Contacts of the strand formed by residues 206 - 212 (chain C) in PDB entry 5LF4
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 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C VAL 3.4 6.3 - - - -
192C ILE* 5.7 7.6 - - + -
195C LEU* 3.4 28.0 - - + -
203C GLY* 4.5 11.1 - - - +
204C LYS 3.7 5.4 - - - +
205C ASN* 1.3 77.3 - - - +
207C GLU* 1.3 61.5 + - - +
208C LEU* 4.1 9.2 + - + -
225C ILE* 4.6 20.1 - - + +
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Residues in contact with GLU 207 (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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44C GLY* 3.3 2.3 - - - -
45C VAL* 2.8 44.1 + - + +
47C LYS 5.0 5.8 + - - +
60C ARG* 5.8 9.0 - - + -
61C LYS 6.0 4.5 - - - +
62C ILE* 4.2 11.8 - - + +
205C ASN 4.0 0.8 - - - -
206C ILE* 1.3 73.7 - - - +
208C LEU* 1.3 59.1 + - - +
220C LEU 6.0 0.2 - - - -
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Residues in contact with LEU 208 (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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42C VAL* 3.7 20.6 - - + -
43C LEU 3.5 9.2 - - - +
44C GLY* 4.5 3.8 - - - -
62C ILE* 4.3 2.0 - - - -
188C ILE* 4.2 8.3 - - + +
191C VAL* 3.9 20.6 - - + -
192C ILE* 3.5 32.5 - - + -
195C LEU* 5.6 0.4 - - + -
206C ILE* 4.1 6.9 + - + +
207C GLU* 1.3 75.0 - - - +
209C ALA* 1.3 74.2 + - - +
210C VAL* 4.3 4.0 - - + -
219C ILE* 3.6 3.9 - - - +
220C LEU* 2.8 53.8 + - + +
225C ILE* 3.6 23.1 - - + +
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Residues in contact with ALA 209 (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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42C VAL* 3.5 3.8 - - - +
43C LEU* 2.9 35.8 + - + +
62C ILE* 3.9 24.4 - - + +
208C LEU* 1.3 76.6 - - - +
210C VAL* 1.3 66.0 + - - +
217C LEU* 3.9 19.7 - - + -
218C LYS 3.4 11.2 - - - +
219C ILE* 4.1 11.2 - - + -
220C LEU* 4.5 0.9 - - - +
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Residues in contact with VAL 210 (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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40C ILE* 3.3 24.0 - - + -
41C VAL 3.5 3.8 - - - -
42C VAL* 3.8 23.6 - - + -
188C ILE* 3.8 22.7 - - + -
208C LEU* 4.3 5.2 - - + -
209C ALA* 1.3 80.3 - - - +
211C MET* 1.3 68.0 + - - +
212C ARG* 3.7 23.1 - - + +
216C SER 4.4 0.2 - - - +
217C LEU* 3.7 7.1 - - - +
218C LYS* 2.9 38.4 + - + +
220C LEU* 5.0 10.3 - - + -
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Residues in contact with MET 211 (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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40C ILE* 3.5 1.6 - - - -
41C VAL* 2.9 48.4 + - + -
64C ALA* 6.2 0.2 - - + -
66C ASP 5.2 1.3 - - - +
67C ASP 4.1 11.2 - - - +
68C ASN* 3.8 28.0 - - - +
69C VAL* 4.1 3.1 - - - +
70C CYS* 3.6 34.5 - - + +
134C VAL* 5.2 0.2 - - + -
135C GLY* 4.2 11.9 - - - -
136C PHE* 3.2 12.8 - - + -
210C VAL* 1.3 74.4 - - - +
212C ARG* 1.3 71.5 + - - +
216C SER* 4.5 11.0 - - - +
217C LEU* 3.7 31.0 - - + +
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Residues in contact with ARG 212 (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* 4.1 8.1 - - - +
40C ILE* 4.0 19.3 - - + +
136C PHE* 3.5 7.4 - - - -
184C ASP* 2.7 37.4 + - - +
188C ILE* 4.7 8.5 - - - +
210C VAL* 3.7 15.5 - - + +
211C MET* 1.3 80.6 - - - +
213C ARG* 1.3 58.3 + - - +
214C ASP 3.1 1.4 + - - -
215C GLN* 2.8 44.6 + - + +
216C SER 3.9 5.5 + - - -
218C LYS* 5.5 6.9 - - - +
228C TYR* 5.7 0.8 + - - -
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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