Contacts of the helix formed by residues 96 - 109 (chain M) in PDB entry 1VQ9
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 96 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4010 C 3.4 36.1 + - - +
4020 U 3.7 11.0 - - - +
95M LYS* 1.3 76.2 - - - +
97M ILE* 1.3 66.4 + - - +
98M GLN* 3.6 25.4 - - - +
99M ARG* 3.1 25.0 + - - +
100M VAL* 3.2 11.9 + - - +
166M ALA* 4.5 5.9 - - - +
169M ARG* 5.5 1.7 + - - -
170M ASN* 3.2 25.6 + - - +
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Residues in contact with ILE 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4020 U 2.9 23.9 + - - +
4030 C 4.9 1.1 - - - +
67M VAL* 3.8 28.4 - - + +
68M ARG* 3.9 30.1 - - - +
69M LYS* 4.4 8.1 - - - -
70M GLY 4.5 11.9 - - - +
95M LYS 5.7 0.2 - - - +
96M ASP* 1.3 70.8 - - - +
98M GLN* 1.3 64.6 + - - +
100M VAL* 3.2 8.3 + - + +
101M ALA* 2.9 20.8 + - - +
127M LYS* 3.8 37.0 - - + +
129M HIS* 4.0 16.2 - - + -
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Residues in contact with GLN 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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96M ASP* 3.2 12.9 + - - +
97M ILE* 1.3 77.6 - - - +
99M ARG* 1.3 58.7 + - - +
101M ALA* 3.2 4.0 + - - +
102M GLU* 3.0 33.4 + - - +
116M ASN* 5.6 0.2 + - - -
117M SER* 2.5 48.0 + - - +
118M TYR* 3.8 5.8 - - - +
119M SER 5.5 0.2 - - - -
129M HIS* 3.5 31.9 + - + +
166M ALA* 3.8 18.6 - - + +
169M ARG* 3.9 21.4 + - - +
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Residues in contact with ARG 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560 C 3.0 26.1 + - - -
1570 G 2.6 35.6 + - - -
95M LYS* 3.6 22.3 - - + +
96M ASP* 3.1 20.0 + - - +
98M GLN* 1.3 79.5 - - - +
100M VAL* 1.3 62.9 + - - +
102M GLU* 3.3 13.5 + - + +
103M GLU* 3.2 28.9 + - + +
159M VAL* 4.3 9.4 + - + +
162M GLY* 3.7 19.5 - - - +
164M THR* 5.6 0.9 - - - -
166M ALA* 3.9 5.4 - - + -
167M GLY* 3.4 34.7 - - - +
170M ASN* 2.9 25.6 - - - +
171M ARG* 4.3 4.8 - - - +
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Residues in contact with VAL 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14700 A 3.6 31.6 - - - +
14710 A 3.4 23.3 + - - +
67M VAL* 4.6 10.8 - - + -
68M ARG* 5.6 2.9 - - - +
95M LYS* 4.6 15.9 - - + +
96M ASP 3.2 17.4 + - - +
97M ILE* 3.2 13.0 + - + +
99M ARG* 1.3 76.8 - - - +
101M ALA* 1.3 62.6 + - - +
103M GLU* 3.5 6.4 + - - +
104M ARG* 3.2 39.1 + - - +
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Residues in contact with ALA 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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65M VAL* 3.8 33.9 - - + +
67M VAL* 4.2 8.9 - - + +
97M ILE 2.9 12.7 + - - +
98M GLN 3.4 9.4 - - - +
100M VAL* 1.3 76.6 - - - +
102M GLU* 1.3 66.8 + - + +
104M ARG* 3.4 1.0 + - - +
105M ALA* 3.1 22.7 + - - +
129M HIS* 4.0 24.2 - - + +
131M VAL* 4.6 2.0 - - + -
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Residues in contact with GLU 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 GLN 3.0 17.3 + - - +
99M ARG* 3.3 10.3 + - - +
101M ALA* 1.3 75.0 - - - +
103M GLU* 1.3 57.6 + - - +
105M ALA* 3.3 3.8 + - - +
106M SER* 3.0 27.9 + - - -
114M VAL* 4.0 13.3 - - + +
116M ASN* 3.9 0.7 - - - +
117M SER* 2.5 41.3 + - - +
131M VAL* 4.1 10.3 - - + -
159M VAL* 3.7 14.8 - - + +
164M THR* 2.7 45.5 + - - +
166M ALA* 3.7 13.5 - - - +
167M GLY 4.6 0.5 + - - -
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Residues in contact with GLU 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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1560 C 4.7 1.9 + - - -
