Contacts of the strand formed by residues 228 - 236 (chain A) in PDB entry 1MS4
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 CYS 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.0 2.7 + - - +
204A PHE* 3.5 17.5 + - - +
205A SER* 2.7 25.2 + - - +
224A SER* 3.2 26.9 - - - +
225A ALA* 3.3 16.2 + - - -
226A PHE 3.4 1.5 - - - -
227A GLY* 1.3 79.0 - - - +
229A SER* 1.3 55.6 + - - +
244A THR* 3.7 23.6 - - - +
245A ARG 3.3 5.2 - - - -
246A VAL* 4.2 4.3 - - - -
252A LEU* 3.8 26.7 - - - -
254A TYR* 3.8 2.7 - - - -
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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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121A THR* 6.4 0.9 - - - -
195A GLN* 3.2 16.8 - - - -
203A VAL* 4.4 15.9 - - - -
227A GLY 3.4 3.4 + - - -
228A CYS* 1.3 73.1 - - - +
230A GLU* 1.3 73.2 + - - +
231A PRO* 3.0 8.5 - - - +
244A THR* 3.9 0.7 - - - -
245A ARG* 2.7 55.6 + - - +
246A VAL* 5.5 0.3 - - - -
247A ASP* 5.6 2.8 + - - -
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Residues in contact with GLU 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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36A LEU* 5.4 0.5 - - - +
96A ASP* 4.5 9.4 - - - +
119A TYR* 4.5 12.1 + - - -
178A GLY* 3.6 22.0 - - - +
179A ALA* 5.3 2.2 - - + -
195A GLN* 2.9 32.2 + - - +
229A SER* 1.3 74.8 - - - +
231A PRO* 1.3 70.2 - - - +
232A VAL* 3.7 5.0 + - - +
243A ASN 4.3 1.4 - - - +
244A THR 4.8 0.2 - - - -
245A ARG* 2.8 42.8 + - + +
251A ARG* 4.8 1.9 + - - -
286A GLN* 3.3 31.5 + - - +
287A SER 5.4 0.9 + - - -
342A TYR* 3.3 18.3 + - - -
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Residues in contact with PRO 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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178A GLY* 3.4 21.0 - - - +
179A ALA 4.8 1.2 - - - +
193A PRO* 3.8 29.0 - - + +
194A VAL 3.6 25.8 - - - +
195A GLN* 4.0 10.1 - - + -
205A SER* 3.7 21.8 - - - +
229A SER 3.0 8.0 - - - +
230A GLU* 1.3 92.2 - - - +
232A VAL* 1.3 60.3 + - - +
242A ILE* 4.0 12.1 - - + -
243A ASN 3.6 7.2 - - - +
244A THR* 4.3 3.6 - - + -
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Residues in contact with VAL 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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178A GLY 5.7 0.9 - - - +
179A ALA 5.0 8.7 - - - +
181A VAL 4.2 19.5 - - - +
193A PRO* 4.2 2.7 - - - -
230A GLU 4.6 3.1 - - - +
231A PRO* 1.3 74.7 - - - +
233A ALA* 1.3 61.4 + - - +
242A ILE* 3.5 1.5 - - - -
243A ASN* 2.8 55.6 + - + +
251A ARG* 4.1 10.8 - - - +
287A SER* 3.5 30.5 - - - +
288A SER* 4.8 0.7 - - - -
289A PHE* 3.7 36.2 - - + +
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Residues in contact with ALA 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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181A VAL 4.6 8.1 + - - +
182A ALA* 4.9 2.3 - - - +
183A ILE* 3.9 21.1 - - + +
191A VAL* 5.7 2.5 - - + -
193A PRO* 3.7 24.6 - - + +
207A ILE* 5.3 3.4 - - + -
232A VAL* 1.3 77.2 - - - +
234A LEU* 1.3 64.8 + - - +
240A LEU* 5.1 7.9 - - + -
241A ILE 3.1 12.1 - - - +
242A ILE* 3.9 16.8 - - + -
289A PHE* 3.9 10.6 - - - +
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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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183A ILE* 3.9 14.6 - - + -
233A ALA* 1.3 74.6 - - - +
235A GLU* 1.3 76.1 + - - +
236A TRP* 3.7 16.6 - - + -
240A LEU* 3.5 6.6 - - - +
241A ILE* 2.9 35.3 + - + -
289A PHE* 3.5 36.3 - - + +
290A THR* 3.6 20.6 - - - +
291A ALA* 4.2 12.6 - - + +
300A MET* 3.4 37.7 - - + -
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Residues in contact with GLU 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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183A ILE* 3.7 17.3 - - + +
184A VAL 4.9 1.2 - - - +
185A ALA* 3.8 16.4 - - - +
186A SER* 3.0 41.8 + - - -
234A LEU* 1.3 77.4 - - - +
236A TRP* 1.3 64.6 + - - +
237A GLU 4.3 0.4 + - - -
238A GLY* 4.2 19.1 - - - +
239A LYS 3.5 18.5 - - - +
240A LEU* 4.3 9.4 - - + +
259A MET* 4.8 4.3 - - - +
291A ALA* 3.9 14.7 - - - +
298A ARG* 5.0 5.0 + - - -
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Residues in contact with TRP 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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234A LEU* 3.7 3.8 - - + +
235A GLU* 1.3 74.7 - - - +
237A GLU* 1.3 102.6 + - + +
238A GLY 3.2 1.3 - - - -
239A LYS* 2.9 34.1 + - - +
241A ILE* 3.5 27.3 - - + +
255A GLU* 5.6 1.3 - - - -
291A ALA* 4.5 8.3 - - + -
298A ARG* 3.4 48.5 - - + -
299A VAL* 3.9 9.9 - - - -
300A MET* 3.7 36.6 - - + -
323A ASP* 3.5 26.7 - - + -
324A ASN* 3.6 24.5 + - + +
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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