Contacts of the helix formed by residues 98 - 108 (chain M) in PDB entry 3J7Y
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96M LEU 3.9 0.6 + - - -
97M SER* 1.3 73.4 - - - +
99M ASN* 1.3 55.6 + - - +
101M LEU* 3.2 8.4 + - + +
102M GLN 2.9 24.4 + - - -
140M LEU* 4.1 11.9 - - + -
141M VAL 3.3 19.8 + - - +
142M GLU* 4.5 2.7 - - - -
144M GLY 3.1 27.7 - - - +
145M ALA* 3.8 10.1 - - + -
148M PHE* 3.5 38.3 - - + -
163M ALA* 3.9 14.4 - - + +
166M ALA* 3.7 24.7 - - + -
167M ILE* 3.9 24.9 - - + -
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Residues in contact with ASN 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M SER* 3.1 5.8 - - - +
98M LEU* 1.3 78.9 - - - +
100M ARG* 1.3 57.8 + - - +
102M GLN* 3.2 7.5 + - - +
103M TYR* 2.9 27.7 + - - +
143M GLU* 4.7 10.3 + - - +
144M GLY* 3.6 23.9 - - - +
147M THR* 5.0 11.3 + - - +
70g SER* 3.1 31.0 + - - +
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Residues in contact with ARG 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3796 ILE* 4.3 16.7 - - + +
3806 TYR* 3.2 33.9 + - - +
1882A A 3.3 17.4 + - - -
1883A G 2.6 36.0 + - - -
1891A A 5.5 6.1 + - - -
96M LEU* 3.9 8.5 - - + -
97M SER* 2.9 21.7 + - - +
99M ASN* 1.3 79.7 - - - +
101M LEU* 1.3 57.9 + - - +
103M TYR* 3.2 17.1 + - + +
104M LEU* 2.9 53.4 + - - +
109M ARG* 4.6 0.2 - - - +
125M ARG 4.1 1.0 + - - -
126M GLY* 2.5 39.0 + - - -
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Residues in contact with LEU 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M LEU* 3.7 25.9 - - + +
97M SER 3.1 2.7 + - - +
98M LEU* 3.2 10.7 + - + +
100M ARG* 1.3 77.8 - - - +
102M GLN* 1.3 58.2 + - - +
104M LEU* 3.2 7.9 + - + +
105M ILE* 2.9 49.3 + - + +
110M VAL* 4.5 15.3 - - + -
116M ILE* 5.2 8.1 - - + -
121M LEU* 5.1 6.3 - - + -
140M LEU* 4.4 14.6 - - + -
148M PHE* 4.3 18.6 - - + -
152M VAL* 5.2 1.8 - - + -
154M ILE* 3.6 31.4 - - + -
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Residues in contact with GLN 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M LEU 2.9 8.9 + - - +
99M ASN* 3.3 13.0 - - - +
101M LEU* 1.3 75.1 - - - +
103M TYR* 1.3 58.4 + - - +
105M ILE* 3.2 14.6 + - - +
106M ASP* 2.9 48.8 + - - +
147M THR 4.2 4.7 - - - +
148M PHE* 3.5 33.6 - - + -
149M THR 3.0 34.0 + - - +
150M ALA* 4.0 6.4 + - - +
69g PRO* 3.4 37.6 + - - +
70g SER* 4.5 7.4 - - - -
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Residues in contact with TYR 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3796 ILE* 6.4 0.9 - - + -
1882A A 3.9 22.4 - - - -
1883A G 3.2 17.7 + - - -
99M ASN 2.9 13.0 + - - +
100M ARG* 3.3 26.2 - - + +
102M GLN* 1.3 77.7 - - - +
104M LEU* 1.3 59.0 + - - +
106M ASP* 3.2 11.2 + - + +
107M LEU* 2.9 61.1 + - + +
109M ARG* 4.1 9.9 - - - -
70g SER* 3.6 19.5 - - - +
72g TRP* 5.1 7.9 - + + -
91g MET* 3.8 0.3 - - - +
93g ASN* 3.1 37.4 + - - -
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Residues in contact with LEU 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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96M LEU* 5.2 3.6 - - + -
100M ARG* 2.9 33.6 + - - +
101M LEU* 3.3 14.6 - - + +
103M TYR* 1.3 78.1 - - + +
105M ILE* 1.3 61.1 + - - +
107M LEU* 3.2 12.6 + - - +
108M GLY 3.2 4.3 + - - -
109M ARG* 2.5 62.5 - - + +
110M VAL* 4.1 20.2 - - + -
121M LEU* 4.4 13.2 - - + -
124M GLY 5.3 0.4 - - - +
126M GLY* 3.7 36.1 - - - +
127M VAL 5.2 0.2 - - - +
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Residues in contact with ILE 105 (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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101M LEU* 2.9 36.8 + - + +
102M GLN* 3.2 20.4 + - - +
104M LEU* 1.3 75.9 - - - +
106M ASP* 1.3 66.4 - - - +
108M GLY* 3.3 13.5 + - - +
110M VAL* 3.9 21.9 - - + +
112M PRO* 3.9 35.8 - - + +
116M ILE* 5.8 0.7 - - + -
148M PHE* 5.6 0.2 - - + -
149M THR 5.4 2.5 - - - +
150M ALA* 3.9 27.8 - - + -
152M VAL* 4.6 3.6 - - + -
61g PRO* 4.6 4.7 - - - +
63g HIS* 4.8 3.9 - - + -
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Residues in contact with ASP 106 (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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102M GLN* 2.9 38.1 + - - +
103M TYR* 3.4 7.6 - - + +
105M ILE* 1.3 78.7 - - - +
107M LEU* 1.3 69.5 + - + +
108M GLY 3.3 1.6 + - - -
60g PRO* 4.0 4.5 - - - +
61g PRO* 3.5 9.0 - - - +
63g HIS* 3.0 29.0 + - - +
68g THR* 3.1 33.8 - - + +
69g PRO* 2.6 23.0 - - - +
70g SER* 3.7 5.2 - - - -
72g TRP* 5.1 7.9 - - + -
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Residues in contact with LEU 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M TYR* 2.9 58.8 + - + +
104M LEU 3.2 5.5 + - - +
106M ASP* 1.3 81.2 - - + +
108M GLY* 1.3 54.8 + - - +
109M ARG* 3.4 30.2 + - - +
57g ILE* 6.3 0.4 - - + -
58g PRO* 4.1 10.7 - - - +
59g ASP 4.5 0.2 - - - -
60g PRO* 3.4 26.4 - - + +
72g TRP* 4.2 30.5 - - + +
91g MET* 3.1 31.2 - - + +
92g HIS* 5.1 4.6 - - + -
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Residues in contact with GLY 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M LEU 3.2 4.2 + - - -
105M ILE 3.3 5.7 + - - -
106M ASP 3.2 5.1 - - - -
107M LEU* 1.3 75.3 - - - +
109M ARG* 1.3 63.3 + - - +
110M VAL 3.6 10.5 + - - +
111M ASP* 4.2 6.2 + - - +
112M PRO* 5.9 0.2 - - - +
58g PRO* 4.5 7.6 - - - -
59g ASP 5.3 1.1 - - - -
60g PRO* 4.7 0.4 - - - -
61g PRO* 3.4 20.6 - - - -
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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