Contacts of the strand formed by residues 227 - 232 (chain A) in PDB entry 2PHA
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 ILE 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A HIS* 4.6 0.7 - - - -
119A GLY 3.4 3.8 - - - +
121A ILE* 3.2 31.0 - - + -
216A LEU* 4.3 15.0 - - + -
219A LEU* 5.4 3.6 - - + -
220A LEU* 3.9 27.8 - - + -
225A ARG* 3.8 10.3 - - - +
226A PRO* 1.3 75.4 - - - +
228A HIS* 1.3 66.3 + - - +
229A LEU* 4.4 2.0 - - + +
264A ILE* 4.5 18.6 - - + -
267A THR* 3.9 21.5 - - + +
269A LEU* 2.7 19.7 + - + +
270A LEU* 3.3 7.1 - - + +
271A SER* 2.9 29.8 + - - -
272A GLY 3.2 3.1 + - - -
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Residues in contact with HIS 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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94A SER* 5.9 0.7 - - - -
107A SER* 3.3 21.3 - - - -
108A ILE* 3.5 40.5 - - + +
111A HIS* 3.2 24.8 + - - +
118A LEU* 3.5 24.2 - - + +
119A GLY 2.7 8.7 + - - -
120A VAL* 3.2 9.2 - - + +
121A ILE 2.9 24.9 + - - -
226A PRO 4.2 0.2 + - - -
227A ILE* 1.3 73.6 - - - +
229A LEU* 1.3 60.6 + - - +
230A SER* 3.9 10.2 - - - -
272A GLY* 3.2 15.6 - - - -
273A LEU 4.5 0.2 - - - -
274A ASP* 2.6 30.4 + - - -
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Residues in contact with LEU 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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121A ILE* 3.3 31.0 - - + +
123A VAL* 3.7 26.5 - - + -
227A ILE* 4.0 2.1 - - + -
228A HIS* 1.3 72.8 - - - +
230A SER* 1.3 62.1 + - - +
231A PHE* 4.3 9.2 - - + -
260A ILE* 5.1 1.6 - - + -
261A THR* 3.6 30.5 - - + -
264A ILE* 4.3 18.4 - - + -
270A LEU* 4.1 8.7 - - + -
272A GLY 2.7 10.3 + - - +
273A LEU* 3.1 30.9 - - + +
274A ASP* 2.9 23.2 + - - +
303A CYS* 3.9 5.2 - - - -
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Residues in contact with SER 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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101A HIS* 2.5 36.3 + - - -
104A ALA* 4.1 2.0 - - - +
120A VAL* 4.8 0.4 - - - -
121A ILE 3.0 7.9 + - - -
122A TRP* 3.7 27.8 - - - -
123A VAL 3.1 25.6 + - - +
228A HIS* 3.8 9.7 + - - -
229A LEU* 1.3 71.9 - - - +
231A PHE* 1.3 57.8 + - - +
232A ASP 3.8 0.2 + - - -
274A ASP* 3.5 23.6 + - - +
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Residues in contact with PHE 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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101A HIS* 4.9 2.5 - - - -
123A VAL* 3.8 35.4 - - + -
229A LEU* 3.6 10.7 + - + -
230A SER* 1.3 71.0 - - - +
232A ASP* 1.3 74.3 + - - +
233A VAL* 3.7 7.7 + - + +
236A LEU* 3.8 29.2 - - + -
257A GLY* 4.4 6.1 - - - -
260A ILE* 4.7 3.1 - - + -
261A THR* 4.1 16.4 - - + -
273A LEU* 4.9 2.9 - - + -
274A ASP* 2.7 20.2 + - - +
275A ILE* 3.5 10.1 - - + -
276A MET* 3.0 26.0 + - - +
299A ILE* 3.2 50.7 - - + -
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Residues in contact with ASP 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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101A HIS* 3.8 8.3 - - + -
123A VAL 3.0 13.9 + - - +
124A ASP* 3.3 17.0 - - - +
230A SER 3.8 1.2 + - - -
231A PHE* 1.3 78.4 - - - +
233A VAL* 1.3 59.7 + - - +
234A ASP* 2.9 19.9 + - - +
235A GLY* 2.7 30.1 + - - -
276A MET 3.7 3.8 - - - -
277A GLU* 3.1 27.7 - - + +
323A MN 2.6 15.4 + - - -
324A MN 2.6 26.4 + - - +
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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