN* 5.0 4.7 + - - -
111N VAL* 3.2 16.3 + - + +
112N SER* 3.0 24.2 + - - +
114N GLY* 1.3 74.9 - - - +
116N LYS* 1.3 68.3 + - + +
118N VAL* 3.0 31.8 - - - +
119N THR* 3.1 13.7 + - + +
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Residues in contact with LYS 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 SER* 2.8 31.1 + - - +
113N GLU* 3.5 39.0 + - - +
115N THR* 1.3 73.5 - - + +
117N ALA* 1.3 69.0 + - + +
119N THR* 2.9 27.1 + - - -
120N LYS* 2.9 12.6 + - + +
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Residues in contact with ALA 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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21M ALA 4.0 20.1 - - - +
23M LEU* 4.1 10.5 - - + -
49M VAL* 4.2 11.6 - - + +
53M ALA* 3.8 21.3 - - + -
113N GLU 2.8 20.5 + - - +
114N GLY 3.9 1.6 - - - +
116N LYS* 1.3 77.5 - - + +
118N VAL* 1.3 63.8 + - - +
120N LYS* 3.0 5.7 + - - +
121N TYR* 2.8 23.6 + - - +
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Residues in contact with VAL 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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46M GLY* 3.8 32.3 - - - +
49M VAL* 3.8 16.5 - - + +
50M TYR* 4.8 6.3 - - + -
91N SER* 4.9 9.6 - - - +
114N GLY 3.2 9.5 + - - +
115N THR* 3.0 31.3 + - - +
117N ALA* 1.3 78.8 - - - +
119N THR* 1.3 57.4 + - + +
121N TYR* 3.0 6.5 + - + +
122N THR* 2.5 43.2 + - - +
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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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115N THR* 3.2 20.6 - - + +
116N LYS* 2.9 15.9 + - - -
118N VAL* 1.3 79.7 - - + +
120N LYS* 1.3 62.6 + - - +
121N TYR 2.9 4.3 - - - -
122N THR* 3.0 20.9 + - - +
123N SER* 3.3 15.8 + - - -
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Residues in contact with LYS 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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20M ARG* 2.9 27.7 - - - +
21M ALA 3.8 15.3 - - - +
22M GLY* 4.9 8.5 - - - -
116N LYS* 2.9 12.1 + - + +
117N ALA* 3.4 9.0 - - - +
119N THR* 1.3 81.1 + - - +
121N TYR* 1.3 56.6 + - - +
123N SER* 3.8 16.4 + - - +
124N ALA 5.0 0.7 - - - +
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Residues in contact with TYR 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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17M ARG* 3.2 55.2 + - + +
20M ARG* 3.8 30.3 - - + +
21M ALA* 4.2 5.6 - - + -
27M VAL* 5.9 0.4 - - + -
45M ALA* 4.4 25.0 + - + +
46M GLY* 5.7 0.4 - - - -
49M VAL* 4.1 24.7 - - + -
117N ALA 2.8 11.2 + - - +
118N VAL* 3.3 11.0 - - + +
119N THR 2.9 0.2 - - - -
120N LYS* 1.3 78.3 - - - +
122N THR* 1.3 69.8 + - - +
123N SER 3.3 1.2 + - - -
124N ALA* 3.5 15.2 + - - +
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Residues in contact with THR 122 (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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118N VAL* 2.5 34.4 + - - +
119N THR* 3.0 10.0 + - - +
121N TYR* 1.3 77.8 - - - +
123N SER* 1.3 51.5 + - - +
124N ALA* 2.7 18.7 + - - +
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Residues in contact with SER 123 (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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119N THR 3.3 12.7 + - - -
120N LYS* 3.8 14.7 + - - +
121N TYR 3.7 1.6 - - - -
122N THR* 1.3 72.3 - - - +
124N ALA* 1.3 68.3 + - - +
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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