Contacts of the strand formed by residues 221 - 228 (chain A) in PDB entry 3MIB
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 VAL 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A THR* 4.2 9.6 - - + -
213A VAL 3.7 18.4 - - - +
214A ILE* 3.7 36.6 - - + -
215A PRO* 3.8 9.2 - - + -
218A GLU* 3.7 22.2 - - + +
220A VAL* 1.3 78.3 - - - +
222A ASN* 1.3 73.9 + - - +
293A CYS 3.8 0.5 - - - +
294A VAL* 3.7 1.0 - - - -
295A PHE* 2.8 42.4 + - + +
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Residues in contact with ASN 222 (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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212A THR* 4.8 1.9 - - - +
220A VAL* 3.8 12.4 + - - +
221A VAL* 1.3 82.3 - - - +
223A ALA* 1.3 60.7 + - - +
224A ASP* 3.8 7.7 + - - +
292A ARG* 3.5 41.4 + - - +
293A CYS 3.5 1.1 - - - -
294A VAL* 3.5 36.2 - - - +
351A ASN* 4.3 4.0 + - - +
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Residues in contact with ALA 223 (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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209A SER* 3.4 16.4 - - - +
212A THR* 3.4 27.8 - - + +
221A VAL 4.0 0.8 + - - -
222A ASN* 1.3 71.4 - - - +
224A ASP* 1.3 62.8 + - - +
291A ALA 3.7 0.9 - - - +
292A ARG* 3.3 3.6 - - - -
293A CYS 3.0 29.2 + - - +
295A PHE* 3.9 22.7 - - + -
315A CYS* 4.1 6.4 - - - -
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Residues in contact with ASP 224 (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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209A SER* 5.1 1.2 + - - -
222A ASN* 3.8 8.1 - - - +
223A ALA* 1.3 75.4 - - - +
225A ILE* 1.3 65.9 + - - +
291A ALA 3.4 2.9 - - - -
292A ARG* 2.8 46.0 + - - +
336A LYS 4.5 0.5 - - - +
337A ASN* 3.7 33.5 + - - +
340A PRO 5.1 1.4 - - - +
343A PHE* 3.6 30.3 - - + +
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Residues in contact with ILE 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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207A MET* 3.5 21.4 - - + +
208A MET* 3.7 14.6 - - - +
209A SER* 3.5 39.3 - - - +
223A ALA 4.5 0.7 - - - +
224A ASP* 1.3 80.0 - - - +
226A SER* 1.3 62.3 + - - +
290A ALA* 3.2 3.3 - - - -
291A ALA* 2.7 45.6 + - + +
315A CYS* 3.6 17.5 - - - +
317A LEU* 5.7 1.1 - - + +
334A CYS* 3.4 31.6 - - - +
335A THR 4.7 0.2 - - - -
336A LYS 3.3 17.0 - - - +
337A ASN* 4.3 0.4 - - - -
343A PHE* 3.3 3.0 - - - -
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Residues in contact with SER 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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225A ILE* 1.3 76.5 - - - +
227A CYS* 1.3 65.4 + - - +
288A ILE* 4.3 4.5 - - - -
289A LEU 3.1 10.5 - - - -
334A CYS* 3.4 3.8 - - - -
336A LYS 2.8 16.1 + - - +
337A ASN* 2.8 23.1 + - - +
338A VAL* 2.9 30.4 + - - +
339A ALA* 3.0 11.2 + - - -
342A MET* 4.2 11.7 - - - -
343A PHE* 3.7 13.2 - - - -
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Residues in contact with CYS 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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205A TYR* 3.3 17.8 + - - +
226A SER* 1.3 74.3 - - - +
228A GLN* 1.3 63.4 + - - +
229A TYR 3.7 0.3 + - - -
288A ILE* 3.4 4.0 - - - -
289A LEU* 2.8 34.4 + - - +
334A CYS* 2.0 49.9 - - - -
336A LYS* 4.1 23.8 - - - -
338A VAL* 3.8 9.9 - - + -
362A GOL 3.8 13.9 - - - +
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Residues in contact with GLN 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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227A CYS* 1.3 72.9 - - - +
229A TYR* 1.3 69.9 + - - +
230A LYS* 3.2 36.2 + - + +
286A GLY* 3.8 22.9 + - - +
287A ASP 3.5 10.3 - - - +
288A ILE* 4.4 15.3 - - + +
338A VAL* 4.0 12.5 - - + +
362A GOL 2.9 19.9 + - - -
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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