Contacts of the strand formed by residues 194 - 198 (chain C) in PDB entry 5MLE
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 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASN* 2.9 24.0 + - - +
163C SER* 3.5 1.7 - - - -
164C PHE 3.1 25.3 + - - -
188C ILE* 3.7 4.5 - - - +
193C ALA* 1.3 79.2 - - - +
195C ALA* 1.3 64.8 + - - +
196C GLN* 3.5 3.1 + - + +
249C PRO* 4.1 21.8 - - + +
250C LEU 4.9 0.4 - - - +
251C TYR* 3.8 29.6 - - + +
275C TYR* 5.6 2.5 - - + -
391C VAL* 3.8 33.2 - - + +
392C PHE* 4.2 19.7 - - + -
475C PRO* 3.9 20.9 - - + -
478C VAL* 5.0 5.4 - - + -
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Residues in contact with ALA 195 (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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164C PHE 3.9 3.1 - - - -
166C VAL* 6.1 0.2 - - + -
185C LEU* 3.9 22.4 - - + -
188C ILE* 3.7 15.9 - - + +
194C ILE* 1.3 73.4 - - - +
196C GLN* 1.3 62.8 + - - +
248C CYS* 3.9 18.4 - - - -
249C PRO 3.1 16.9 + - - +
250C LEU* 3.5 10.4 - - + +
251C TYR 3.0 24.3 + - - -
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Residues in contact with GLN 196 (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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107C HIS* 3.1 26.4 - - - -
138C HIS* 3.6 24.8 + - - +
163C SER* 5.2 0.9 - - - -
164C PHE 2.7 19.6 + - - +
165C LEU* 3.5 16.1 - - + +
166C VAL* 3.2 21.0 + - - +
194C ILE* 3.5 7.4 + - + +
195C ALA* 1.3 77.2 - - - +
197C VAL* 1.3 68.0 + - - +
251C TYR* 3.2 46.3 - - + +
253C THR* 3.9 4.2 - - + +
392C PHE* 4.0 5.2 - - + -
608C NI 3.2 19.4 - - - +
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 4.4 3.8 - - - -
166C VAL* 3.5 25.6 - - + -
168C MET* 4.2 13.5 - - - -
181C ILE* 5.6 2.7 - - + -
185C LEU* 5.6 3.8 - - + -
195C ALA 5.4 0.2 - - - -
196C GLN* 1.3 82.2 - - - +
198C HIS* 1.3 58.3 + - - +
199C ALA* 3.5 30.2 + - + +
239C ALA* 4.4 14.4 - - + -
250C LEU* 4.0 21.8 - - + -
251C TYR 3.1 10.1 + - - +
252C ILE* 4.3 7.6 - - + +
253C THR* 2.8 33.9 + - - +
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Residues in contact with HIS 198 (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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75C ARG* 6.1 1.6 - - - -
165C LEU* 4.5 5.7 - - + +
166C VAL 3.2 9.3 + - - +
167C TYR* 3.8 36.8 - + + -
168C MET* 3.2 22.9 + - - +
169C ALA* 4.1 12.8 + - + +
170C PHE* 4.1 15.5 - + - -
197C VAL* 1.3 71.7 - - - +
199C ALA* 1.3 59.7 + - - +
200C GLU* 2.9 36.5 + - + -
253C THR* 3.8 8.1 - - - +
254C LYS* 4.4 14.8 + - + -
304C SER* 3.1 26.6 + - - -
305C PRO* 4.0 8.0 - - + +
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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