Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 2VZE
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 ALA 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLY 5.3 1.0 - - - +
132A ILE* 3.6 34.8 - - + +
213A GLN 3.6 2.6 + - - -
214A GLU* 1.3 77.8 - - + +
216A SER* 1.3 57.9 + - - +
217A ALA 5.1 0.2 - - - +
232A GLU* 3.5 33.3 + - + +
233A HIS 3.8 5.6 - - - -
234A SER* 4.5 0.7 - - - +
235A TYR* 3.2 16.1 + - - -
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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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127A ILE* 4.3 4.0 - - - +
131A LEU 3.6 1.2 + - - +
132A ILE* 3.3 9.0 - - - -
133A PHE* 3.1 41.8 + - - -
214A GLU 3.3 0.4 + - - -
215A ALA* 1.3 73.5 - - - +
217A ALA* 1.3 59.1 + - - +
233A HIS 2.8 8.7 + - - -
234A SER 3.8 7.0 - - - -
235A TYR* 3.3 52.2 - - - -
238A LEU* 5.0 3.3 - - - +
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Residues in contact with ALA 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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132A ILE* 3.8 3.5 - - - +
133A PHE* 3.2 38.6 - - + +
216A SER* 1.3 78.6 - - - +
218A ILE* 1.3 64.6 + - - +
219A TYR* 4.1 12.3 - - + -
231A ALA 4.4 0.4 - - - -
232A GLU* 3.4 5.9 - - - +
233A HIS* 2.9 30.9 + - + +
238A LEU* 3.8 16.2 - - + -
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Residues in contact with ILE 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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108A ARG* 3.7 41.1 - - - +
132A ILE* 3.8 13.2 - - + +
133A PHE 3.0 6.3 + - - -
134A MET* 3.2 44.2 - - + +
135A PRO* 4.0 2.3 - - - +
217A ALA* 1.3 77.4 - - - +
219A TYR* 1.3 65.7 + - - +
220A PHE* 4.0 5.9 + - + -
230A MET* 3.5 40.6 - - + -
231A ALA 3.3 6.5 - - - +
232A GLU* 4.5 7.6 - - + +
427A VAL* 4.2 17.9 - - + -
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TRP* 4.8 2.9 - - - -
133A PHE* 4.0 4.5 - + - -
135A PRO* 3.6 36.1 - - + +
217A ALA* 4.1 22.2 - - + -
218A ILE* 1.3 75.3 - - - +
220A PHE* 1.3 68.9 + - - +
221A THR* 4.2 0.5 - - - -
231A ALA* 2.8 39.6 + - - +
233A HIS* 4.8 6.3 - + - -
238A LEU* 4.9 1.8 - - + -
263A THR 5.3 0.2 - - - -
264A GLY 3.5 25.6 - - - -
265A TRP 3.9 3.8 + - - -
266A ILE* 3.6 43.2 - - + -
269A ILE* 3.5 28.3 + - + +
364A THR* 3.5 23.1 - - + -
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Residues in contact with PHE 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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134A MET* 4.6 17.9 - - + -
135A PRO 5.1 8.3 + - - +
147A TYR* 4.2 10.8 - + - -
148A ARG* 3.5 79.5 + - + +
151A MET* 4.3 5.6 - - + -
152A SER* 4.2 2.2 - - - -
218A ILE* 4.6 11.0 - - + -
219A TYR* 1.3 78.6 - - - +
221A THR* 1.3 60.0 - - - +
228A PRO* 4.2 18.6 - - + -
229A LYS 3.2 9.2 - - - -
230A MET* 3.4 37.9 - - + +
264A GLY 5.7 0.7 - - - +
364A THR* 5.3 0.9 + - - +
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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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219A TYR 4.2 2.2 - - - -
220A PHE* 1.3 76.8 - - - +
222A SER* 1.3 62.1 + - - +
228A PRO* 4.1 3.9 - - - +
229A LYS* 2.8 42.5 + - + +
231A ALA* 4.1 12.3 - - + -
364A THR* 3.7 15.6 + - - -
365A GLU* 4.0 18.4 - - - +
426A TYR* 4.1 16.4 - - + -
472A ARG* 3.0 34.7 + - - +
1570A AMP 4.8 0.3 + - - -
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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