Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 4R3O
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.0 18.8 - - + -
52A THR 3.2 13.7 - - - +
53A GLN* 4.2 4.0 - - - -
54A LYS* 3.8 12.3 - - - +
199A ILE* 4.4 20.9 - - + -
202A LEU* 4.3 6.3 - - + -
210A PHE* 3.6 46.9 - - + -
211A LYS 4.3 7.9 - - - +
212A PRO 3.9 12.5 - - - +
214A GLU* 1.3 86.3 - - - +
216A GLU* 1.3 64.9 + - - +
217A VAL* 4.4 2.2 - - + -
235A ILE* 4.0 29.4 - - + +
239A LEU* 4.7 3.6 - - + -
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE 3.9 0.2 - - - +
51A VAL* 3.2 5.2 - - - +
52A THR* 2.9 44.1 + - - +
53A GLN 4.5 4.0 - - - +
54A LYS* 3.9 24.0 + - + +
67A THR* 3.2 28.7 + - - +
68A HIS* 2.9 40.0 + - - +
69A LEU* 4.0 19.4 + - + +
215A ILE* 1.3 76.6 - - - +
217A VAL* 1.3 63.3 + - - +
229A ILE* 5.6 4.8 - - + +
235A ILE* 4.4 4.9 - - + -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.9 14.1 - - + -
50A ILE 3.2 12.1 - - - +
51A VAL* 3.9 18.2 - - + -
69A LEU* 3.7 3.3 - - - +
195A VAL* 4.8 8.1 - - + -
199A ILE* 4.5 12.8 - - + -
215A ILE* 4.4 13.2 - - + -
216A GLU* 1.3 79.3 - - - +
218A GLY* 1.3 68.6 + - - +
219A VAL* 5.0 1.6 - - + -
229A ILE* 3.8 3.0 - - - +
230A LEU* 3.1 55.4 + - + +
235A ILE* 4.3 17.0 - - + +
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.6 1.7 - - - -
50A ILE* 2.9 35.8 + - - +
69A LEU* 3.3 19.9 - - - +
141A ILE* 4.5 0.7 - - - -
217A VAL* 1.3 77.4 - - - +
219A VAL* 1.3 63.5 + - - +
227A PHE* 3.9 15.3 - - - -
228A ARG 3.7 6.7 - - - -
229A ILE* 4.6 0.7 - - - -
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A CYS* 5.0 0.4 - - + -
48A ALA 3.4 15.5 - - - +
49A VAL* 3.6 18.2 - - + -
141A ILE* 4.2 3.4 - - - -
191A PHE* 3.4 35.7 - - + -
195A VAL* 5.0 1.1 - - + -
217A VAL* 5.0 1.3 - - + -
218A GLY* 1.3 73.0 - - - +
220A VAL* 1.3 72.1 + - - +
221A THR* 4.9 3.8 - - - +
226A LYS 4.3 0.2 - - - +
227A PHE* 3.5 6.5 - - - -
228A ARG* 3.0 52.2 + - + +
230A LEU* 3.7 22.2 - - + -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A CYS* 3.2 4.7 - - - +
48A ALA* 2.9 57.4 + - + +
75A ASN 4.5 2.7 - - - +
141A ILE* 3.8 13.7 - - + +
142A GLY* 3.9 19.3 - - - +
143A ILE* 3.5 25.7 - - + +
219A VAL* 1.3 77.7 - - - +
221A THR* 1.3 67.0 + - - +
224A ASN 4.4 2.2 - - - -
225A PRO 3.1 28.7 - - - +
226A LYS 4.9 0.9 - - - -
227A PHE* 4.7 7.4 - - + +
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.2 23.1 - - + +
47A CYS* 3.9 9.6 - - + -
143A ILE* 3.2 9.9 - - - +
191A PHE* 4.3 23.2 - - + -
219A VAL* 4.9 3.8 - - - +
220A VAL* 1.3 75.8 + - - +
222A VAL* 1.3 61.9 + - - +
223A GLU* 4.3 9.0 - - + +
224A ASN* 3.1 43.2 + - - +
225A PRO* 3.1 9.9 - - - +
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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