Contacts of the strand formed by residues 195 - 199 (chain C) in PDB entry 1EFP
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 ARG 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C ALA* 3.4 4.5 - - - +
194C ARG* 1.3 96.1 - - + +
196C VAL* 1.3 66.9 + - - +
219C LEU* 2.8 61.2 + - + +
220C GLY 5.0 1.7 + - - +
221C ALA* 3.0 20.0 - - + +
222C ALA 2.9 21.8 + - - -
251C GLU* 4.7 12.7 + - + -
252C LEU* 3.3 28.1 - - + +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C LEU* 3.8 37.7 - - + +
193C ALA* 4.1 13.5 - - + -
195C ARG* 1.3 80.5 - - - +
197C VAL* 1.3 66.2 + - - +
198C SER* 3.7 21.1 - - - +
221C ALA* 4.1 0.2 - - - -
222C ALA* 3.4 5.2 - - + +
224C GLY* 4.1 1.6 - - - +
241C VAL* 5.0 0.4 - - + -
248C VAL* 4.6 4.0 - - + -
250C PRO* 3.7 27.6 - - + -
252C LEU* 2.8 9.4 + - - +
253C TYR* 3.3 16.5 - - + -
254C VAL* 2.8 26.2 + - - +
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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
----------------------------------------------------------
195C ARG* 6.0 0.2 - - + -
196C VAL* 1.3 76.9 - - - +
198C SER* 1.3 60.8 + - - +
212C ILE* 3.9 25.8 - - + +
215C LEU* 4.2 17.7 - - + -
216C ALA* 3.9 31.4 - - + +
219C LEU* 4.3 15.9 - - + -
221C ALA* 4.1 9.2 - - + -
222C ALA 2.9 7.3 + - - -
223C VAL* 3.2 13.2 - - - +
224C GLY 2.9 16.9 + - - -
252C LEU* 6.2 0.2 - - + -
254C VAL* 3.5 15.0 - - + +
256C VAL* 4.3 13.7 - - + -
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Residues in contact with SER 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C VAL* 3.7 4.7 - - - +
197C VAL* 1.3 72.8 - - - +
199C GLY* 1.3 59.4 + - - +
212C ILE* 4.5 1.8 - - - -
224C GLY* 3.1 28.1 + - - -
225C ALA* 3.8 1.7 + - - -
241C VAL* 4.2 0.7 - - - +
253C TYR* 2.7 35.4 + - - -
254C VAL 2.9 10.4 + - - -
256C VAL* 3.1 33.4 + - - +
258C ILE* 3.8 14.9 - - - +
264C HIS* 4.7 0.4 - - - -
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Residues in contact with GLY 199 (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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197C VAL 4.3 0.2 + - - -
198C SER* 1.3 74.3 - - - +
200C GLY* 1.3 62.2 + - - -
203C LEU* 3.5 19.3 - - - -
209C PHE* 3.7 11.8 - - - -
212C ILE* 4.3 5.7 - - - +
224C GLY 3.0 8.9 + - - -
225C ALA* 3.3 21.8 - - - +
226C SER 3.4 3.8 + - - -
229C ALA* 3.6 6.9 - - - +
256C VAL 3.6 2.7 - - - -
258C ILE* 4.0 2.7 - - - -
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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