Contacts of the helix formed by residues 95 - 104 (chain M) in PDB entry 2JA7
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 PHE 95 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21M LEU* 3.4 36.1 - - + -
92M HIS* 2.4 55.0 + + + +
94M GLY* 1.3 70.9 - - - -
96M ILE* 1.3 66.9 + - - +
97M ALA 3.0 3.1 - - - -
98M LYS* 2.5 22.6 + - + +
99M ILE* 3.0 12.0 + - + -
233M TRP 5.2 1.3 - - - -
234M MET* 3.4 49.8 - - + -
236M LEU* 6.3 0.4 - - + -
1410M PHE* 3.7 33.0 - - + -
1411M GLU* 4.7 3.8 - - + -
1414M ALA* 3.7 15.7 - - + -
1211N ASN* 5.8 1.8 - - - -
1212N ILE* 4.6 2.5 - - + -
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Residues in contact with ILE 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M PHE* 3.7 40.2 - - + -
92M HIS 3.4 2.8 + - - +
93M VAL* 4.0 26.0 - - + +
94M GLY 3.5 0.2 - - - -
95M PHE* 1.3 74.9 - - - +
97M ALA* 1.3 69.4 + - - +
98M LYS 3.0 0.9 + - - -
99M ILE* 3.1 11.2 + - - +
100M LYS* 3.0 23.1 + - + +
176M LYS* 4.3 33.2 - - + +
178M GLY 5.1 1.3 - - - +
179M LEU* 4.2 32.5 - - + -
181M LEU* 4.9 12.5 - - + +
297M GLN* 4.9 1.6 - - - +
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Residues in contact with ALA 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M GLY 4.3 11.3 + - - +
95M PHE 2.7 4.3 + - - +
96M ILE* 1.3 80.2 - - - +
98M LYS* 1.3 58.5 + - + +
100M LYS* 3.5 7.5 - - - +
101M LYS* 3.1 33.1 + - + +
176M LYS* 6.4 0.4 - - - -
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Residues in contact with LYS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PHE* 2.5 16.4 + - + +
97M ALA* 1.3 74.2 - - + +
99M ILE* 1.3 69.4 + - - +
100M LYS 2.5 4.0 + - - -
101M LYS* 2.6 19.2 + - + +
102M VAL* 2.6 15.6 + - + +
135M PHE* 4.0 35.9 - - + -
223M GLY* 4.1 13.3 + - - -
224M PHE* 4.5 13.8 - - + -
234M MET* 4.0 21.5 - - + -
1411M GLU* 4.2 26.3 - - + +
1414M ALA* 4.7 12.4 + - + +
1415M SER* 3.2 25.3 + - - -
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Residues in contact with ILE 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M PHE* 3.5 49.8 - - + -
92M HIS 4.6 0.2 - - - +
95M PHE* 3.0 13.2 + - + +
96M ILE* 3.6 9.6 - - - +
98M LYS* 1.3 78.5 - - - +
100M LYS* 1.3 62.4 + - - +
102M VAL* 4.5 2.2 - - - -
103M CYS* 3.3 16.6 + - - -
181M LEU* 4.3 4.7 - - + -
207M ILE* 4.0 18.2 - - + -
211M PHE* 3.5 19.6 - - + -
234M MET* 3.5 44.1 - - + +
235M ILE* 3.7 9.9 - - + -
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Residues in contact with LYS 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 T 5.8 2.6 + - - -
96M ILE* 3.0 11.2 + - + +
97M ALA* 3.5 11.2 - - - +
98M LYS 2.5 4.0 + - - -
99M ILE* 1.3 69.8 - - - +
101M LYS* 1.3 57.5 - - + +
102M VAL 2.7 15.4 + - - -
103M CYS* 2.8 18.2 + - - +
104M GLU* 3.1 47.7 + - - +
139M TRP* 5.1 7.1 - - - -
174M ILE* 4.3 26.2 + - + +
175M ARG* 4.9 6.7 - - - +
176M LYS* 4.9 10.8 - - - +
181M LEU* 3.6 35.4 - - + +
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Residues in contact with LYS 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 T 3.6 22.6 + - - -
97M ALA* 3.1 19.7 + - + +
98M LYS* 2.6 11.9 + - + +
100M LYS* 1.3 81.0 - - + +
102M VAL* 1.3 59.0 + - - +
104M GLU* 3.9 6.3 - - - +
105M CYS* 3.3 10.7 + - - -
135M PHE* 4.0 25.1 - - + -
139M TRP* 3.1 70.5 - - + +
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Residues in contact with VAL 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M LYS* 2.6 28.8 + - + +
99M ILE 3.7 5.8 - - - +
100M LYS 2.7 2.8 + - - -
101M LYS* 1.3 72.6 - - - +
103M CYS* 1.3 56.5 + - - +
105M CYS* 2.6 33.6 + - - +
106M VAL* 3.0 7.4 + - + -
135M PHE* 4.3 17.3 - - + -
211M PHE* 3.6 22.0 - - + -
214M ILE* 4.3 19.1 - - + -
222M LEU* 4.4 13.7 - - + -
224M PHE* 4.6 9.0 - - + -
231M PRO* 5.1 3.1 - - + -
234M MET* 4.2 19.3 - - + -
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Residues in contact with CYS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M ILE* 3.3 14.5 + - - -
100M LYS* 2.8 9.3 + - - +
102M VAL* 1.3 80.1 - - - +
104M GLU* 1.3 58.0 + - - +
105M CYS 2.8 4.0 + - - -
106M VAL* 2.4 31.1 + - - +
108M MET* 3.4 26.3 - - + +
171M GLN* 4.6 2.1 - - - +
174M ILE* 3.8 21.5 - - + -
181M LEU* 5.3 1.6 - - - -
202M LEU* 5.2 0.2 - - - -
207M ILE* 3.4 24.7 - - - -
210M ILE* 5.9 0.7 - - - -
211M PHE* 3.7 15.9 - - - -
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Residues in contact with GLU 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100M LYS* 3.1 43.4 + - + +
101M LYS* 3.9 1.1 - - - +
103M CYS* 1.3 74.7 - - - +
105M CYS* 1.3 58.4 + - - +
114M LEU* 3.9 4.1 - - - +
139M TRP* 3.4 32.9 + - + +
142M CYS 3.2 23.4 - - - +
143M LYS* 3.8 18.1 - - - +
171M GLN* 4.8 1.8 - - - +
172M PRO 5.8 1.1 - - - +
173M THR* 4.8 5.2 - - - +
174M ILE* 3.5 43.9 + - + +
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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
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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