Contacts of the helix formed by residues 103 - 118 (chain E) in PDB entry 1NJI
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 ASN 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A G 3.7 8.1 - - - +
657A G 3.7 11.5 + - - +
663A C 3.7 30.3 + - - +
664A U 3.6 7.1 + - - +
749A C 2.7 48.1 + - - -
750A A 3.4 11.2 + - - +
102E LEU* 1.3 77.4 - - - +
104E ASP* 1.3 67.2 + - - +
105E LYS* 4.3 0.9 - - + +
106E GLU* 3.0 23.2 + - + +
107E ARG* 2.8 20.3 + - - +
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Residues in contact with ASP 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A U 3.2 40.4 + - - +
678A G 4.9 0.2 + - - -
680A G 4.3 7.4 - - - +
681A G 5.0 2.8 - - - +
102E LEU 3.3 2.1 + - - +
103E ASN* 1.3 69.8 - - - +
105E LYS* 1.3 53.8 + - + +
107E ARG* 2.8 35.1 + - - +
108E GLN* 2.7 51.7 + - - +
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Residues in contact with LYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A G 3.6 14.6 - - - +
658A C 3.1 40.9 + - - +
662A U 3.4 13.7 + - - -
663A C 3.0 37.9 + - - +
664A U 4.9 2.1 + - - +
103E ASN* 3.1 1.9 - - + +
104E ASP* 1.3 76.4 - - + +
106E GLU* 1.3 58.7 + - - +
108E GLN* 3.9 11.0 - - - +
109E LEU* 2.9 30.8 + - - +
112E ARG* 5.4 1.3 + - - +
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A G 3.2 40.1 + - - +
657A G 3.3 35.5 + - - +
750A A 5.1 0.9 - - - -
30E LEU* 4.3 13.8 - - + +
33E LYS* 2.8 36.9 + - + +
34E ALA* 5.6 0.2 - - - +
102E LEU* 4.2 13.5 - - + +
103E ASN* 3.0 21.3 + - + +
105E LYS* 1.3 79.7 - - - +
107E ARG* 1.3 62.1 + - - +
109E LEU* 3.7 6.2 - - - +
110E ALA* 3.2 20.6 + - - +
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A C 5.0 0.4 - - - -
677A C 3.1 38.2 + - - +
678A G 2.6 31.3 + - - -
34E ALA* 4.5 9.0 - - + -
102E LEU* 3.9 32.2 + - + +
103E ASN 2.8 11.2 + - - +
104E ASP* 2.8 41.9 + - - +
106E GLU* 1.3 75.3 - - - +
108E GLN* 1.3 80.4 + - - +
110E ALA* 3.1 7.5 + - - +
111E VAL* 3.0 28.6 + - + +
220E THR* 5.0 0.9 - - - +
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Residues in contact with GLN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A G 2.7 31.5 + - - +
679A G 4.7 9.9 + - - -
104E ASP* 2.7 37.2 + - - +
105E LYS* 4.0 10.6 - - - +
107E ARG* 1.3 86.9 - - - +
109E LEU* 1.3 62.6 + - - +
111E VAL* 3.0 12.2 + - + +
112E ARG* 2.9 56.5 + - - +
246E ARG* 5.2 3.7 + - - +
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A G 4.1 23.6 - - - +
658A C 4.3 7.0 - - - +
24E THR* 4.2 21.3 - - + -
25E PRO* 5.9 0.7 - - + +
27E ARG* 5.2 5.6 - - + +
30E LEU* 3.6 27.8 - - + -
105E LYS 2.9 18.8 + - - +
106E GLU* 3.7 5.8 - - - +
108E GLN* 1.3 77.2 - - - +
110E ALA* 1.3 56.1 + - - +
112E ARG* 3.2 16.0 + - + +
113E SER* 2.8 29.0 + - - -
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LEU* 3.4 36.5 - - + +
31E ILE* 3.8 6.1 - - - +
34E ALA* 3.8 16.8 - - + -
106E GLU 3.2 9.8 + - - +
107E ARG 3.1 9.7 + - - +
109E LEU* 1.3 79.9 - - - +
111E VAL* 1.3 57.6 + - - +
113E SER* 3.3 7.3 + - - -
114E ALA* 2.8 30.8 + - - +
220E THR* 4.3 3.0 + - - +
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Residues in contact with VAL 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A C 4.4 13.7 - - - +
