Contacts of the helix formed by residues 49 - 63 (chain J) 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 ARG 49 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11180 A 4.1 18.8 + - - +
11190 G 2.6 49.3 + - - +
12440 U 4.6 2.8 + - - +
48J GLY* 1.3 69.6 - - - -
50J GLU* 1.3 66.9 + - - +
51J GLU* 3.0 42.6 + - - +
52J GLN* 3.0 26.7 + - + +
53J ILE* 3.1 13.7 + - - +
55J GLU* 5.6 3.8 + - - -
128J LYS* 4.1 21.4 - - - +
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Residues in contact with GLU 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J GLY 3.6 5.3 + - - -
49J ARG* 1.3 71.9 - - - +
51J GLU* 1.3 77.2 + - - +
53J ILE* 4.4 1.1 - - - -
54J VAL* 3.0 38.8 + - + +
129J PHE 5.3 2.7 - - - +
130J VAL* 3.5 42.5 - - + +
134J GLU* 4.6 13.7 - - - +
138J THR* 4.5 9.5 + - - -
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Residues in contact with GLU 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ARG* 3.0 41.6 + - - +
50J GLU* 1.3 90.7 + - - +
52J GLN* 1.3 60.9 + - - +
54J VAL* 4.1 4.0 - - - +
55J GLU* 3.2 26.6 + - - +
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Residues in contact with GLN 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11190 G 2.9 75.2 + - - +
12440 U 4.8 1.2 + - - -
93160 CL 3.8 3.8 - - - +
49J ARG* 3.0 36.2 + - + +
51J GLU* 1.3 76.1 - - - +
53J ILE* 1.3 80.2 + - + +
55J GLU* 3.2 11.8 + - - +
56J LYS* 3.0 28.2 + - - +
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11190 G 5.7 1.8 - - + +
46J ILE* 3.6 30.1 - - + -
47J THR 3.2 33.9 - - - +
48J GLY* 3.8 13.2 - - - -
49J ARG 3.1 11.8 + - - +
50J GLU* 3.8 4.3 - - - +
52J GLN* 1.3 95.3 - - + +
54J VAL* 1.3 62.8 + - + +
56J LYS* 3.1 15.0 + - - +
57J TYR* 3.2 25.6 - - + -
130J VAL* 3.8 19.1 - - + -
135J ILE* 4.0 21.8 - - + -
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Residues in contact with VAL 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J GLU* 3.0 38.9 + - + +
51J GLU* 4.1 4.0 - - - +
53J ILE* 1.3 73.4 - - + +
55J GLU* 1.3 61.6 + - - +
57J TYR* 3.2 6.7 + - - +
58J GLU* 2.8 51.0 + - + +
130J VAL* 5.5 0.2 - - + -
135J ILE* 4.7 20.4 - - + +
138J THR* 3.4 37.0 - - + +
139J LEU* 5.1 2.9 - - + -
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Residues in contact with GLU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ARG* 5.6 3.8 + - - -
51J GLU* 3.2 15.9 + - - +
52J GLN* 3.2 15.4 + - - +
54J VAL* 1.3 78.8 - - - +
56J LYS* 1.3 62.6 + - - +
58J GLU* 3.3 14.4 + - - +
59J LYS* 3.1 23.9 + - - +
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Residues in contact with LYS 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12360 A 4.0 19.2 - - + -
12370 U 4.2 9.7 + - - -
12410 G 4.8 0.4 + - - -
12420 A 3.1 36.0 + - - +
93160 CL 3.4 28.5 - - + +
52J GLN* 3.0 17.2 + - - +
53J ILE* 3.1 10.5 + - - +
55J GLU* 1.3 77.6 - - - +
57J TYR* 1.3 70.5 + - + +
59J LYS* 3.4 8.0 + - - +
60J ARG* 3.3 50.2 + - - +
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Residues in contact with TYR 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12420 A 4.0 17.7 + - - -
12430 C 5.5 0.5 + - - -
19J MET* 4.3 13.0 - - - -
46J ILE* 4.2 16.8 - - + +
53J ILE* 3.2 42.5 + - + +
54J VAL 3.2 5.4 + - - +
56J LYS* 1.3 88.3 - - + +
58J GLU* 1.3 64.7 + - - +
60J ARG* 3.4 18.6 + - - +
61J VAL* 3.2 24.9 + - - +
71J TYR* 3.2 37.1 - + - -
78J ILE* 3.6 24.2 - - + +
132J LEU* 5.8 0.2 - - + -
135J ILE* 4.3 19.7 - - + -
139J LEU* 4.0 16.2 - - + -
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Residues in contact with GLU 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28020 C 3.8 17.9 + - - -
28030 C 5.4 2.6 - - - +
54J VAL* 2.8 39.0 + - + +
55J GLU* 3.8 15.3 - - - +
56J LYS 3.3 0.2 - - - -
57J TYR* 1.3 74.1 - - - +
59J LYS* 1.3 61.2 + - - +
61J VAL* 3.0 8.0 + - - +
62J ASP* 2.9 35.9 + - - +
138J THR* 4.1 15.1 - - - +
139J LEU* 3.7 20.9 - - + -
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Residues in contact with LYS 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12360 A 3.0 77.3 + - + +
55J GLU 3.1 16.8 + - - +
56J LYS* 3.6 8.1 - - - +
58J GLU* 1.3 77.4 - - - +
60J ARG* 1.3 56.6 + - - +
62J ASP* 3.0 13.2 + - + +
63J ILE* 2.9 43.4 + - + +
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Residues in contact with ARG 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12360 A 3.0 32.6 + - + +
12410 G 2.9 26.5 + - - -
12420 A 2.5 43.4 + - - -
56J LYS* 3.3 38.2 + - - +
57J TYR* 3.6 23.0 - - - +
58J GLU 3.2 0.6 - - - -
59J LYS* 1.3 75.8 - - - +
61J VAL* 1.3 50.9 + - - +
63J ILE* 3.8 11.1 + - - -
69J TYR* 3.9 11.2 - - + -
71J TYR* 3.2 54.8 + - + +
9146J NA 2.6 24.9 - - - -
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Residues in contact with VAL 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26770 A 4.6 8.0 + - - +
28030 C 6.2 0.2 - - - +
57J TYR 3.2 14.0 + - - +
58J GLU* 3.0 11.9 + - - +
60J ARG* 1.3 78.9 - - - +
62J ASP* 1.3 66.3 + - - +
63J ILE 3.6 0.5 - - - +
71J TYR* 4.5 17.5 - - + +
73J LYS* 4.2 38.6 - - + +
139J LEU* 4.3 20.0 - - + +
9146J NA 2.7 15.8 - - - -
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Residues in contact with ASP 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12350 G 5.6 1.9 - - - +
28030 C 4.9 8.3 + - - -
58J GLU* 2.9 22.2 + - - +
59J LYS* 3.0 17.0 + - + +
61J VAL* 1.3 82.2 - - - +
63J ILE* 1.3 65.9 + - - +
64J GLY* 3.6 1.6 + - - -
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Residues in contact with ILE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12350 G 3.2 50.5 - - + +
12360 A 3.0 54.7 - - + +
59J LYS* 2.9 34.5 + - + +
60J ARG* 4.0 8.7 - - - +
61J VAL 3.4 1.1 - - - +
62J ASP* 1.3 78.3 - - - +
64J GLY* 1.3 63.3 + - - +
69J TYR* 4.0 15.3 - - + +
9146J NA 2.4 26.7 - - - -
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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