Contacts of the helix formed by residues 89 - 111 (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 ASN 89 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P GLY 3.7 9.2 + - - +
86P ALA 5.0 1.2 + - - -
88P GLN* 1.3 72.3 - - - +
90P SER* 1.3 65.5 + - - +
91P LYS* 3.8 13.7 - - - +
92P GLU* 2.8 47.7 + - + +
93P ASP* 2.9 28.2 + - - +
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Residues in contact with SER 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8150 U 4.9 4.5 + - - -
81060 MG 4.1 14.9 - - - -
85P GLY* 4.7 5.1 + - - -
88P GLN* 3.2 7.9 + - - -
89P ASN* 1.3 72.8 + - - +
91P LYS* 1.3 67.2 + - - +
93P ASP* 3.1 8.6 + - - +
94P TRP* 3.0 22.7 + - - +
97P ARG* 4.6 2.8 + - - +
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Residues in contact with LYS 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8150 U 5.7 0.7 - - - -
8160 G 2.6 46.0 + - - +
8170 G 3.1 27.8 + - - +
15390 U 4.0 26.4 - - - +
15400 G 5.6 0.7 - - - +
15970 A 2.9 35.2 + - - -
89P ASN* 3.5 11.6 - - - +
90P SER* 1.3 80.7 + - - +
92P GLU* 1.3 62.0 + - - +
94P TRP* 3.2 7.4 + - + +
95P GLU* 2.9 44.7 + - + +
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Residues in contact with GLU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 6.0 1.1 - - - +
16400 C 5.2 6.2 + - - -
17970 A 5.6 4.2 - - - +
89P ASN* 2.8 42.7 + - + +
91P LYS* 1.3 80.4 - - - +
93P ASP* 1.3 60.3 + - - +
95P GLU* 3.2 21.1 + - - +
96P SER* 3.2 19.6 + - - -
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Residues in contact with ASP 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17930 C 4.6 10.6 + - - +
17940 G 5.6 1.2 - - - +
17990 G 4.9 2.6 + - - -
88P GLN* 3.7 33.9 + - + +
89P ASN 2.9 17.0 + - - +
90P SER* 3.5 8.5 - - - +
92P GLU* 1.3 76.1 - - - +
94P TRP* 1.3 60.2 + - - +
96P SER* 3.3 10.2 + - - -
97P ARG* 2.8 57.6 + - - +
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Residues in contact with TRP 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8140 G 4.1 15.0 - - - -
8150 U 3.5 52.4 + - - +
8160 G 4.1 3.1 - - - +
15970 A 3.1 34.8 + - - -
15980 A 3.4 15.5 - - - -
90P SER 3.0 12.3 + - - +
91P LYS* 3.2 11.4 + - - +
93P ASP* 1.3 75.5 - - - +
95P GLU* 1.3 65.5 + - - +
97P ARG* 3.8 29.3 - - - +
98P ILE* 2.9 56.6 + - + +
101P GLN* 6.1 2.2 - - - -
126P ALA 4.0 5.8 - - - -
127P GLY 4.0 20.0 - - - -
129P GLY* 4.3 11.9 - - - -
131P PHE 6.2 0.2 - - - -
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Residues in contact with GLU 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 4.0 26.3 + - - +
15970 A 3.3 46.1 - - - +
91P LYS* 2.9 39.4 + - + +
92P GLU* 3.5 22.9 - - - +
93P ASP 3.2 0.2 - - - -
94P TRP* 1.3 78.0 - - - +
96P SER* 1.3 65.0 + - - +
98P ILE* 4.3 0.4 - - - -
99P ARG* 3.1 52.1 + - - +
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Residues in contact with SER 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 3.1 38.5 + - - +
17950 G 4.8 2.8 + - - -
17960 A 3.9 11.7 + - - -
92P GLU 3.2 11.6 + - - -
93P ASP* 3.4 16.6 - - - -
94P TRP 3.2 0.2 - - - -
95P GLU* 1.3 79.5 - - - +
97P ARG* 1.3 62.1 + - - +
99P ARG* 3.8 4.6 - - - +
100P ALA* 3.1 24.5 + - - +
