Contacts of the helix formed by residues 45 - 53 (chain C) in PDB entry 1L3B
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 GLY 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.3 4.5 - - - -
42C CYS 3.0 12.1 + - - -
43C GLY 3.2 0.6 - - - -
44C THR* 1.3 79.4 - - - +
46C GLY* 1.3 71.2 + - - +
47C VAL 3.5 1.3 - - - -
48C THR* 3.8 5.6 - - - -
49C LEU* 2.9 28.6 + - - +
71C THR* 3.3 24.9 - - - -
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.7 20.7 - - - -
16C PRO* 5.0 5.3 - - - +
17C THR* 5.4 2.0 - - - +
22C ARG* 3.8 23.1 - - - -
42C CYS 4.4 1.8 + - - -
44C THR* 3.6 4.6 - - - -
45C GLY* 1.3 81.9 - - - +
47C VAL* 1.3 63.5 + - - +
49C LEU* 2.9 15.1 + - - +
50C GLU* 3.2 9.9 + - - +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 4.4 14.8 + - - +
22C ARG* 4.2 10.0 - - + +
25C ILE* 4.2 31.6 - - + -
26C MSE 5.1 2.9 - - - -
39C ASP* 3.3 29.8 - - - +
42C CYS 5.3 1.9 + - - +
46C GLY* 1.3 73.1 - - - +
48C THR* 1.3 64.1 + - - +
49C LEU 3.2 0.3 + - - -
50C GLU* 3.2 8.2 + - - +
51C LEU* 3.1 35.1 + - + +
105C VAL* 4.0 18.6 - - + -
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Residues in contact with THR 48 (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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39C ASP* 3.2 26.0 + - - +
42C CYS* 3.5 15.2 - - - +
45C GLY* 3.4 4.8 + - - -
46C GLY 3.2 0.8 - - - -
47C VAL* 1.3 77.2 - - - +
49C LEU* 1.3 56.3 + - - +
51C LEU* 3.7 1.5 + - - +
52C ALA* 3.0 27.7 + - - +
58C VAL* 4.4 13.5 - - + +
60C ALA* 3.8 6.3 - - + +
71C THR* 3.8 25.8 - - + -
75C LEU* 4.2 4.9 - - + -
84C VAL* 3.7 30.1 - - + -
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Residues in contact with LEU 49 (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 ILE* 4.7 9.2 - - + -
7C PHE* 4.2 13.2 - - + -
45C GLY 2.9 17.8 + - - +
46C GLY* 3.1 11.9 - - - +
48C THR* 1.3 74.9 - - - +
50C GLU* 1.3 72.2 + - - +
52C ALA* 3.4 14.6 - - - +
53C GLY 3.6 0.9 + - - -
71C THR 4.5 0.7 - - - +
74C ASN* 3.6 13.2 - - + +
75C LEU* 3.5 44.0 - - + +
78C HIS* 3.7 27.4 - - + -
80C LEU* 3.6 38.3 - - + +
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Residues in contact with GLU 50 (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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1C MSE 3.3 50.1 - - + +
2C ILE* 3.5 19.5 - - - +
7C PHE* 4.7 0.3 - - - -
22C ARG* 3.4 18.7 + - + +
26C MSE 3.2 36.5 - - + +
46C GLY 3.2 13.0 + - - +
47C VAL* 3.2 6.9 + - - +
49C LEU* 1.3 86.2 - - - +
51C LEU* 1.3 65.1 + - - +
53C GLY* 3.5 6.9 + - - -
54C ARG* 3.3 18.2 + - - -
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Residues in contact with LEU 51 (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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26C MSE 3.5 28.0 - - + -
29C ALA* 4.4 4.3 - - + -
31C PRO* 4.1 12.8 - - + -
37C ALA* 3.9 21.5 - - + -
38C VAL 5.0 2.2 - - - +
39C ASP* 4.8 7.9 - - + +
47C VAL* 3.1 31.1 + - + +
50C GLU* 1.3 78.8 - - - +
52C ALA* 1.3 53.0 + - - +
54C ARG* 2.6 28.1 + - - -
55C VAL* 3.1 19.4 + - + +
58C VAL* 4.0 22.4 - - + -
103C ILE* 4.4 20.2 - - + -
105C VAL* 4.7 10.8 - - + -
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Residues in contact with ALA 52 (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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48C THR 3.0 20.1 + - - +
49C LEU 3.4 8.5 - - - +
51C LEU* 1.3 75.1 - - - +
53C GLY* 1.3 56.8 + - - +
54C ARG 3.3 3.5 + - - -
55C VAL 4.1 1.9 - - - +
58C VAL* 3.7 13.3 - - - +
75C LEU* 4.0 7.0 - - + -
80C LEU* 4.0 19.0 - - + +
83C ASN* 2.8 26.7 + - - +
84C VAL* 3.7 20.0 - - + -
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Residues in contact with GLY 53 (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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49C LEU 3.6 3.6 + - - -
50C GLU 3.5 5.9 + - - -
51C LEU 2.9 1.8 + - - -
52C ALA* 1.3 79.0 - - - +
54C ARG* 1.3 70.7 + - - +
80C LEU* 4.2 17.2 - - - +
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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