Contacts of the strand formed by residues 224 - 229 (chain A) in PDB entry 4RM9
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLY 3.8 1.4 - - - +
221A ASP* 3.0 31.6 + - - +
223A LEU* 1.3 80.3 - - - +
225A LEU* 1.3 66.5 + - - +
226A ASN* 4.8 3.0 - - - +
240A PHE 3.4 10.5 - - - -
241A PRO* 4.3 0.4 - - - -
242A TRP* 3.1 23.2 - - - +
572A ARG* 4.1 2.0 - - - +
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Residues in contact with LEU 225 (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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218A LEU* 4.3 17.0 - - + -
219A GLY 3.4 2.0 - - - +
220A VAL* 3.7 28.5 - - + -
224A GLY* 1.3 75.9 - - - +
226A ASN* 1.3 67.1 + - - +
227A ILE* 4.8 0.7 - - - -
238A ILE 4.1 0.2 - - - +
239A GLY* 3.4 1.7 - - - -
240A PHE* 2.8 47.5 + - + +
242A TRP* 3.6 29.6 - - + -
245A ILE* 3.7 21.5 - - + -
248A ILE* 5.4 0.4 - - + -
257A ILE* 4.0 25.4 - - + -
267A PHE* 4.8 8.1 - - + -
269A PHE* 5.3 1.1 - - + -
284A CYS* 3.9 10.1 - - - -
572A ARG* 5.8 0.2 + - - -
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Residues in contact with ASN 226 (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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203A ILE* 4.2 11.3 - - - +
217A TRP 3.7 0.2 - - - +
218A LEU* 3.4 7.7 - - - +
219A GLY 2.7 41.7 + - - +
221A ASP* 4.4 12.3 + - - +
224A GLY 4.8 3.1 - - - -
225A LEU* 1.3 82.5 + - - +
227A ILE* 1.3 64.3 + - - +
228A TYR* 3.4 32.1 + - + -
236A PRO* 3.7 17.9 - - + +
238A ILE 3.5 2.9 - - - -
239A GLY* 4.3 1.0 - - - -
564A LYS* 6.0 0.6 - - - +
568A LEU* 3.7 27.5 - - - +
571A ILE* 4.0 5.4 - - - +
572A ARG* 4.9 3.3 + - - -
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Residues in contact with ILE 227 (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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208A ILE* 5.0 4.9 - - + -
216A LEU* 4.2 6.3 - - + -
217A TRP 3.4 8.7 - - - +
218A LEU* 5.1 2.7 - - + -
225A LEU 4.5 0.7 - - - +
226A ASN* 1.3 80.6 - - - +
228A TYR* 1.3 64.3 + - - +
236A PRO* 3.4 1.9 - - - +
237A LYS* 2.7 33.3 + - - +
238A ILE* 2.9 31.9 + - + +
240A PHE* 3.6 33.7 - - + -
267A PHE* 4.2 11.0 - - + -
583A PHE* 3.8 31.4 - - + -
586A LEU* 4.0 27.4 - - + -
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Residues in contact with TYR 228 (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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199A GLU 4.6 1.0 + - - -
203A ILE* 3.2 30.1 - - - +
205A TYR* 3.6 20.9 + + - -
216A LEU* 3.3 13.5 - - - +
217A TRP* 2.9 52.4 + - + -
219A GLY* 3.9 12.3 - - - -
226A ASN* 3.4 31.5 + - + -
227A ILE* 1.3 76.9 - - - +
229A GLU* 1.3 63.5 + - - +
232A ASP 3.4 22.7 - - - +
233A LYS* 3.1 20.9 - - - -
234A LEU 4.1 1.3 - - - -
235A THR 3.6 2.0 - - - -
236A PRO* 3.3 38.2 - - + +
237A LYS* 4.6 1.8 - - - +
586A LEU* 5.5 0.2 - - - -
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Residues in contact with GLU 229 (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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216A LEU* 3.9 14.6 - - + -
217A TRP* 3.7 4.9 - - - -
228A TYR* 1.3 75.1 - - - +
230A LYS* 1.3 66.8 + - - +
231A ASP 3.0 5.0 + - - +
232A ASP* 3.1 23.1 + - + +
235A THR 5.0 0.6 + - - -
237A LYS* 3.5 39.2 + - + +
586A LEU* 4.9 19.3 - - + +
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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