Contacts of the helix formed by residues 46 - 52 (chain J) in PDB entry 2NVT
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 CYS 46 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J CYS* 3.8 6.7 - - - -
10J CYS* 2.9 17.3 - - - -
12J LYS* 4.2 17.9 - - - -
14J VAL* 4.5 2.7 - - + -
41J LEU* 3.5 33.7 - - + +
43J ARG* 3.0 21.2 + - + +
45J CYS* 1.3 74.1 - - - +
47J ARG* 1.3 64.3 + - - +
49J MET* 3.3 19.4 - - - +
50J ILE* 3.9 2.4 + - - +
101J ZN 2.3 37.8 - - - -
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Residues in contact with ARG 47 (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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1036B ALA* 3.2 25.2 + - - +
1037B LEU* 2.6 31.5 + - - +
1039B GLY 4.4 0.6 - - - +
33J GLY* 3.1 29.7 + - - -
36J LEU* 3.5 36.3 - - + +
37J SER* 3.3 24.2 + - - +
41J LEU* 3.2 28.4 + - + +
42J LYS* 4.0 9.8 + - - +
43J ARG 3.4 0.4 + - - -
44J TYR* 2.7 30.8 + - - +
46J CYS* 1.3 74.4 - - - +
48J ARG* 1.3 55.9 + - - +
50J ILE* 3.2 4.7 + - - +
51J LEU* 3.2 28.8 + - - +
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Residues in contact with ARG 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLN* 3.7 10.0 + - - +
803B LEU* 4.6 20.0 - - + -
821B GLN* 6.3 0.2 - - - +
822B ASN* 3.0 33.0 + - - +
824B ILE* 3.4 13.3 - - + +
850B LEU* 4.1 7.5 - - - +
1009B ASP* 2.5 31.2 + - - -
1036B ALA* 4.5 7.3 - - + +
1089B PRO* 5.4 2.2 - - + -
8J PHE* 3.8 8.9 - - - +
9J SER* 2.8 18.7 + - - -
44J TYR 2.7 13.7 + - - +
45J CYS* 2.7 42.2 + - - +
47J ARG* 1.3 68.6 - - - +
49J MET* 1.3 84.2 + - - +
50J ILE 3.2 2.5 + - - -
51J LEU* 4.7 3.1 - - - +
52J THR* 2.3 39.9 + - - +
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Residues in contact with MET 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLN* 4.1 10.3 + - - +
3J VAL* 5.8 0.2 - - - +
4J PRO* 4.2 26.3 - - - +
6J ARG 4.6 1.1 - - - +
7J CYS* 3.0 35.2 - - + -
8J PHE* 3.1 48.0 - - + +
14J VAL* 3.8 19.5 - - + -
45J CYS 3.2 8.6 + - - +
46J CYS* 3.3 16.2 - - - +
47J ARG 3.3 0.6 - - - -
48J ARG* 1.3 102.6 - - - +
50J ILE* 1.3 59.6 + - + +
53J HIS* 3.7 17.3 + - - +
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Residues in contact with ILE 50 (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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3J VAL* 4.3 16.6 - - + -
14J VAL* 4.1 29.8 - - + +
17J LYS* 5.0 9.2 - - + -
18J TRP* 3.9 16.0 - - + +
21J TYR* 3.4 40.6 - - + -
36J LEU* 3.9 18.6 - - + -
39J LEU* 5.8 0.9 - - + -
41J LEU* 4.4 11.9 - - + -
46J CYS 4.1 10.8 - - - +
47J ARG 3.2 6.5 + - - +
48J ARG 3.2 0.2 - - - -
49J MET* 1.3 79.1 - - + +
51J LEU* 1.3 65.5 + - - +
52J THR 3.4 1.3 - - - -
53J HIS* 3.1 22.2 + - - +
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Residues in contact with LEU 51 (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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801B LYS* 3.2 34.0 + - - +
803B LEU* 4.9 9.2 - - + -
1035B ALA 3.8 13.9 - - - +
1036B ALA* 4.8 5.2 - - - +
1039B GLY* 3.2 35.9 - - - +
1040B ASN 4.9 3.6 - - - +
21J TYR* 3.8 9.0 - - + +
32J GLU* 3.5 33.7 - - + -
36J LEU* 4.5 11.9 - - + -
47J ARG 3.2 13.7 + - - +
48J ARG* 4.8 1.8 - - - -
50J ILE* 1.3 80.3 - - - +
52J THR* 1.3 61.0 + - - +
53J HIS 3.5 2.3 + - - +
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Residues in contact with THR 52 (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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800B GLN* 3.2 31.8 + - + +
801B LYS* 2.6 50.0 + - - +
802B PRO 4.6 0.4 - - - -
803B LEU* 4.2 5.8 - - + +
822B ASN* 2.5 36.5 + - - +
48J ARG* 2.3 37.7 + - - +
51J LEU* 1.3 76.8 - - - +
53J HIS* 1.3 62.9 + - - +
54J VAL 3.3 0.9 + - - -
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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