Contacts of the strand formed by residues 36 - 41 (chain C) in PDB entry 1E3S
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 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLY* 5.0 4.2 + - - +
11C LEU 3.0 7.2 + - - +
12C VAL* 3.3 34.1 - - + +
13C ALA* 3.0 27.8 + - - +
30C LEU* 5.9 0.2 - - - +
34C GLY 5.4 0.9 - - - +
35C ALA* 1.3 79.2 - - - +
37C ALA* 1.3 61.3 + - - +
57C ASN* 3.4 35.2 - - + +
82C PHE* 4.0 25.7 - - + -
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Residues in contact with ALA 37 (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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13C ALA* 3.4 7.9 - - + +
15C ILE* 4.6 10.8 - - + -
27C ALA* 4.4 19.7 - - + +
30C LEU* 5.7 3.4 - - + -
31C VAL* 3.8 20.8 - - + +
36C THR* 1.3 76.0 - - - +
38C VAL* 1.3 63.6 + - - +
39C LEU* 4.1 2.0 - - + -
57C ASN 3.0 8.6 + - - +
58C CYS* 3.2 12.2 - - - -
59C ILE* 3.2 23.0 + - - +
82C PHE* 4.6 2.3 - - - -
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Residues in contact with VAL 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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12C VAL* 5.2 2.5 - - + -
13C ALA 2.9 14.7 + - - +
14C VAL* 3.6 15.6 - - + +
15C ILE* 3.0 24.8 + - - -
37C ALA* 1.3 76.0 - - - +
39C LEU* 1.3 63.2 + - - +
40C LEU* 3.5 1.6 + - + +
59C ILE* 3.6 17.7 - - + +
61C ALA* 4.0 26.0 - - + -
74C ALA* 4.9 3.8 - - + +
77C LEU* 5.9 0.2 - - + -
78C ALA* 3.7 30.3 - - + -
82C PHE* 3.8 24.2 - - + -
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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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15C ILE* 3.7 7.2 - - + -
18C GLY* 3.7 33.0 - - - +
19C ALA* 4.7 1.3 - - - +
24C LEU* 5.0 2.9 - - + -
27C ALA* 3.6 31.2 - - + -
37C ALA* 4.7 2.5 - - + -
38C VAL* 1.3 74.6 - - - +
40C LEU* 1.3 57.8 + - - +
41C ASP* 3.9 0.4 - - + -
47C GLY* 4.0 22.0 - - - +
50C GLU* 4.4 9.9 - - + -
51C ALA* 4.1 9.2 - - + +
54C LEU* 5.4 0.7 - - + -
58C CYS* 3.7 26.9 - - - -
59C ILE 2.9 13.1 + - - +
60C PHE* 3.4 13.7 - - + -
61C ALA* 2.9 29.1 + - - -
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Residues in contact with LEU 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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14C VAL* 4.4 21.8 - - + -
15C ILE 3.0 12.2 + - - +
16C THR* 3.3 14.5 - - + -
17C GLY 2.8 31.4 + - - -
18C GLY 3.6 0.4 + - - +
38C VAL* 3.5 2.3 + - + +
39C LEU* 1.3 70.1 - - - +
41C ASP* 1.3 60.4 + - - +
61C ALA* 3.5 7.9 - - + +
63C ALA* 3.8 32.8 - - + +
65C VAL* 3.9 26.7 - - + +
71C VAL* 4.8 17.9 - - + +
74C ALA* 3.7 25.1 - - + -
75C LEU* 5.1 3.6 - - + -
128C VAL* 5.4 1.8 - - + -
301C NAD 4.5 0.8 + - + -
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Residues in contact with ASP 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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17C GLY* 3.2 10.1 - - - -
18C GLY 5.1 0.2 - - - -
19C ALA* 3.1 32.3 + - + +
39C LEU 3.9 1.6 + - - -
40C LEU* 1.3 75.9 - - - +
42C VAL* 1.3 77.4 + - - +
45C SER* 3.7 10.7 - - - +
60C PHE* 3.7 9.3 - - + -
61C ALA 3.7 3.8 + - - -
62C PRO* 3.3 7.3 - - - +
63C ALA 3.0 25.3 + - - -
301C NAD 2.6 56.9 + - - -
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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