Contacts of the helix formed by residues 32 - 41 (chain J) in PDB entry 5ANC
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 TYR 32 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J ASN 4.3 15.9 - - - -
15J VAL* 4.7 2.0 - - - -
16J ALA* 3.6 7.2 - - - +
31J CYS* 1.3 77.6 - - - +
33J LYS* 1.3 93.4 + - + +
34J ASN* 3.1 37.4 + - + -
35J LYS* 3.0 37.3 + - + +
36J VAL* 3.1 15.1 + - - +
50J VAL 3.8 5.5 + - - -
52J GLN* 4.1 18.2 - - - +
98J LYS* 5.1 8.3 + - - -
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Residues in contact with LYS 33 (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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14J ASN* 4.8 7.2 - - - +
15J VAL* 4.7 16.2 + - - +
16J ALA* 3.5 13.2 - - + +
32J TYR* 1.3 103.6 - - + +
34J ASN* 1.3 58.3 + - - +
36J VAL* 5.2 0.2 - - - -
37J VAL* 3.3 25.3 + - - +
93J VAL* 4.6 2.8 - - - +
94J GLN* 3.4 30.5 + - + +
95J VAL* 4.2 2.3 + - - -
96J SER* 3.1 32.2 + - - +
99J GLU* 4.5 0.3 - - - +
2551N C 4.4 16.2 + - - -
2552N U 4.1 16.4 + - - -
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Residues in contact with ASN 34 (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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32J TYR* 3.1 28.8 - - + -
33J LYS* 1.3 74.9 - - - +
35J LYS* 1.3 64.3 + - + +
36J VAL 3.3 1.1 - - - -
37J VAL* 3.2 4.2 + - - +
38J GLY* 2.9 26.2 + - - -
96J SER* 2.7 20.5 + - - -
98J LYS* 3.6 34.7 + - - +
99J GLU* 4.3 18.4 + - + +
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Residues in contact with LYS 35 (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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32J TYR* 3.0 30.6 + - + +
34J ASN* 1.3 80.7 - - + +
36J VAL* 1.3 57.4 + - - +
38J GLY* 3.2 3.0 + - - -
39J TRP* 2.9 28.9 + - - +
45J LYS* 4.3 13.8 - - - +
49J GLU* 2.7 45.3 + - - +
50J VAL* 3.6 31.8 - - + +
52J GLN* 4.2 21.1 + - - +
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Residues in contact with VAL 36 (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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16J ALA* 4.8 0.7 - - + -
18J VAL* 4.2 11.0 - - + -
31J CYS* 3.3 35.9 - - + -
32J TYR 3.1 8.1 + - - +
33J LYS 4.8 0.2 - - - +
35J LYS* 1.3 76.2 - - - +
37J VAL* 1.3 56.8 + - - +
39J TRP* 3.2 4.6 + - - +
40J ARG* 2.9 44.1 + - - +
50J VAL 4.8 0.9 - - - +
88J LEU* 3.7 35.6 - - + +
93J VAL* 3.5 29.6 - - + -
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Residues in contact with VAL 37 (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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33J LYS 3.3 19.1 - - - +
34J ASN 3.2 8.6 + - - +
36J VAL* 1.3 77.5 - - - +
38J GLY* 1.3 61.5 + - - +
40J ARG* 3.2 15.0 + - + +
41J SER* 3.1 29.1 + - - +
93J VAL* 4.8 10.3 - - + -
95J VAL* 3.9 24.2 - - + -
99J GLU* 3.4 29.2 - - + +
103J GLN* 6.1 5.2 - - - +
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Residues in contact with GLY 38 (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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34J ASN 2.9 14.3 + - - -
35J LYS* 3.2 4.2 + - - -
37J VAL* 1.3 77.6 - - - +
39J TRP* 1.3 61.8 + - - +
41J SER* 3.4 11.0 + - - +
43J VAL* 3.0 37.4 + - - +
45J LYS* 6.4 0.9 - - - -
99J GLU* 5.3 0.6 + - - -
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Residues in contact with TRP 39 (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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35J LYS 2.9 12.3 + - - +
36J VAL* 3.2 13.0 + - - +
38J GLY* 1.3 79.1 - - - +
40J ARG* 1.3 65.8 + - + +
41J SER 3.4 1.0 + - - -
42J GLY 3.5 9.9 + - - -
43J VAL 3.6 9.1 + - - -
44J GLU* 3.0 53.7 + - + +
45J LYS* 3.2 33.2 - - - +
46J ASP* 3.8 24.5 - - - -
47J LEU* 4.5 7.0 - - + -
50J VAL* 3.6 20.8 - - + +
85J LYS* 4.1 23.3 - - + +
88J LEU* 3.5 36.0 - - + +
89J THR* 4.4 18.0 - - + +
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Residues in contact with ARG 40 (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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18J VAL* 4.6 0.6 - - - +
36J VAL* 2.9 26.3 + - - +
37J VAL* 3.2 20.4 + - + +
39J TRP* 1.3 83.7 - - + +
41J SER* 1.3 61.2 + - - +
42J GLY 3.7 0.9 - - - -
88J LEU 2.9 28.9 + - - +
89J THR* 3.5 22.5 + - + +
91J GLY 3.0 25.2 + - - +
93J VAL* 3.7 28.3 - - - +
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Residues in contact with SER 41 (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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37J VAL* 3.1 19.0 + - - +
38J GLY* 3.4 7.6 - - - +
40J ARG* 1.3 82.9 + - - +
42J GLY* 1.3 54.3 + - - +
43J VAL* 3.6 8.8 + - - +
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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