Contacts of the helix formed by residues 117 - 125 (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 ASP 117 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115M PRO* 3.4 9.6 + - + +
116M ILE* 1.3 78.6 - - - +
118M LEU* 1.3 71.3 + - - +
119M THR* 2.6 41.6 + - - +
120M GLN* 3.2 16.0 + - + +
121M LEU* 3.2 14.5 + - - +
155M GLU* 3.8 12.7 - - + +
179M TYR* 2.5 27.7 + - - -
187M VAL* 4.5 0.5 - - - +
260M LYS* 2.9 28.0 + - + -
266M PHE* 6.1 0.2 - - - -
267M PHE* 5.4 7.9 - - + -
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Residues in contact with LEU 118 (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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117M ASP* 1.3 78.2 + - - +
119M THR* 1.3 58.1 + - - +
121M LEU* 3.2 11.0 + - + +
122M VAL* 2.9 39.9 + - + +
127M VAL 5.3 0.9 - - - +
129M ILE* 3.5 22.7 - - + -
137M GLY* 4.3 0.2 - - - -
138M VAL* 3.7 21.8 - - + -
155M GLU 3.9 8.3 + - - +
156M VAL* 6.4 0.2 - - - -
157M GLN* 3.2 31.6 - - - +
179M TYR* 4.0 8.7 - - + +
184M LEU* 3.3 30.7 - - + -
187M VAL* 4.0 17.9 - - + -
188M CYS* 4.9 0.4 - - - -
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Residues in contact with THR 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ASP* 2.6 28.7 + - - +
118M LEU* 1.3 77.9 - - - +
120M GLN* 1.3 67.8 + - - +
122M VAL* 3.2 7.2 + - - +
123M ASN* 2.8 40.0 + - - +
187M VAL* 3.2 42.6 - - + +
188M CYS 5.5 0.2 - - - -
190M PRO* 5.5 2.0 - - + -
265M ILE 6.0 0.7 - - - +
266M PHE* 4.7 8.5 - - + -
51g LEU* 4.3 27.9 - - + +
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Residues in contact with GLN 120 (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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110M VAL* 4.5 10.7 - - + +
111M ASP* 5.1 10.4 + - - +
114M GLN* 4.3 20.8 + - - +
115M PRO 3.7 22.7 - - - +
116M ILE* 4.7 8.4 - - + +
117M ASP* 3.2 15.9 + - + +
119M THR* 1.3 89.1 + - - +
121M LEU* 1.3 58.7 + - - +
123M ASN* 3.2 11.3 + - - +
124M GLY* 2.9 25.3 + - - -
50g ARG* 4.1 25.5 + - - +
51g LEU* 5.3 5.5 - - - +
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Residues in contact with LEU 121 (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* 3.4 34.8 - - + -
101M LEU* 5.1 3.6 - - + -
104M LEU* 4.4 11.7 - - + -
110M VAL* 4.0 22.5 - - + +
116M ILE* 3.6 30.7 - - + -
117M ASP 3.2 7.4 + - - +
118M LEU* 3.2 13.1 + - + +
120M GLN* 1.3 80.3 - - - +
122M VAL* 1.3 56.4 - - - +
124M GLY* 3.2 2.3 + - - -
125M ARG 2.9 23.9 + - - -
126M GLY 3.3 10.3 + - - -
127M VAL* 4.2 19.5 - - + -
138M VAL* 4.2 15.0 - - + -
154M ILE* 5.3 0.2 - - + -
155M GLU 5.6 0.2 - - - +
156M VAL* 4.8 8.5 - - + -
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Residues in contact with VAL 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F LEU* 3.4 21.5 - - + +
118M LEU* 2.9 31.6 + - + +
119M THR* 3.5 8.3 - - - +
121M LEU* 1.3 77.7 - - - +
123M ASN* 1.3 65.1 + - - +
125M ARG* 3.1 23.6 + - - +
127M VAL 3.5 21.5 - - - +
128M THR* 5.3 1.1 - - - -
129M ILE* 4.3 13.9 - - + +
188M CYS* 3.2 34.8 - - + +
189M LYS* 5.4 0.7 - - + -
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Residues in contact with ASN 123 (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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280F TYR* 4.4 3.5 - - - -
283F LEU* 4.5 3.5 - - - +
119M THR* 2.8 28.8 + - - +
120M GLN* 3.5 14.1 - - - +
122M VAL* 1.3 83.0 - - - +
124M GLY* 1.3 57.6 + - - +
125M ARG* 2.6 31.3 + - - +
188M CYS 4.8 3.6 - - - +
190M PRO* 5.2 4.9 - - - +
50g ARG 4.9 1.6 + - - -
51g LEU* 2.8 31.3 + - - +
52g LEU 3.4 3.4 + - - -
53g PRO* 3.1 33.6 - - + +
54g ALA* 5.3 1.6 + - - +
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Residues in contact with GLY 124 (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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280F TYR* 3.1 25.4 + - - -
104M LEU* 5.3 0.2 - - - -
109M ARG* 4.2 26.4 + - - -
110M VAL* 4.3 11.9 - - - -
120M GLN 2.9 14.5 + - - -
121M LEU 3.2 4.2 + - - -
123M ASN* 1.3 74.3 - - - +
125M ARG* 1.3 66.5 - - - +
126M GLY 3.6 0.9 - - - -
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Residues in contact with ARG 125 (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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1883A G 3.8 18.9 + - - +
280F TYR* 3.4 44.5 - - + +
281F ARG* 2.9 63.8 + - - +
282F PRO 3.7 4.6 + - - -
283F LEU* 3.5 31.8 - - + +
290F TYR* 3.8 18.6 - - - -
100M ARG* 4.1 0.3 + - - -
104M LEU* 4.6 1.8 - - - -
109M ARG* 4.3 4.7 + - - +
121M LEU 2.9 4.2 + - - -
122M VAL* 3.1 17.0 + - - +
123M ASN 2.6 30.9 + - - -
124M GLY* 1.3 76.8 - - - +
126M GLY* 1.3 65.1 + - - +
127M VAL 4.5 3.8 - - - +
128M THR* 5.4 2.0 - - - -
53g PRO* 4.2 10.5 - - - +
54g ALA 4.7 1.0 - - - +
55g THR* 4.7 2.0 - - - +
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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