Contacts of the strand formed by residues 40 - 46 (chain C) in PDB entry 5LEZ
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 ILE 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C GLY* 2.8 31.4 + - - -
38C ARG 3.7 0.8 - - - +
39C ASP* 1.3 83.1 - - - +
41C VAL* 1.3 77.2 + - - +
42C VAL* 4.2 6.3 - - + -
136C PHE* 4.0 2.2 - - - -
142C PRO* 4.6 0.5 - - - +
183C THR 5.5 0.2 - - - -
184C ASP* 3.2 42.6 - - + +
187C THR* 4.0 28.3 - - + +
188C ILE* 4.4 4.5 - - + -
210C VAL* 3.4 38.1 - - + -
211C MET 3.6 14.4 - - - +
212C ARG* 4.1 9.6 - - + +
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Residues in contact with VAL 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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35C VAL 3.6 5.6 - - - +
36C ARG* 4.1 13.5 - - - -
40C ILE* 1.3 81.7 - - - +
42C VAL* 1.3 64.5 + - - +
134C VAL* 3.8 30.1 - - + +
135C GLY 4.0 8.5 - - - +
136C PHE* 4.1 6.1 - - + -
142C PRO* 3.8 23.3 - - + -
143C ARG 4.0 16.6 - - - +
210C VAL* 3.5 2.3 - - - -
211C MET* 2.9 51.5 + - + +
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Residues in contact with VAL 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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33C VAL 4.6 0.2 - - - -
34C GLY* 3.3 4.5 - - - -
35C VAL 3.1 31.1 + - - +
40C ILE* 4.2 6.7 - - + -
41C VAL* 1.3 79.8 - - - +
43C LEU* 1.3 70.5 + - - +
134C VAL* 4.8 2.6 - - - +
187C THR* 3.7 26.5 - - + -
188C ILE* 4.1 14.4 - - + +
191C VAL* 3.7 26.0 - - + -
208C LEU* 3.7 23.6 - - + -
209C ALA 3.5 12.1 - - - +
210C VAL* 4.0 13.9 - - + -
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Residues in contact with LEU 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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33C VAL 3.2 17.0 - - - +
34C GLY* 3.9 9.0 - - - -
42C VAL* 1.3 84.6 - - - +
44C GLY* 1.3 58.9 + - - +
62C ILE* 3.6 23.2 - - + +
70C CYS* 3.9 15.0 - - - -
71C MET* 3.9 4.9 - - - -
72C ALA* 3.9 27.1 - - + +
132C LEU* 4.0 22.9 - - + +
134C VAL* 3.5 35.4 - - + -
191C VAL* 4.4 0.7 - - - -
208C LEU* 3.5 2.9 - - - +
209C ALA* 3.0 34.8 + - + +
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Residues in contact with GLY 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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32C ALA* 3.5 0.7 - - - +
33C VAL* 2.7 36.8 + - - +
43C LEU* 1.3 75.1 - - - +
45C VAL* 1.3 64.6 + - - +
62C ILE* 4.3 0.2 - - - -
72C ALA* 5.6 0.3 - - - +
191C VAL* 3.9 15.1 - - - +
195C LEU* 3.9 9.5 - - - +
207C GLU 3.3 11.2 - - - -
208C LEU* 4.2 4.0 - - - -
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Residues in contact with VAL 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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30C SER* 4.5 4.5 - - - -
31C THR 3.3 13.5 - - - +
32C ALA* 4.1 8.1 - - + -
44C GLY* 1.3 76.7 - - - +
46C GLU* 1.3 75.5 + - - +
61C LYS* 4.1 34.3 - - + -
62C ILE* 3.6 31.4 - - + -
72C ALA* 4.6 9.9 - - + -
73C PHE 5.4 2.0 - - - +
195C LEU* 3.4 8.7 - - - +
206C ILE* 3.5 2.8 - - - -
207C GLU* 3.0 38.9 + - + +
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Residues in contact with GLU 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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30C SER* 3.5 15.1 - - - -
31C THR* 2.9 51.0 + - - +
45C VAL* 1.3 85.8 - - - +
47C LYS* 1.3 78.2 + - + +
48C LYS* 3.4 9.4 + - - +
61C LYS* 5.4 1.2 - - - -
163C ARG* 3.2 35.5 + - - +
195C LEU* 3.6 9.9 - - + +
198C VAL* 4.6 15.1 - - + +
199C VAL* 4.7 15.9 - - + -
200C GLN* 4.9 4.9 + - - +
205C ASN 3.7 3.8 - - - -
207C GLU* 5.7 0.7 - - - +
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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