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Residues in contact with ARG 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8140 G 5.9 0.2 + - - -
8150 U 4.8 4.9 + - - -
17930 C 3.8 23.3 + - - +
17940 G 4.2 14.9 + - - +
90P SER* 4.6 2.4 + - - +
93P ASP* 2.8 41.4 + - - +
94P TRP* 3.8 38.6 - - + +
96P SER* 1.3 79.8 - - - +
98P ILE* 1.3 57.9 + - - +
100P ALA* 3.2 3.5 + - - +
101P GLN* 2.9 41.2 + - - +
131P PHE 5.4 3.6 + - - -
132P ASP* 3.4 26.1 + - - +
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Residues in contact with ILE 98 (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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15970 A 3.7 34.5 - - - +
94P TRP* 2.9 58.7 + - + +
95P GLU 4.0 0.9 - - - +
97P ARG* 1.3 73.1 - - - +
99P ARG* 1.3 63.2 + - - +
101P GLN* 4.4 8.3 - - + +
102P ARG* 3.0 65.6 + - + +
126P ALA* 4.4 23.1 - - + +
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Residues in contact with ARG 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 2.9 37.0 + - - -
15410 G 3.1 18.8 + - - -
15970 A 2.7 50.3 + - - +
95P GLU* 3.1 37.0 + - - +
96P SER* 3.8 3.8 - - - +
98P ILE* 1.3 81.5 - - - +
100P ALA* 1.3 57.1 + - - +
102P ARG* 3.4 6.5 + - - +
103P THR* 2.8 36.4 + - - +
106P ARG* 4.6 0.5 + - - -
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Residues in contact with ALA 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 3.8 8.3 - - - +
17950 G 3.4 38.6 + - - +
96P SER 3.1 16.6 + - - +
97P ARG 3.6 4.0 - - - +
99P ARG* 1.3 78.5 - - - +
101P GLN* 1.3 56.6 + - - +
103P THR* 3.5 6.2 + - - -
104P LYS* 3.1 27.5 + - - +
134P VAL* 3.9 16.3 - - + +
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Residues in contact with GLN 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 5.3 0.4 - - - +
94P TRP* 6.1 2.4 - - - -
97P ARG* 2.9 31.0 + - - +
98P ILE* 3.8 9.3 - - - +
99P ARG 3.3 0.2 - - - -
100P ALA* 1.3 79.4 - - - +
102P ARG* 1.3 57.1 + - - +
104P LYS* 3.4 7.5 - - - +
105P LEU* 3.1 31.8 + - - +
126P ALA* 3.7 30.7 - - + +
129P GLY* 6.0 0.3 - - - -
131P PHE* 2.8 41.6 + - - +
132P ASP 3.9 1.8 + - - -
133P SER* 3.6 31.2 - - - +
134P VAL* 4.3 6.3 - - + +
137P LEU* 3.8 10.1 - - + +
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Residues in contact with ARG 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15960 U 3.1 43.6 + - - +
15970 A 3.1 24.1 + - - -
15980 A 2.9 40.2 + - - -
98P ILE* 3.0 47.7 + - + +
99P ARG* 3.9 4.0 - - - +
100P ALA 3.3 0.2 - - - -
101P GLN* 1.3 74.3 - - - +
103P THR* 1.3 65.9 + - - +
104P LYS 3.1 1.6 - - - -
105P LEU* 3.3 7.3 + - - +
106P ARG* 2.9 35.7 + - - +
119P TYR* 5.2 1.9 + - - -
123P TYR* 3.6 35.4 + - + -
126P ALA* 5.3 3.8 - - + -
127P GLY* 4.2 10.9 - - - +
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Residues in contact with THR 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17950 G 6.1 0.4 - - - -
99P ARG* 2.8 25.6 + - - +
100P ALA* 3.9 6.7 - - - -
102P ARG* 1.3 76.5 - - - +
104P LYS* 1.3 62.2 + - - +
106P ARG* 3.3 30.6 + - - +
107P GLU* 3.0 47.6 + - + +
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Residues in contact with LYS 104 (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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100P ALA 3.1 15.1 + - - +
