Contacts of the strand formed by residues 42 - 48 (chain C) in PDB entry 3LON
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 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ILE* 4.2 4.5 - - + -
36C VAL 2.9 21.1 - - - +
37C SER* 3.1 15.8 + - - +
41C GLN* 1.3 82.4 + - - +
43C PHE* 1.3 67.6 + - - +
109C ARG* 2.9 41.9 + - - +
137C GLY* 3.4 16.2 - - - -
26D VAL* 4.6 1.8 - - + -
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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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35C ILE* 3.8 0.2 - - - -
36C VAL* 2.9 49.8 + - + +
37C SER* 4.8 0.2 - - - -
38C THR* 4.0 19.1 - - + -
41C GLN* 4.1 17.9 - - + +
42C THR* 1.3 81.7 - - - +
44C LEU* 1.3 72.6 + - - +
54C THR* 3.1 32.5 - - + -
55C VAL* 4.0 10.3 - - + -
58C GLY* 3.3 34.1 - - - -
59C ALA* 3.4 17.5 - - + -
109C ARG* 3.7 4.7 + - - -
137C GLY* 3.2 18.2 - - - +
139C SER* 3.3 15.9 - - - +
23D VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 44 (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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33C VAL* 4.1 16.2 - - + -
34C GLN 3.4 7.2 - - - +
35C ILE* 3.8 21.8 - - + -
36C VAL* 4.1 2.9 - - - -
43C PHE* 1.3 82.4 - - - +
45C ALA* 1.3 56.6 + - - +
54C THR* 2.7 27.5 + - - -
107C VAL* 3.8 14.8 - - + +
108C THR 4.1 1.8 - - - -
109C ARG* 3.6 31.2 - - + +
137C GLY 3.7 8.1 - - - +
138C SER* 3.3 24.7 - - - +
139C SER 2.9 7.7 + - - +
140C GLY* 3.2 9.9 - - - -
141C GLY* 3.5 24.7 - - - +
29D ILE* 5.1 0.2 - - + -
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Residues in contact with ALA 45 (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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33C VAL* 3.3 7.4 - - - +
34C GLN* 2.9 35.0 + - - +
36C VAL* 4.0 14.8 - - + -
44C LEU* 1.3 76.0 - - - +
46C THR* 1.3 65.2 + - - +
52C CYS* 3.5 25.1 - - - -
53C TRP 3.0 14.1 - - - +
54C THR* 4.0 8.3 - - - -
85C TRP* 4.7 2.5 - - + -
140C GLY 4.0 0.9 - - - -
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Residues in contact with THR 46 (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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32C GLU 3.5 7.0 - - - +
33C VAL* 4.2 2.2 - - + +
34C GLN* 4.2 0.4 - - - -
45C ALA* 1.3 74.6 + - - +
47C CYS* 1.3 63.0 + - - +
48C ILE* 3.8 14.1 - - + -
53C TRP* 2.7 44.5 + - - +
94C LEU* 3.8 28.7 - - + -
140C GLY 2.7 23.4 + - - -
141C GLY* 3.4 13.3 - - - -
142C PRO* 3.4 16.6 - - + +
153C LEU* 4.0 10.5 - - - -
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Residues in contact with CYS 47 (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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32C GLU 2.8 11.8 + - - +
34C GLN* 3.4 30.5 - - - -
46C THR* 1.3 72.2 - - - +
48C ILE* 1.3 63.3 + - - +
51C VAL 3.1 5.6 - - - +
52C CYS* 3.8 19.7 - - - -
87C ALA* 3.8 11.2 - - + -
88C PRO* 3.9 0.9 - - - -
91C SER* 3.7 16.8 - - - -
92C ARG 3.6 19.3 - - - +
93C SER* 3.5 10.7 - - - +
94C LEU* 2.8 25.8 + - - +
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Residues in contact with ILE 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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46C THR* 3.6 14.0 + - + -
47C CYS* 1.3 80.2 - - - +
49C ASN* 1.3 76.1 + - - +
50C GLY 3.3 0.9 - - - -
51C VAL* 2.8 13.3 + - - +
53C TRP* 2.9 30.1 + - + +
94C LEU* 3.6 22.0 - - + +
96C PRO* 4.0 22.0 - - + -
142C PRO* 5.8 0.7 - - + -
150C ALA* 3.7 21.8 - - + -
152C GLY 5.5 2.0 - - - +
153C LEU* 3.9 17.5 - - + -
172C VAL* 4.3 7.0 - - + -
175C LEU* 3.6 27.1 - - + -
176C GLU* 6.2 1.1 - - + -
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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