Contacts of the helix formed by residues 35 - 43 (chain C) in PDB entry 1JT0
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 SER 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.1 13.2 - - - +
34C SER* 1.3 78.7 + - - +
36C LYS* 1.3 66.9 + - - +
37C GLY 3.2 0.2 - - - -
38C ASN* 3.9 1.7 - - - +
39C LEU* 3.0 23.2 + - - +
11F T 3.7 1.6 - - - +
12F A 2.7 63.5 + - - -
13F G 3.8 10.5 - - - -
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Residues in contact with LYS 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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25C THR* 3.0 30.6 + - - -
26C GLY* 4.1 13.8 - - - +
29C VAL* 4.2 13.3 - - + +
35C SER* 1.3 73.2 - - - +
37C GLY* 1.3 59.9 + - - +
39C LEU* 3.2 4.4 + - + +
40C TYR* 2.8 47.3 + - + +
25E G 3.6 9.9 + - - -
26E G 2.7 54.2 + - - +
27E T 3.5 16.4 - - - +
13F G 3.5 5.4 + - + +
14F A 3.6 12.1 - - - +
15F C 5.3 0.7 - - - +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 1.3 76.1 - - - +
38C ASN* 1.3 57.5 + - - +
40C TYR* 3.2 3.1 + - - +
41C TYR* 2.8 30.0 + - - +
28E C 4.2 3.6 - - - -
11F T 4.0 3.5 - - - +
12F A 3.3 21.1 - - - -
13F G 2.8 31.2 + - - -
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Residues in contact with ASN 38 (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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3C LEU* 3.6 13.7 - - - +
7C ILE* 4.2 2.4 - - - +
34C SER* 3.1 28.1 + - - +
35C SER* 3.5 3.3 + - - +
36C LYS 3.3 0.4 - - - -
37C GLY* 1.3 74.6 - - - +
39C LEU* 1.3 61.6 + - - +
41C TYR* 3.0 0.9 + - - +
42C HIS* 2.8 59.9 + - - -
10F A 3.6 2.8 - - - +
11F T 3.0 55.1 + - + +
12F A 3.7 13.5 + - - +
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Residues in contact with LEU 39 (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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7C ILE* 3.6 40.9 - - + +
25C THR* 4.3 17.0 - - + -
28C ILE* 4.2 18.8 - - + -
29C VAL* 4.7 7.6 - - + -
35C SER 3.0 20.3 + - - +
36C LYS* 3.5 5.4 - - + +
38C ASN* 1.3 75.9 - - - +
40C TYR* 1.3 95.2 + - + +
43C PHE* 3.0 45.0 + - + +
46C LYS* 6.3 1.3 - - - +
49C LEU* 4.3 13.0 - - + -
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Residues in contact with TYR 40 (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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25C THR* 3.5 13.2 - - + +
36C LYS* 2.8 25.3 + - + +
37C GLY* 4.0 2.5 - - - +
39C LEU* 1.3 101.1 - - + +
41C TYR* 1.3 62.9 + - - +
43C PHE* 2.7 19.4 - - + +
44C LYS* 3.5 27.4 - - - -
45C THR* 4.2 4.0 - - - -
46C LYS 4.3 2.3 + - - -
25E G 3.2 15.8 - - - +
26E G 2.7 65.3 + + + -
27E T 3.4 26.9 - - + +
28E C 6.0 0.9 - - - +
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Residues in contact with TYR 41 (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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37C GLY 2.8 10.1 + - - +
38C ASN 3.0 2.4 + - - +
40C TYR* 1.3 80.7 - - - +
42C HIS* 1.3 101.8 + + - +
43C PHE* 3.3 2.4 + - - +
9F T 2.8 41.9 + + + +
10F A 3.0 40.1 + + + -
11F T 3.1 34.5 - - + -
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Residues in contact with HIS 42 (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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2C ASN 5.7 1.8 + - - -
4C LYS* 3.8 47.6 + - + +
7C ILE* 4.9 1.8 - - - +
38C ASN* 2.8 42.1 + - - +
41C TYR* 1.3 104.3 - + - +
43C PHE* 1.3 86.4 + - + +
52C GLU* 5.0 0.5 - - - +
10F A 4.0 14.5 + - + -
11F T 2.7 30.5 + - - -
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Residues in contact with PHE 43 (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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4C LYS* 3.5 34.8 - - + -
7C ILE* 3.6 24.2 - - + -
8C LEU* 3.8 13.9 - - + -
39C LEU* 3.0 30.7 + - + +
40C TYR* 2.7 30.5 - - + +
41C TYR 3.2 2.0 - - - -
42C HIS* 1.3 95.2 - + + +
44C LYS* 1.3 62.4 + - - +
45C THR 4.6 8.3 - - - +
48C ASN 5.0 0.7 - - - -
49C LEU* 3.6 40.4 - - + +
52C GLU* 3.5 25.1 - - - -
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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