1810 G 5.3 0.2 + - - -
14700 A 5.1 1.1 - - - -
14710 A 4.5 12.3 - - - +
95M LYS* 3.0 37.0 + - - +
99M ARG* 3.2 19.9 + - + +
100M VAL* 3.8 6.1 - - - +
101M ALA 3.2 0.4 - - - -
102M GLU* 1.3 76.4 - - - +
104M ARG* 1.3 66.9 + - + +
106M SER* 3.1 3.8 + - - -
107M ARG* 3.0 38.8 + - - +
159M VAL* 4.0 25.0 - - + +
160M PHE* 3.5 40.0 - - + +
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Residues in contact with ARG 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14680 G 4.2 16.4 + - - -
14690 C 3.0 50.3 + - - +
14700 A 5.2 2.2 + - - -
14710 A 2.9 39.5 + - - +
36M ALA* 5.7 5.1 - - - +
37M VAL* 4.5 6.7 - - + -
65M VAL* 4.4 10.8 - - + -
66M SER 4.2 5.2 + - - -
67M VAL* 3.6 34.9 - - - +
68M ARG* 4.9 1.0 - - - +
100M VAL* 3.2 26.2 + - - +
101M ALA 3.9 4.5 - - - +
102M GLU 3.4 0.2 - - - -
103M GLU* 1.3 76.9 - - + +
105M ALA* 1.3 64.2 + - - +
107M ARG* 3.0 25.2 + - - +
108M THR* 3.0 17.1 + - - -
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Residues in contact with ALA 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M VAL* 4.5 6.5 - - + -
63M ALA* 5.2 1.1 - - + -
65M VAL* 3.8 19.8 - - + +
101M ALA 3.1 10.8 + - - +
102M GLU 3.4 8.5 - - - +
104M ARG* 1.3 79.0 - - - +
106M SER* 1.3 63.3 + - - +
108M THR* 3.1 16.1 + - - -
109M PHE* 3.1 21.9 - - + -
131M VAL* 4.1 23.1 - - + -
133M LEU* 4.1 8.5 - - + -
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Residues in contact with SER 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 GLU 3.0 9.1 + - - -
103M GLU 3.1 6.9 + - - -
105M ALA* 1.3 76.5 - - - +
107M ARG* 1.3 58.7 + - - +
109M PHE 3.0 11.3 - - - +
110M PRO* 3.4 2.1 - - - +
112M LEU 3.6 2.3 + - - -
114M VAL* 3.6 19.5 - - - +
133M LEU* 4.0 9.1 - - - +
159M VAL* 3.8 12.9 - - - +
160M PHE* 4.0 9.6 - - - -
9147M NA 2.5 42.5 - - - -
9318M CL 3.1 18.4 - - - +
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Residues in contact with ARG 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330 U 4.4 1.7 + - - -
1810 G 4.1 17.8 + - - -
1820 G 5.9 0.4 + - - -
14690 C 5.3 2.8 - - - +
14710 A 3.0 39.8 + - - -
14720 C 2.7 34.0 + - - +
103M GLU* 3.0 25.8 + - - +
104M ARG* 3.0 15.3 + - - +
106M SER* 1.3 73.4 - - - +
108M THR* 1.3 67.8 + - - +
110M PRO* 3.1 17.5 - - - +
160M PHE* 3.5 31.4 - - + -
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Residues in contact with THR 108 (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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1330 U 2.6 29.9 + - - +
1340 U 3.8 17.3 - - - +
37M VAL* 3.4 36.0 - - + +
104M ARG 3.0 8.0 + - - -
105M ALA 3.4 8.5 - - - -
107M ARG* 1.3 76.7 - - - +
109M PHE* 1.3 80.7 + - + +
110M PRO* 2.8 2.8 - - - +
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Residues in contact with PHE 109 (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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1340 U 3.4 42.4 - - - +
1350 G 3.9 10.1 - - - -
37M VAL* 4.0 8.5 - - + -
39M ARG* 4.3 15.0 - - + -
61M ILE* 4.4 9.0 - - + -
63M ALA* 3.7 30.7 - - + -
105M ALA* 3.1 27.4 + - - +
106M SER* 3.0 4.1 - - - +
107M ARG 3.1 0.4 - - - -
108M THR* 1.3 93.3 - - + +
110M PRO* 1.3 58.3 - - - +
111M ASN 3.2 2.9 - - - -
112M LEU* 2.9 33.6 + - + +
133M LEU* 3.8 16.8 - - + -
9147M NA 2.7 20.8 - - - -
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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