Contacts of the helix formed by residues 26 - 36 (chain C) in PDB entry 3N1Y
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 THR 26 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU 4.8 0.5 + - - -
25C ASP* 1.3 76.0 - - - +
27C MET* 1.3 58.3 + - - +
28C ASP* 3.2 17.0 - - + +
29C GLN* 2.9 25.7 + - - -
30C VAL* 2.8 27.5 + - - +
64C ARG 2.6 31.4 - - - +
65C GLY* 3.7 20.1 + - - -
66C MET 3.3 6.1 - - - -
67C ILE* 4.0 8.8 - - - +
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Residues in contact with MET 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C THR* 1.3 74.7 - - - +
28C ASP* 1.3 57.2 + - - +
30C VAL* 3.2 9.3 + - - -
31C ALA* 2.9 26.9 + - - +
51C LEU 5.8 0.7 - - - -
52C ARG* 6.2 0.2 - - - +
53C VAL* 3.2 45.0 - - + +
62C PHE* 3.5 22.2 - - + +
63C PRO 3.2 26.9 - - - +
64C ARG* 3.4 5.6 - - - +
66C MET* 2.8 35.5 + - + +
68C VAL* 4.1 17.5 - - + +
71C ALA* 3.6 31.2 - - + -
73C LEU* 5.3 3.1 - - + -
79C LEU* 5.7 2.0 - - - -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C THR* 3.0 13.2 - - + +
27C MET* 1.3 77.9 - - - +
29C GLN* 1.3 60.1 + - + +
31C ALA* 3.3 7.3 + - - +
32C GLU* 3.0 25.8 + - - +
51C LEU 4.2 10.2 - - - +
64C ARG* 3.1 65.9 + - - +
65C GLY* 5.5 0.2 - - - -
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU 4.2 3.3 - - - +
25C ASP* 3.5 23.1 - - + +
26C THR* 2.9 37.0 + - - +
28C ASP* 1.3 77.0 - - + +
30C VAL* 1.3 65.8 + - - +
32C GLU* 3.4 8.9 + - - +
33C LYS* 3.1 30.5 + - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 5.0 0.2 - - + -
21C VAL* 3.9 26.6 - - + +
25C ASP* 4.0 5.2 - - + -
26C THR 2.8 17.9 + - - +
27C MET* 3.4 15.0 - - - +
29C GLN* 1.3 75.9 - - - +
31C ALA* 1.3 65.3 + - - +
33C LYS* 3.0 6.0 + - - +
34C CYS* 3.0 33.8 + - - -
53C VAL* 4.1 13.9 - - + -
68C VAL* 3.6 30.1 - - + -
79C LEU* 4.4 19.5 - - + -
81C ILE* 4.7 0.2 - - + -
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 4.3 0.7 - - - -
27C MET 2.9 17.6 + - - +
28C ASP* 3.6 5.6 - - - +
30C VAL* 1.3 78.4 - - - +
32C GLU* 1.3 56.9 + - - +
34C CYS* 3.6 3.1 - - - +
35C ALA* 2.8 31.2 + - - +
51C LEU* 3.8 37.4 - - + +
53C VAL* 4.1 8.1 - - + -
81C ILE* 3.9 17.9 - - + -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP 3.0 14.1 + - - +
29C GLN* 3.5 12.8 - - - +
31C ALA* 1.3 77.6 - - - +
33C LYS* 1.3 65.0 + - + +
35C ALA* 3.4 10.2 + - - +
36C TYR* 3.3 20.4 + - - +
51C LEU* 5.4 3.1 - - - +
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 3.9 14.8 - - + +
20C PRO 4.0 15.6 + - - +
21C VAL* 4.2 7.1 - - + +
22C ASP* 3.8 13.3 - - - +
25C ASP* 2.5 39.1 + - - +
29C GLN* 3.1 12.2 + - - +
30C VAL* 3.0 9.2 + - - +
32C GLU* 1.3 79.2 - - + +
34C CYS* 1.3 60.3 + - - +
36C TYR* 3.4 18.2 - - - +
37C HIS* 3.5 14.4 - - - -
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Residues in contact with CYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.9 18.8 - - - -
8C SER* 3.4 36.0 + - - +
10C PHE* 4.0 6.9 - - + -
17C GLN* 5.3 0.2 - - - +
19C VAL* 4.2 11.0 - - - -
30C VAL* 3.0 19.5 + - - +
31C ALA 3.6 7.6 - - - +
33C LYS* 1.3 76.1 - - - +
35C ALA* 1.3 65.0 + - - +
37C HIS* 3.0 17.5 + - - +
38C SER* 3.6 7.1 + - - -
81C ILE* 3.8 28.0 - - + -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.4 17.7 - - + -
31C ALA 2.8 17.7 + - - +
32C GLU* 3.6 12.6 - - - +
34C CYS* 1.3 76.2 - - - +
36C TYR* 1.3 62.6 + - - +
38C SER 2.8 0.5 + - - -
39C ILE* 2.7 49.3 + - + +
51C LEU* 4.0 11.2 - - + -
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A LEU* 5.8 0.2 - - - +
391A GLU* 2.8 37.1 + - - -
32C GLU 3.3 9.6 + - - +
33C LYS* 3.4 15.3 - - - +
34C CYS 3.2 0.2 - - - -
35C ALA* 1.3 78.0 - - - +
37C HIS* 1.3 82.0 + + - +
38C SER 3.7 0.2 + - - -
39C ILE 4.3 3.7 - - - +
41C ARG* 3.0 36.5 + - - +
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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