Contacts of the strand formed by residues 213 - 218 (chain C) in PDB entry 3ZXR
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 LEU 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 3.4 32.4 - - + +
40B SER* 4.9 3.4 + - - -
41B ALA* 4.2 5.9 - - - +
203C LEU* 3.8 17.9 - - + +
206C LEU* 3.8 10.8 - - + -
207C ILE* 3.5 39.6 - - + +
211C PHE* 3.5 29.6 + - + +
212C ILE* 1.3 80.3 - - - +
214C GLU* 1.3 64.8 + - - +
228C ILE* 3.8 22.7 - - + -
229C ASN 3.4 18.8 - - - +
230C TYR* 4.4 4.5 - - + -
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Residues in contact with GLU 214 (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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37B ILE* 3.2 22.9 - - - +
38B PRO* 3.5 5.6 - - - +
41B ALA* 4.5 7.4 - - + +
212C ILE* 4.9 2.0 - - + +
213C LEU* 1.3 80.1 - - - +
215C LYS* 1.3 66.9 + - + +
229C ASN* 2.8 20.5 + - + +
231C GLN* 3.5 36.3 - - + +
232C PHE* 4.7 2.6 + - - -
501C IQ1 3.2 41.5 + - - +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.7 26.6 - - + -
36B THR 3.1 13.5 - - - +
37B ILE* 4.0 7.2 - - + +
38B PRO* 4.5 1.5 - - - +
52B ALA* 4.4 17.2 + - - +
53B PHE* 5.7 1.0 - - - +
186C TYR* 5.6 4.0 + - - -
187C PHE* 6.4 0.2 - - - -
203C LEU* 4.5 6.1 - - - -
213C LEU* 5.1 0.4 - - - +
214C GLU* 1.3 84.8 - - + +
216C GLY* 1.3 59.3 + - - +
217C HIS* 4.2 23.0 + - + -
227C GLU 4.6 0.4 - - - -
228C ILE* 3.3 3.8 - - - +
229C ASN* 2.6 60.1 + - + +
501C IQ1 5.8 2.2 - - - -
504C MG 4.3 0.2 - - - -
506C PO4 4.1 19.7 + - - -
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Residues in contact with GLY 216 (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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35B PHE* 3.7 0.9 - - - +
36B THR* 2.8 37.3 + - - +
199C ARG* 4.6 6.0 + - - -
203C LEU* 4.4 12.6 - - - +
215C LYS* 1.3 74.4 - - - +
217C HIS* 1.3 64.9 + - - +
227C GLU 3.2 9.9 - - - -
228C ILE* 3.9 12.1 - - - -
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Residues in contact with HIS 217 (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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34B HIS* 4.4 1.3 - - - +
35B PHE* 3.5 20.9 - - + +
186C TYR* 3.7 15.6 + + - -
187C PHE* 3.7 17.4 - + + -
199C ARG* 3.5 18.8 - - - +
215C LYS* 4.2 32.0 + - + -
216C GLY* 1.3 78.1 - - - +
218C HIS* 1.3 79.2 + - - +
219C GLU* 3.5 24.7 - - + -
226C ALA* 3.4 2.1 - - - -
227C GLU* 2.8 68.5 + - + +
504C MG 4.5 1.0 - - - -
505C P3S 4.7 1.1 - - - -
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Residues in contact with HIS 218 (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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34B HIS* 5.4 0.8 + - - +
180C VAL* 4.1 17.6 - - + +
185C GLY* 3.0 22.6 + - - +
186C TYR* 4.1 1.2 - - - -
187C PHE* 3.7 21.0 - - + +
193C ASP* 3.3 37.5 - - + +
195C TYR* 4.0 20.6 - + - -
199C ARG* 3.5 19.3 - - - +
217C HIS* 1.3 88.6 + - - +
219C GLU* 1.3 84.7 + - - +
221C GLY 3.4 17.7 - - - -
224C GLY* 4.0 5.8 - - - -
225C GLN 3.1 22.2 + - - -
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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