Contacts of the strand formed by residues 227 - 235 (chain A) in PDB entry 1RHM
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 ARG 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A TYR* 3.9 3.3 - - - -
162A GLU* 3.2 33.2 + - + +
163A GLY* 3.8 18.8 - - - -
164A LEU* 3.3 26.6 - - - +
199A GLU* 4.5 7.7 + - - -
201A ARG* 4.2 4.6 - - - +
221A GLU* 3.0 29.5 + - - +
222A ASP 3.4 16.5 + - - -
224A HIS* 2.9 51.3 + - + +
226A LYS* 1.3 79.7 - - + +
228A SER* 1.3 61.6 + - - +
229A SER 4.3 4.7 - - - +
273A LEU* 5.4 0.4 - - + -
276A LYS* 2.8 33.0 + - - +
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Residues in contact with SER 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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154A LYS 4.0 5.1 - - - +
155A MET* 3.5 30.0 + - - +
156A TYR* 2.8 48.2 + - - +
162A GLU* 2.8 24.5 + - - -
227A ARG* 1.3 74.5 - - - +
229A SER* 1.3 62.5 + - - +
276A LYS* 3.6 21.1 - - - +
277A PRO* 3.8 7.1 - - - +
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Residues in contact with SER 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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155A MET* 4.6 7.4 - - - +
162A MET 3.0 8.5 + - - -
163A GLY* 3.2 22.2 - - - -
164A LEU 3.8 0.9 + - - -
198A TYR* 2.9 29.9 + - - -
224A HIS* 5.3 0.7 + - - -
227A ARG* 3.6 6.3 - - - +
228A SER* 1.3 79.5 - - - +
230A PHE* 1.3 62.5 + - - +
231A VAL* 4.4 2.6 - - - +
273A LEU* 4.3 11.1 - - - +
276A LYS* 4.7 0.9 - - - +
277A PRO* 3.3 29.4 - - - -
279A LEU* 5.7 2.0 - - - -
398B LEU* 6.3 0.2 - - - -
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Residues in contact with PHE 230 (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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164A LEU* 4.0 17.5 - - + -
166A ILE* 4.0 17.3 - - + -
215A MET* 4.8 3.4 - - - -
218A VAL* 3.8 23.6 - - + -
224A HIS* 4.6 9.6 - + - +
229A SER* 1.3 76.3 - - - +
231A VAL* 1.3 72.1 + - - +
232A CYS* 3.7 32.1 - - + -
265A PHE* 3.7 39.7 - + - -
273A LEU* 3.7 23.3 - - + +
277A PRO 3.2 7.4 + - - +
278A LYS* 4.6 14.8 - - + -
279A LEU 2.9 26.2 + - - -
280A PHE* 4.2 9.0 - + - -
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Residues in contact with VAL 231 (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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164A LEU 3.0 12.2 + - - +
165A CYS* 2.9 25.3 - - + -
166A ILE 2.8 24.1 + - - -
193A PHE* 4.1 20.2 - - + -
198A TYR* 3.6 27.4 - - + +
229A SER* 4.4 1.1 - - - +
230A PHE* 1.3 88.3 - - - +
232A CYS* 1.3 65.5 + - - +
233A VAL* 4.4 9.2 - - + -
279A LEU* 3.4 34.1 - - + +
281A ILE* 4.6 4.7 - - + -
400B PHE* 5.9 0.2 - - + -
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Residues in contact with CYS 232 (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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166A ILE* 3.3 9.6 - - + +
168A ILE* 4.8 0.9 - - - -
215A MET* 4.1 26.5 - - - -
230A PHE* 3.7 23.5 - - + -
231A VAL* 1.3 74.5 - - - +
233A VAL* 1.3 72.9 + - - +
234A LEU* 4.1 20.4 - - - +
261A ILE* 5.9 0.4 - - - -
279A LEU 3.0 7.3 + - - -
280A PHE* 3.4 22.1 - - + +
281A ILE 3.0 23.4 + - - +
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Residues in contact with VAL 233 (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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165A CYS* 4.8 1.1 - - - -
166A ILE 2.7 14.3 + - - +
167A ILE* 4.4 13.7 - - + -
168A ILE* 2.8 26.9 + - - +
189A LEU* 3.6 37.2 - - + -
193A PHE* 4.7 4.7 - - + -
231A VAL* 4.4 9.6 - - + -
232A CYS* 1.3 77.6 - - - +
234A LEU* 1.3 69.4 + - - +
235A LEU* 3.7 18.2 - - + -
281A ILE* 3.3 40.2 - - + +
350B ILE* 5.0 0.4 - - + -
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Residues in contact with LEU 234 (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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168A ILE* 3.5 38.1 - - + -
211A ILE* 5.0 8.3 - - + -
215A MET* 6.2 0.9 - - - -
232A CYS* 4.1 13.9 - - - +
233A VAL* 1.3 76.5 - - - +
235A LEU* 1.3 66.8 + - - +
236A SER* 4.1 3.1 - - - -
243A ILE* 4.7 17.7 - - + -
258A LEU* 4.0 14.4 - - + -
261A ILE* 3.6 31.2 - - + -
280A PHE* 5.1 5.6 - - + -
281A ILE 2.9 9.5 + - - +
282A ILE* 4.5 19.5 - - + +
283A GLN 3.0 27.8 + - - +
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Residues in contact with LEU 235 (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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167A ILE* 4.3 7.4 - - + -
168A ILE* 2.9 15.0 + - - +
169A ASN* 2.9 32.8 - - + +
170A ASN* 3.0 24.4 + - - +
179A ARG* 3.5 4.9 + - - +
182A THR* 3.9 6.1 - - - +
185A ASP* 4.3 1.8 - - + -
186A ALA* 4.2 15.0 - - - +
189A LEU* 4.3 3.6 - - + -
233A VAL* 3.7 19.1 - - + -
234A LEU* 1.3 82.8 - - - +
236A SER* 1.3 63.4 + - - +
283A GLN* 3.7 22.0 - - + -
341B ARG* 3.7 24.9 - - - +
350B ILE* 4.2 11.7 - - + -
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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