Contacts of the strand formed by residues 219 - 224 (chain A) in PDB entry 3EBV
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A VAL* 3.8 2.9 - - - -
176A VAL 3.8 2.0 - - - -
180A TYR* 4.5 4.5 - - - +
206A ALA* 4.3 21.8 - - + -
209A GLN* 3.6 35.2 - - + +
210A LEU* 3.7 17.5 - - + +
214A LEU* 4.2 9.2 - - + -
215A ALA 3.7 12.1 - - - +
216A PRO 3.1 6.1 + - - +
217A SER 3.4 0.8 - - - -
218A GLN* 1.3 85.3 - - - +
220A GLY* 1.3 62.5 + - - +
221A LEU* 5.0 1.3 - - + -
265A LEU* 3.6 23.0 - - + +
266A ARG* 3.2 23.7 + - - +
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Residues in contact with GLY 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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175A VAL* 3.6 4.7 - - - +
176A VAL 2.9 17.7 + - - +
177A ASN* 3.5 20.4 - - - -
178A MSE 3.6 12.8 + - - +
180A TYR* 3.7 8.7 + - - -
209A GLN* 5.3 0.2 - - - +
219A VAL* 1.3 75.5 - - - +
221A LEU* 1.3 67.2 + - - -
222A GLY 3.6 0.6 + - - -
267A GLY 3.4 13.9 - - - -
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Residues in contact with LEU 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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180A TYR* 3.7 28.3 - - + +
202A LEU* 4.3 12.3 - - + +
206A ALA* 3.9 16.6 - - + -
219A VAL* 5.0 3.6 - - + -
220A GLY* 1.3 71.7 - - - -
222A GLY* 1.3 57.4 + - - +
223A LEU* 3.6 16.0 - - + +
240A VAL* 4.5 4.5 - - + +
243A ALA* 3.9 27.4 - - + -
244A LEU* 3.9 25.4 - - + +
247A LEU* 4.3 11.0 - - + -
265A LEU* 4.8 3.4 - - + -
267A GLY 2.9 17.6 + - - +
268A ALA* 3.2 10.5 - - + +
269A MSE 2.8 27.3 + - - +
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Residues in contact with GLY 222 (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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178A MSE 3.0 21.4 + - - +
180A TYR* 2.9 30.0 + - - +
181A TYR* 3.3 7.2 - - - -
220A GLY 3.6 2.0 + - - -
221A LEU* 1.3 69.2 - - - +
223A LEU* 1.3 68.0 + - - +
269A MSE 3.3 26.9 - - - +
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Residues in contact with LEU 223 (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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180A TYR 4.0 10.5 - - - +
181A TYR* 3.6 8.2 - - - -
202A LEU* 4.0 21.1 - - + -
221A LEU* 3.6 26.2 - - + +
222A GLY* 1.3 82.9 - - - +
224A PRO* 1.3 72.6 - - + +
233A GLY 3.7 22.9 - - - +
235A VAL* 3.8 16.6 - - + +
240A VAL* 3.8 27.1 - - + -
269A MSE 2.9 5.9 + - - -
270A THR* 2.8 27.4 + - - -
271A TRP 3.2 3.6 + - - -
283A TRP* 4.1 15.3 - - + +
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Residues in contact with PRO 224 (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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181A TYR* 3.5 22.2 - - + -
223A LEU* 1.3 90.6 - - + +
225A ALA* 1.3 64.9 + - - +
226A SER 3.3 17.2 + - - +
229A ALA* 4.0 3.4 - - + -
230A ALA* 3.5 32.5 - - + -
233A GLY 3.7 16.2 - - - +
234A TYR* 3.4 28.6 - - + +
235A VAL 5.0 0.2 - - - +
270A THR* 3.4 0.2 - - - -
271A TRP* 3.5 9.0 - - + +
283A TRP* 3.7 10.2 + - - -
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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