Contacts of the strand formed by residues 214 - 220 (chain D) in PDB entry 4ZM9
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 GLY 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D VAL* 4.0 8.1 - - - -
209D ALA* 3.6 1.2 - - - -
210D ASP 2.8 35.8 + - - -
213D ILE* 1.3 76.4 - - - +
215D ALA* 1.3 62.9 + - - -
235D LEU* 3.8 16.8 - - - +
268D VAL 3.0 13.2 - - - -
269D SER* 3.9 3.8 - - - -
270D LYS* 3.9 3.7 - - - +
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D VAL* 3.8 10.9 - - + +
180D VAL* 4.0 14.4 - - + -
181D ALA 3.5 31.9 - - - +
182D TYR 4.4 0.2 - - - +
208D TYR 3.1 9.6 - - - +
209D ALA* 4.0 3.1 - - + -
214D GLY* 1.3 75.4 - - - +
216D VAL* 1.3 65.1 + - - +
235D LEU* 4.1 0.6 - - - +
267D VAL* 3.3 4.2 - - - +
268D VAL* 2.8 33.7 + - + +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D VAL* 3.6 4.3 - - - -
182D TYR* 3.5 5.9 - - - +
207D GLY* 2.9 23.1 - - - -
208D TYR 2.9 11.4 + - - +
215D ALA* 1.3 80.0 - - - +
217D SER* 1.3 70.1 + - - +
218D THR* 3.9 18.2 - - + -
231D ALA* 3.9 21.1 - - + +
234D THR* 4.2 8.5 - - - +
235D LEU* 3.7 25.4 - - + -
265D LEU* 4.1 12.1 - - + -
266D ILE 3.3 11.9 - - - +
267D VAL* 3.7 18.4 - - + -
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Residues in contact with SER 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D HIS* 3.0 23.5 + - - -
170D GLY* 3.5 0.9 - - - -
171D ALA 4.0 6.1 - - - -
172D VAL* 3.5 6.5 - - - +
182D TYR* 4.5 1.8 - - - -
183D ALA 3.4 13.7 + - - -
184D THR* 2.6 23.6 + - - -
206D GLY 3.6 5.8 - - - -
216D VAL* 1.3 74.6 - - - +
218D THR* 1.3 60.8 + - - +
265D LEU* 3.2 4.3 - - - +
266D ILE* 3.0 42.5 + - - +
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Residues in contact with THR 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D HIS* 3.4 14.9 + - - -
168D THR* 3.8 9.5 - - - +
184D THR* 3.9 6.8 - - - +
199D ASP* 3.1 17.2 + - - +
205D ALA 3.0 28.2 + - - +
206D GLY* 3.0 9.0 + - - +
216D VAL* 3.9 16.2 - - + -
217D SER* 1.3 78.6 + - - +
219D THR* 1.3 64.0 + - - +
225D ILE* 3.8 3.2 - - - +
230D LEU* 3.8 25.6 - - + -
231D ALA* 4.0 9.0 - - + +
264D GLY 3.3 8.1 - - - -
265D LEU* 4.0 4.0 - - + +
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D HIS* 3.6 13.9 - - + +
10D GLY* 3.3 14.5 - - - -
11D GLY* 3.4 15.3 + - - +
168D THR* 3.6 2.1 - - - -
218D THR* 1.3 76.8 - - - +
220D GLY* 1.3 58.3 + - - +
225D ILE* 3.5 12.5 - - - +
230D LEU* 5.2 0.5 - - - +
263D GLY* 3.2 2.5 - - - -
264D GLY 2.8 42.5 + - - +
283D MET* 3.7 25.4 - - + -
402D GLY 4.4 4.9 - - - -
403D FLC 2.1 31.0 + - - +
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Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ILE* 4.8 0.2 - - - +
219D THR* 1.3 74.7 + - - +
221D HIS* 1.3 61.3 + - - -
222D GLY 3.1 8.5 + - - -
225D ILE* 3.6 2.7 - - - +
262D LEU 3.5 10.5 - - - -
263D GLY* 3.6 2.9 - - - -
402D GLY 3.2 4.3 + - - +
403D FLC 2.4 61.6 + - - +
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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