Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 5FJV
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 THR 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN* 6.0 0.4 - - - -
196A LEU* 4.0 1.6 - - - +
209A ASN* 4.5 8.7 - - + +
210A ALA* 1.3 83.8 - - - +
212A GLY* 1.3 61.1 + - - +
213A THR* 3.7 15.8 - - - +
230A THR 3.5 0.2 - - - +
231A TYR* 3.1 11.0 - - - -
232A ALA* 2.7 55.3 + - + +
233A PHE* 4.7 0.2 - - - -
234A VAL* 5.9 0.4 - - + -
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Residues in contact with GLY 212 (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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189A GLN* 3.2 32.3 + - - +
192A GLN* 3.8 12.0 + - - +
196A LEU* 4.3 4.0 - - - +
211A THR* 1.3 72.0 - - - +
213A THR* 1.3 66.8 + - - +
229A VAL* 4.5 0.2 - - - -
230A THR 3.7 4.5 - - - -
231A TYR* 3.8 18.8 - - - -
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Residues in contact with THR 213 (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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189A GLN* 3.9 2.8 + - - -
211A THR* 3.7 19.7 - - - +
212A GLY* 1.3 80.9 - - - +
214A TYR* 1.3 65.7 + - - +
215A ASN* 3.5 16.1 + - - -
228A ASP* 4.2 1.2 - - - +
229A VAL* 3.5 5.4 - - - +
230A THR* 2.9 41.0 + - - +
232A ALA* 5.6 1.1 - - + +
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Residues in contact with TYR 214 (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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182A LYS* 3.1 27.3 + - - +
186A ASP* 3.0 18.6 + - - -
187A LEU* 3.3 45.3 - - + -
188A GLU* 5.6 0.2 - - - -
189A GLN* 3.7 17.5 + - + +
213A THR* 1.3 73.6 + - - +
215A ASN* 1.3 86.9 + - - +
216A SER* 4.0 8.1 - - - -
227A PRO* 3.3 13.4 - - + +
228A ASP 3.5 4.3 - - - -
229A VAL* 4.5 4.5 - - + -
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Residues in contact with ASN 215 (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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213A THR* 3.5 22.0 + - - -
214A TYR* 1.3 91.0 - - - +
216A SER* 1.3 64.7 + - - +
217A LYS* 5.6 5.4 - - + -
227A PRO* 3.4 0.5 - - - +
228A ASP* 3.0 51.1 + - - +
230A THR* 4.5 6.1 + - - -
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Residues in contact with SER 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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182A LYS* 3.8 11.9 - - - +
214A TYR* 4.0 15.3 - - - -
215A ASN* 1.3 81.1 + - - +
217A LYS* 1.3 72.8 + - - +
225A ILE* 3.8 24.9 - - - +
226A TYR 3.9 9.7 + - - -
227A PRO* 4.6 0.9 - - - -
228A ASP* 4.3 0.6 + - - -
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Residues in contact with LYS 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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174A LYS* 5.7 2.0 - - - +
215A ASN* 5.6 3.4 - - + -
216A SER* 1.3 88.7 + - - +
218A LYS* 1.3 64.9 + - - +
219A TYR* 3.4 23.0 - - + +
225A ILE* 3.0 8.8 - - - -
226A TYR 2.9 31.2 + - - -
228A ASP* 5.5 2.9 - - - +
199B TYR* 2.8 45.8 + - + -
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Residues in contact with LYS 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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217A LYS* 1.3 79.5 - - - +
219A TYR* 1.3 69.7 + - - +
220A ASP* 4.0 15.3 + - - +
221A CYS 5.5 0.8 - - - +
222A CYS 3.8 16.4 + - - +
223A ALA* 3.1 33.5 - - - +
224A GLU 3.8 10.1 - - - +
225A ILE* 4.2 11.4 - - + +
199B TYR* 3.5 6.9 + - - -
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Residues in contact with TYR 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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122A TYR* 3.9 10.0 + + - -
174A LYS* 3.4 27.3 + - - -
217A LYS* 3.4 34.5 - - + +
218A LYS* 1.3 79.8 + - - +
220A ASP* 1.3 62.2 + - - +
221A CYS* 2.7 21.0 + - - -
222A CYS 3.3 18.0 + - - +
224A GLU 4.3 1.0 + - - -
226A TYR* 3.5 31.0 + + + +
227A PRO 5.1 0.2 + - - -
228A ASP* 3.5 17.2 + - - +
300A EPJ 3.5 34.1 - - + -
84B TRP* 4.4 4.3 - + + -
199B TYR* 2.8 45.3 - + + +
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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