101P GLN* 3.4 11.9 - - - +
102P ARG 3.1 0.2 - - - -
103P THR* 1.3 77.9 - - - +
105P LEU* 1.3 62.9 + - - +
107P GLU* 3.0 28.2 + - + +
108P LEU* 3.1 34.3 + - + +
134P VAL* 4.2 15.1 - - + +
137P LEU* 4.1 17.9 - - + -
138P GLU* 2.6 39.7 + - + -
141P ILE* 6.0 0.4 - - + -
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Residues in contact with LEU 105 (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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101P GLN 3.1 17.7 + - - +
102P ARG* 3.3 5.6 + - - +
104P LYS* 1.3 79.2 - - - +
106P ARG* 1.3 60.6 + - - +
108P LEU* 4.0 7.1 - - + +
109P ARG* 3.3 13.0 + - - +
114P LEU* 4.4 5.6 - - + +
119P TYR* 3.1 29.7 - - + +
122P LEU* 3.6 29.4 - - + +
123P TYR* 3.3 47.6 - - + +
126P ALA* 4.6 8.3 - - + -
137P LEU* 3.4 27.1 - - + -
141P ILE* 4.3 7.2 - - + -
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Residues in contact with ARG 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15950 G 4.7 7.2 + - - +
15960 U 4.4 17.9 + - - -
99P ARG 4.6 0.6 + - - -
102P ARG* 2.9 22.7 + - - +
103P THR* 3.3 47.2 + - - +
104P LYS 3.1 0.2 - - - -
105P LEU* 1.3 75.7 - - - +
107P GLU* 1.3 67.2 + - + +
109P ARG* 3.7 22.9 + - - +
110P ASP* 2.9 38.7 + - - +
119P TYR* 4.1 10.8 + - + +
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Residues in contact with GLU 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P THR* 3.0 30.5 - - + +
104P LYS* 3.0 20.3 + - + +
106P ARG* 1.3 80.0 - - + +
108P LEU* 1.3 67.7 + - + +
109P ARG 3.1 0.3 + - - -
110P ASP* 3.3 4.5 + - - +
111P GLU* 2.9 34.7 + - - +
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Residues in contact with LEU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P LYS* 3.1 40.2 + - + +
105P LEU* 4.1 3.4 - - + +
107P GLU* 1.3 77.8 - - + +
109P ARG* 1.3 59.5 + - - +
111P GLU* 3.5 23.6 - - - +
112P GLY 3.3 2.6 + - - -
113P THR* 3.1 42.6 + - + +
114P LEU* 3.3 28.0 + - + -
138P GLU* 6.3 0.4 - - + -
141P ILE* 3.4 36.1 - - + -
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Residues in contact with ARG 109 (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 2.6 39.5 + - - -
15950 G 3.2 27.3 + - - -
16070 A 5.7 1.2 + - - -
105P LEU 3.3 15.3 + - - +
106P ARG* 3.8 20.9 - - - +
107P GLU 3.1 1.0 - - - -
108P LEU* 1.3 75.6 - - - +
110P ASP* 1.3 73.6 + - - +
111P GLU 2.9 4.0 - - - -
112P GLY* 2.8 21.8 + - - -
114P LEU* 3.9 21.3 - - - +
116P SER* 4.7 9.0 - - - +
119P TYR* 3.1 43.4 - - + -
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Residues in contact with ASP 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P ARG* 2.9 28.9 + - - +
107P GLU* 3.3 4.1 + - - +
109P ARG* 1.3 94.2 + - - +
111P GLU* 1.3 58.2 + - - +
112P GLY* 3.3 0.6 + - - -
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Residues in contact with GLU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P GLU* 2.9 28.6 + - - +
108P LEU* 3.5 20.0 - - - +
109P ARG 2.9 0.2 - - - -
110P ASP* 1.3 79.7 - - - +
112P GLY* 1.3 54.5 + - - +
113P THR* 2.8 22.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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