Contacts of the helix formed by residues 115 - 128 (chain P) in PDB entry 1VQN
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 SER 115 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P LEU* 1.3 73.9 - - - +
116P SER* 1.3 66.8 + - - +
117P SER* 3.5 11.9 + - - -
118P GLN* 2.6 59.6 + - - +
119P TYR* 2.7 10.3 + - - +
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Residues in contact with SER 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15930 C 3.7 29.0 + - - +
15940 C 3.8 11.7 + - - -
109P ARG* 4.7 7.6 - - - +
114P LEU 4.0 1.2 + - - -
115P SER* 1.3 71.7 - - - +
117P SER* 1.3 61.9 + - - +
119P TYR* 3.4 8.3 - - - +
120P ARG* 2.8 28.8 + - - +
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Residues in contact with SER 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15930 C 2.7 38.3 + - - -
115P SER* 2.8 13.8 + - - -
116P SER* 1.3 77.2 + - - +
118P GLN* 1.3 64.0 + - - +
120P ARG* 3.6 1.8 - - - +
121P ASP* 3.1 24.3 + - - +
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Residues in contact with GLN 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P THR 4.2 5.1 + - - +
114P LEU* 3.5 23.6 - - + +
115P SER* 2.6 56.4 + - - +
117P SER* 1.3 73.4 - - - +
119P TYR* 1.3 63.8 + - - +
121P ASP* 3.4 6.0 + - - +
122P LEU* 3.1 32.0 + - + +
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Residues in contact with TYR 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15940 C 3.1 33.2 - - - -
15950 G 2.6 25.1 + - - -
102P ARG 5.2 0.7 + - - -
105P LEU* 3.1 46.3 - - + +
106P ARG* 4.1 8.4 + - - +
109P ARG* 3.1 43.9 + - + -
114P LEU* 4.4 14.7 - - + +
115P SER 2.7 10.3 + - - +
116P SER 3.4 7.4 - - - +
118P GLN* 1.3 77.4 - - - +
120P ARG* 1.3 57.0 + - - +
122P LEU* 3.2 4.0 + - - +
123P TYR* 2.7 62.2 + + + +
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Residues in contact with ARG 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15930 C 3.9 38.4 - - + +
15940 C 2.9 55.0 + - - +
15950 G 2.7 53.3 + - - -
116P SER 2.8 17.8 + - - +
117P SER* 3.6 9.6 - - - +
118P GLN 3.3 0.2 - - - -
119P TYR* 1.3 81.4 - - - +
121P ASP* 1.3 63.2 + - - +
123P TYR* 2.9 23.5 - - - +
124P ASP* 2.9 51.2 + - - +
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Residues in contact with ASP 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8020 G 4.7 5.1 + - - -
117P SER 3.1 15.8 + - - +
118P GLN* 3.7 6.5 - - - +
120P ARG* 1.3 80.0 - - - +
122P LEU* 1.3 65.6 + - + +
124P ASP* 4.2 4.7 - - - +
125P LYS* 3.3 56.7 + - - +
140P TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P LEU* 3.6 19.3 - - + -
114P LEU* 3.9 20.2 - - + -
118P GLN* 3.1 21.7 + - + +
119P TYR 3.7 3.1 - - - +
121P ASP* 1.3 79.3 - - - +
123P TYR* 1.3 60.6 + - - +
125P LYS* 3.2 4.9 + - + +
126P ALA* 2.8 29.6 + - - +
131P PHE* 3.7 12.1 - - + -
137P LEU* 4.4 2.5 - - + -
140P TYR* 3.5 39.0 - - + -
141P ILE* 3.7 33.0 - - + -
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Residues in contact with TYR 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15950 G 3.3 26.3 - + - -
15960 U 2.5 51.1 + + - -
102P ARG* 3.6 36.5 + - + -
105P LEU* 3.3 17.6 - - + +
119P TYR* 2.7 52.2 + + + +
120P ARG* 2.9 39.5 - - - +
122P LEU* 1.3 73.2 - - - +
124P ASP* 1.3 64.3 + - - +
126P ALA* 3.3 3.7 + - - +
127P GLY* 3.1 19.5 + - - -
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Residues in contact with ASP 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8000 G 4.2 1.3 + - - +
8010 U 3.3 35.4 + - - +
15930 C 5.8 1.0 - - - -
15940 C 5.5 0.3 + - - -
15950 G 3.7 7.8 - - - +
120P ARG* 2.9 58.4 + - - +
121P ASP* 4.2 4.9 - - - +
123P TYR* 1.3 75.3 - - - +
125P LYS* 1.3 66.2 + - + +
127P GLY* 3.3 3.5 + - - +
128P GLY 3.1 15.9 + - - -
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Residues in contact with LYS 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8010 U 3.8 16.6 - - - +
8020 G 3.4 27.0 - - - +
121P ASP* 3.3 37.1 + - - +
122P LEU* 3.2 6.5 + - - +
124P ASP* 1.3 76.1 - - + +
126P ALA* 1.3 64.8 + - - +
128P GLY 3.1 5.5 + - - -
130P GLU* 2.9 51.5 + - + +
131P PHE* 4.0 13.5 - - + -
140P TYR* 2.7 31.9 + - + +
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Residues in contact with ALA 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P TRP* 4.0 7.6 - - - -
98P ILE* 4.4 13.5 - - + +
101P GLN* 3.7 25.6 - - + +
102P ARG* 5.3 2.7 - - + -
105P LEU* 4.6 8.3 - - + -
122P LEU 2.8 13.2 + - - +
123P TYR* 3.4 12.6 - - - +
124P ASP 3.2 0.2 - - - -
125P LYS* 1.3 72.8 - - - +
127P GLY* 1.3 54.4 + - - +
128P GLY 2.9 4.0 - - - -
129P GLY* 2.6 28.1 + - - -
130P GLU 4.5 0.7 - - - +
131P PHE* 3.8 16.7 - - + -
137P LEU* 5.7 0.2 - - + -
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Residues in contact with GLY 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8000 G 3.7 13.8 + - - +
8140 G 5.1 4.2 + - - +
8150 U 5.6 1.9 - - - +
15960 U 5.1 4.7 - - - -
15980 A 4.9 1.8 + - - -
94P TRP* 4.0 16.4 - - - -
98P ILE* 4.5 1.7 - - - +
102P ARG* 4.2 21.5 - - - -
123P TYR* 3.1 11.5 + - - -
124P ASP* 3.3 5.6 + - - -
125P LYS 3.3 0.2 - - - -
126P ALA* 1.3 78.1 - - - +
128P GLY* 1.3 56.0 - - - +
129P GLY 3.1 1.4 + - - -
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Residues in contact with GLY 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8000 G 3.1 31.1 + - - -
8010 U 3.3 31.5 - - - +
8130 C 4.7 0.9 - - - +
8140 G 4.3 5.0 + - - -
124P ASP 3.1 8.1 + - - -
125P LYS 3.1 3.6 + - - -
126P ALA 2.9 2.2 + - - -
127P GLY* 1.3 75.8 - - - +
129P GLY* 1.3 62.7 + - - +
130P GLU* 3.4 5.3 + - - +
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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