Contacts of the strand formed by residues 220 - 226 (chain D) in PDB entry 4F9P
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 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D GLN 3.6 10.5 - - - -
175D LYS* 4.2 4.3 - - - -
176D SER 4.9 3.4 - - - -
218D ASP 4.0 0.4 + - - -
219D PHE* 1.3 77.7 - - - +
221D ILE* 1.3 69.9 + - - +
222D TYR* 4.0 6.7 - - - -
238D THR 3.7 1.0 - - - +
240D LEU* 3.2 34.2 + - - +
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Residues in contact with ILE 221 (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 TYR 4.0 0.2 - - - +
174D GLN* 2.8 46.6 + - - +
176D SER* 6.1 2.2 - - - +
220D GLY* 1.3 79.2 - - - +
222D TYR* 1.3 67.5 + - - +
223D PHE* 3.5 33.6 - - + -
236D THR 4.9 1.3 - - - +
237D GLY* 4.2 12.8 - - - -
238D THR 3.4 8.3 - - - +
239D LYS* 4.1 20.9 - - + -
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Residues in contact with TYR 222 (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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142D GLN* 3.2 9.8 + - - +
157D LEU* 3.7 31.9 - - + -
171D TRP* 5.4 1.6 - - + -
172D TYR 3.2 10.5 - - - +
173D ARG* 3.5 28.2 - - + +
183D LEU* 4.1 10.1 - - + -
198D PHE* 4.4 15.5 - + - -
209D LEU* 3.9 15.7 - - + -
211D ILE* 5.2 4.9 - - + -
218D ASP* 2.2 42.0 + - - +
219D PHE 4.3 1.8 - - - -
220D GLY* 4.0 18.2 - - - -
221D ILE* 1.3 81.9 - - - +
223D PHE* 1.3 62.4 + - - +
237D GLY* 3.3 1.0 - - - -
238D THR* 2.8 41.8 + - - +
240D LEU* 4.4 12.5 - - + +
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Residues in contact with PHE 223 (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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39D GLN* 6.0 1.3 - - - -
44D GLY* 5.8 4.9 - - - -
45D LEU* 4.6 31.6 - - + -
142D GLN* 3.5 5.2 - - - +
170D HIS 3.7 0.2 - - - +
171D TRP* 3.3 9.1 - - - -
172D TYR* 2.9 48.9 + - + +
174D GLN* 3.7 29.8 - - + -
180D PRO* 5.9 2.5 - - + -
221D ILE* 3.5 32.5 - - + -
222D TYR* 1.3 75.6 - - - +
224D CYS* 1.3 65.1 + - - +
234D PHE* 4.9 7.0 - - + -
235D GLY 3.3 20.0 - - - -
236D THR 3.6 22.2 - - - -
237D GLY* 3.7 6.3 - - - -
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Residues in contact with CYS 224 (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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140D LEU* 4.1 1.8 - - - -
142D GLN* 3.2 21.6 + - - +
159D CYS* 2.1 51.4 - - + -
169D LEU* 4.1 7.6 - - + -
170D HIS 3.2 9.2 - - - +
171D TRP* 3.9 9.2 - - + -
172D TYR* 5.3 0.7 - - - -
223D PHE* 1.3 76.4 - - - +
225D GLN* 1.3 65.5 + - - +
234D PHE* 3.5 22.3 - - - +
235D GLY* 3.4 15.3 + - - +
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Residues in contact with GLN 225 (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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47D TRP* 5.6 1.6 - - - -
100D ASP* 4.5 4.2 - - - +
169D LEU* 2.8 34.1 - - - +
170D HIS* 2.8 39.2 + - + +
172D TYR* 3.8 17.8 + - + -
224D CYS* 1.3 76.8 - - - +
226D GLN* 1.3 71.6 + - - +
232D HIS* 3.1 42.9 + - - +
233D THR 2.9 19.1 + - - +
234D PHE* 3.3 27.3 - - + +
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Residues in contact with GLN 226 (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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138D ILE* 3.9 27.8 - - + -
165D ILE* 3.9 25.1 - - + -
168D ASN 3.7 5.8 - - - +
169D LEU* 5.5 0.2 - - + -
225D GLN* 1.3 93.8 + - - +
227D SER* 1.3 59.5 + - - +
228D ASN 3.3 6.1 - - - +
229D SER 5.0 0.5 - - - +
232D HIS* 3.6 13.7 - - - +
233D THR* 3.6 9.3 + - - +
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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