Contacts of the strand formed by residues 216 - 221 (chain A) in PDB entry 4FJV
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 VAL 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 4.0 10.5 - - + +
59A SER* 3.6 18.6 - - - +
60A TYR* 3.6 40.8 - - + +
189A ILE* 4.1 6.3 - - + -
190A ALA 3.2 6.0 + - - +
191A LEU* 3.4 22.7 - - + -
192A GLN 2.8 25.8 + - - -
214A PRO* 3.7 4.3 - - - +
215A SER* 1.3 88.1 - - - +
217A TYR* 1.3 65.9 + - - +
218A LEU* 3.7 19.5 - - + -
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Residues in contact with TYR 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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39A PHE* 3.4 36.3 - + + -
59A SER* 4.7 1.2 + - - -
192A GLN* 3.4 40.4 - - + +
194A GLU* 5.9 0.4 - - + -
214A PRO* 3.8 38.3 + - + +
215A SER 4.7 4.7 - - - -
216A VAL* 1.3 78.2 - - - +
218A LEU* 1.3 69.6 + - - +
227A ILE* 3.8 2.8 - - - +
228A LEU* 2.9 42.0 + - + +
230A ALA* 4.0 26.3 - - + +
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Residues in contact with LEU 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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52A PHE* 3.7 33.0 - - + +
55A ALA* 4.0 28.3 - - + +
56A LEU* 4.7 3.1 - - + +
191A LEU* 3.7 23.6 - - + -
192A GLN 2.9 10.0 + - - +
193A VAL* 3.6 5.1 - - + -
194A GLU* 2.9 28.6 + - - +
216A VAL* 3.7 14.4 - - + -
217A TYR* 1.3 83.5 - - - +
219A LEU* 1.3 58.9 + - - +
220A TYR 3.9 0.4 - - - -
225A TYR* 4.0 21.1 - - + -
226A ASN 3.2 13.0 - - - +
227A ILE* 4.0 9.0 - - + -
228A LEU* 3.8 4.9 - - - +
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Residues in contact with LEU 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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18A ILE* 3.9 18.8 - - + -
35A LEU* 3.8 15.9 - - + -
42A ILE* 3.9 22.9 - - + -
194A GLU* 3.8 8.5 - - + +
196A VAL* 3.5 35.7 - - + -
218A LEU* 1.3 72.9 - - - +
220A TYR* 1.3 61.3 + - - +
221A LYS* 3.8 21.6 + - + +
224A HIS 3.2 5.9 - - - +
225A TYR* 3.4 2.1 - - - -
226A ASN* 2.8 41.1 + - + +
228A LEU* 3.8 20.6 - - + +
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Residues in contact with TYR 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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193A VAL* 3.6 17.0 - - + -
194A GLU 2.8 15.6 + - - +
195A TYR* 3.5 35.6 + + - -
196A VAL* 3.0 26.9 + - - +
218A LEU 3.9 0.6 + - - -
219A LEU* 1.3 71.1 - - - +
221A LYS* 1.3 61.0 + - - +
223A SER* 3.7 15.6 + - - -
224A HIS 3.3 8.1 - - - -
225A TYR* 3.3 35.0 - + + -
303A GOL 3.1 37.8 + - - -
72B ARG 4.2 2.6 + - - -
73B LEU* 3.5 17.5 - - + -
74B ARG 2.8 35.8 + - - -
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Residues in contact with LYS 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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18A ILE* 4.6 11.4 - - - -
21A ASP* 5.1 8.5 + - - +
22A HIS* 3.0 37.1 + - + +
28A TYR* 3.9 13.5 - - + -
32A ILE* 5.1 2.9 - - + -
196A VAL* 3.7 27.1 - - + +
219A LEU* 3.8 26.4 + - + +
220A TYR* 1.3 77.7 - - - +
222A THR* 1.3 96.2 + - + +
223A SER 3.2 0.7 - - - -
224A HIS* 3.0 21.1 + - - +
226A ASN* 5.6 6.6 - - - +
303A GOL 3.6 4.9 - - - -
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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