107E ARG* 3.0 23.5 + - + +
108E GLN* 3.0 11.8 + - + +
110E ALA* 1.3 73.8 - - - +
112E ARG* 1.3 62.0 + - + +
114E ALA* 3.3 4.7 + - - +
115E LEU* 2.9 35.8 + - + +
218E VAL* 4.4 7.9 - - + +
219E ASN* 5.0 0.4 - - - -
220E THR* 3.4 25.8 - - - +
223E LEU* 4.1 11.4 - - + +
246E ARG* 4.1 36.6 - - + +
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 3.9 16.7 - - + +
24E THR* 3.9 22.4 - - + +
105E LYS* 5.4 1.4 + - - +
108E GLN* 2.9 50.0 + - - +
109E LEU* 3.6 15.7 - - - +
111E VAL* 1.3 75.5 - - + +
113E SER* 1.3 61.9 + - - +
115E LEU* 3.2 12.7 - - + +
116E ALA* 3.0 22.7 + - - +
246E ARG 2.8 39.4 + - - -
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 4.0 11.2 - - - +
25E PRO 3.1 10.9 + - - -
26E VAL* 3.2 4.5 - - - +
27E ARG* 2.5 39.8 + - - -
31E ILE* 3.9 10.5 - - - +
109E LEU* 2.8 19.0 + - - -
110E ALA* 3.7 6.5 - - - -
112E ARG* 1.3 78.3 - - - +
114E ALA* 1.3 62.3 + - - +
116E ALA* 3.3 5.7 + - - +
117E ALA* 3.0 21.7 + - - +
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 3.7 19.7 - - + +
110E ALA 2.8 18.6 + - - +
111E VAL* 3.7 4.3 - - - +
113E SER* 1.3 74.4 - - - +
115E LEU* 1.3 68.7 + - - +
117E ALA* 3.4 10.7 + - - +
118E THR* 3.4 13.3 + - - -
220E THR* 4.5 5.6 - - + -
223E LEU* 3.8 28.8 - - + +
224E ALA* 4.3 13.2 - - + -
229E PRO* 5.5 0.2 - - - -
230E GLY 5.1 1.0 + - - -
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 4.5 12.1 - - + +
22E PHE* 3.5 17.4 - - + -
111E VAL* 2.9 23.1 + - + +
112E ARG* 3.2 16.4 - - + +
114E ALA* 1.3 76.9 - - - +
116E ALA* 1.3 56.5 + - - +
118E THR* 2.8 30.0 + - - +
218E VAL* 5.2 3.6 - - + -
223E LEU* 3.4 25.1 - - + +
235E PHE* 3.9 28.5 - - + -
243E VAL* 3.3 40.6 - - + +
246E ARG* 4.8 6.5 - - + -
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Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL 3.6 15.5 + - - +
22E PHE* 3.7 21.8 - - - +
24E THR 2.9 29.6 - - - +
26E VAL* 4.3 4.5 - - + +
112E ARG 3.0 5.4 + - - +
113E SER 3.4 7.4 - - - +
115E LEU* 1.3 75.9 - - - +
117E ALA* 1.3 61.7 + - - +
118E THR 2.8 7.0 + - - -
119E ALA* 2.9 18.2 + - - +
120E ASP* 4.1 3.6 + - - +
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Residues in contact with ALA 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 3.6 22.8 - - + +
113E SER 3.0 10.3 + - - +
114E ALA 3.8 7.6 - - - +
115E LEU 3.3 0.4 - - - -
116E ALA* 1.3 75.8 - - - +
118E THR* 1.3 61.6 + - - +
119E ALA 3.3 0.5 + - - -
120E ASP* 3.4 15.8 + - - +
123E LEU* 3.9 9.5 - - + +
124E VAL* 4.0 3.6 - - - +
229E PRO* 3.7 17.3 - - + -
230E GLY* 3.6 33.0 - - - +
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Residues in contact with THR 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E PHE* 4.4 1.8 - - + -
114E ALA 3.4 9.6 + - - -
115E LEU* 2.8 18.9 + - - +
116E ALA 2.8 0.6 - - - -
117E ALA* 1.3 80.5 - - - +
119E ALA* 1.3 55.2 + - - +
120E ASP 3.3 0.8 + - - -
124E VAL* 3.8 7.0 - - - +
136E VAL* 3.0 21.5 - - - +
137E PRO* 3.5 28.4 - - + +
223E LEU* 4.5 10.6 + - - +
230E GLY* 4.7 1.3 - - - -
231E ARG 3.7 14.1 + - - +
233E THR* 3.5 29.4 + - - +
235E PHE* 3.8 9.2 - - + -
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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