Contacts of the strand formed by residues 234 - 241 (chain A) in PDB entry 1MF7
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 PHE 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU* 3.7 33.0 - - + -
132A ASP 3.0 21.6 + - - -
133A SER* 3.8 18.8 - - - +
134A ASP* 2.8 28.4 + - - +
232A ASN 4.0 0.4 + - - -
233A ALA* 1.4 75.4 - - - +
235A LYS* 1.3 59.8 + - - +
236A ILE* 4.0 12.3 - - + -
265A ILE* 4.3 10.8 - - + -
319A ILE* 3.6 25.4 - - + -
320A GLY* 3.7 28.0 - - - -
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Residues in contact with LYS 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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134A ASP* 3.7 7.2 - - + +
223A PHE* 3.7 43.3 + - + +
230A ARG 5.5 7.2 - - - +
233A ALA 3.9 9.4 - - - +
234A PHE* 1.3 76.1 - - - +
236A ILE* 1.3 63.1 + - - +
262A GLU* 2.9 48.4 + - - +
263A GLY 3.5 13.8 + - - +
264A VAL* 4.1 11.0 - - + -
265A ILE* 2.8 27.7 + - - +
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Residues in contact with ILE 236 (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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133A SER* 4.0 28.9 - - - +
134A ASP 3.0 8.9 + - - +
135A ILE* 3.4 23.0 - - + -
136A ALA 2.7 31.2 + - - -
223A PHE* 3.5 7.3 - - - -
234A PHE* 4.0 12.1 - - + -
235A LYS* 1.3 78.2 - - - +
237A LEU* 1.3 61.2 + - - +
238A VAL* 4.6 0.4 - - + -
264A VAL* 4.6 0.2 - - - -
265A ILE* 3.4 13.7 - - + +
267A TYR* 4.0 23.6 - - + -
316A ILE* 4.3 17.0 - - + +
319A ILE* 3.3 31.0 - - + -
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Residues in contact with LEU 237 (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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136A ALA* 3.3 13.5 - - + +
138A LEU* 3.8 27.1 - - + +
215A ILE* 4.5 18.6 - - + -
218A VAL* 3.9 32.3 - - + -
219A VAL* 5.8 1.1 - - + -
223A PHE* 4.7 0.2 - - + -
236A ILE* 1.3 75.3 - - - +
238A VAL* 1.3 67.3 + - - +
239A VAL* 3.7 22.0 - - + -
264A VAL* 3.7 18.8 - - + +
265A ILE 2.8 10.6 + - - +
266A ARG* 3.4 17.0 - - + -
267A TYR* 2.8 28.4 + - - +
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Residues in contact with VAL 238 (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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135A ILE* 4.6 1.1 - - + -
136A ALA 2.8 10.9 + - - +
137A PHE* 3.3 42.9 - - + +
138A LEU 2.9 26.2 + - - +
236A ILE* 4.6 4.7 - - + -
237A LEU* 1.3 74.6 - - - +
239A VAL* 1.3 64.6 + - - +
240A ILE* 4.4 2.6 - - + +
267A TYR* 3.4 16.8 - - + +
269A ILE* 3.8 28.3 - - + -
312A LEU* 4.3 7.4 - - + -
316A ILE* 4.0 27.4 - - + -
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Residues in contact with VAL 239 (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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138A LEU* 3.3 25.8 - - + +
176A TYR* 4.8 2.0 - - - +
211A THR* 4.4 19.3 - - + -
215A ILE* 4.6 2.9 - - + -
237A LEU* 3.7 31.4 - - + -
238A VAL* 1.3 72.2 - - - +
240A ILE* 1.3 70.5 + - - +
241A THR* 4.6 3.8 - - - -
266A ARG* 5.5 1.8 - - + -
267A TYR 2.8 16.5 + - - +
268A VAL* 3.4 15.9 - - + -
269A ILE* 2.8 28.2 + - - +
287A ILE* 4.1 16.2 - - + -
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Residues in contact with ILE 240 (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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137A PHE* 4.4 4.7 - - + -
138A LEU 2.9 10.0 + - - +
139A ILE* 3.9 22.7 - - + -
140A ASP* 3.0 26.2 + - - +
153A MET* 3.8 27.4 - - + +
156A PHE* 3.9 31.2 - - + -
157A VAL* 3.9 10.8 - - + -
176A TYR* 4.4 1.4 - - - -
238A VAL* 4.4 6.3 - - + +
239A VAL* 1.3 78.2 - - - +
241A THR* 1.3 62.7 + - - +
269A ILE* 3.5 20.0 - - + +
271A VAL* 3.9 25.1 - - + -
302A PHE* 5.0 1.8 - - + -
305A LEU* 4.9 3.4 - - + -
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Residues in contact with THR 241 (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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140A ASP* 3.8 5.0 + - - -
176A TYR* 3.6 19.2 + - - -
211A THR* 4.5 3.7 + - - -
239A VAL* 4.6 4.3 - - + -
240A ILE* 1.3 75.0 - - - +
242A ASP* 1.3 60.9 + - - +
243A GLY 3.0 22.4 + - - +
268A VAL* 4.1 11.2 - - + -
269A ILE 3.0 11.1 + - - +
270A GLY* 3.5 0.5 - - - -
271A VAL* 2.9 29.1 + - - +
275A PHE* 3.6 17.0 - - + -
283A GLU* 6.1 0.4 - - - +
284A LEU* 4.0 15.3 - - + -
287A ILE* 4.7 8.5 - - + -
302A PHE* 5.8 0.2 - - - -
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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