Contacts of the helix formed by residues 292 - 301 (chain A) in PDB entry 4MBS
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A VAL* 3.7 29.6 - - + -
247A PHE* 3.5 34.8 - - + -
288A THR 3.9 2.7 - - - +
289A HIS* 3.1 23.7 + - + +
290A CYS 3.7 0.2 - - - -
291A CYS* 1.4 77.1 - - - +
293A ASN* 1.4 68.3 + - - +
294A PRO* 3.4 2.5 - - - -
295A ILE* 3.0 28.2 + - + +
296A ILE* 3.3 15.4 + - + +
1107A OLC 3.9 38.4 - - + -
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Residues in contact with ASN 293 (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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48A ASN* 5.6 0.7 - - - +
72A LEU* 3.6 29.3 - - - +
76A ASP* 3.5 22.3 + - - +
119A ILE* 5.0 0.8 - - - +
240A ILE* 4.1 16.0 - - - +
289A HIS* 3.9 26.8 + - - -
292A ILE* 1.4 73.0 - - - +
294A PRO* 1.4 70.0 - - + +
296A ILE* 2.9 34.7 + - + +
297A TYR* 3.1 34.2 + - + +
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Residues in contact with PRO 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.5 43.5 - - - +
48A ASN* 3.8 18.8 - - - +
51A VAL* 4.0 10.0 - - + +
76A ASP* 5.5 0.4 - - - +
290A CYS 4.9 0.7 - - - +
291A CYS* 3.7 15.9 - - - +
292A ILE 3.5 4.3 - - - -
293A ASN* 1.4 91.2 - - + +
295A ILE* 1.4 61.0 + - + +
297A TYR* 3.3 15.6 + - + +
298A ALA* 3.2 21.8 + - - +
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Residues in contact with ILE 295 (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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43A PHE* 3.4 40.6 - - + -
291A CYS 3.7 11.7 - - - +
292A ILE* 3.0 21.7 + - + +
294A PRO* 1.4 73.0 - - + +
296A ILE* 1.3 66.9 + - + +
298A ALA* 3.2 7.5 + - - +
299A PHE* 3.2 50.5 + - + -
1107A OLC 3.9 23.1 - - + -
151B ILE* 4.3 16.8 - - + -
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Residues in contact with ILE 296 (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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236A LEU* 3.8 20.9 - - + -
239A THR* 3.8 14.8 - - + -
240A ILE* 4.2 18.4 - - + -
243A VAL* 3.9 36.1 - - + -
292A ILE* 3.8 13.7 - - + +
293A ASN* 2.9 33.2 + - - +
295A ILE* 1.3 76.4 - - + +
297A TYR* 1.4 56.7 + - + +
299A PHE* 3.1 2.6 + - - -
300A VAL* 2.7 49.5 + - + +
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 6.2 0.2 - - - -
51A VAL* 3.6 44.9 - - + -
69A LEU* 3.5 33.7 + - + +
72A LEU* 3.8 20.1 - - - +
73A ALA* 5.5 1.4 + - + -
236A LEU* 3.7 19.3 - - + -
240A ILE* 3.4 25.3 - - + +
293A ASN* 3.1 34.6 + - + +
294A PRO* 3.7 4.9 - - + +
296A ILE* 1.4 75.6 - - + +
298A ALA* 1.3 58.8 + - - +
301A GLY* 3.1 32.8 + - - +
304A PHE* 3.4 37.5 - + + +
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Residues in contact with ALA 298 (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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294A PRO 3.2 10.6 + - - +
295A ILE* 3.4 13.0 - - - +
296A ILE 3.2 0.2 - - - -
297A TYR* 1.3 77.9 - - - +
299A PHE* 1.4 65.8 + - + +
304A PHE* 4.8 7.0 - - - -
305A ARG* 3.6 24.6 - - - +
144B PHE* 5.8 1.7 - - - -
147B VAL* 4.4 19.3 - - + +
151B ILE* 5.8 0.9 - - + -
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Residues in contact with PHE 299 (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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235A ARG* 5.1 5.2 + - - -
295A ILE* 3.2 34.8 + - + +
296A ILE* 3.1 3.3 + - - +
298A ALA* 1.4 81.0 - - + +
300A VAL* 1.3 67.3 + - + +
301A GLY 3.7 2.1 - - - +
305A ARG* 5.4 3.8 - - - +
144B PHE* 3.5 38.0 - + - -
147B VAL* 3.6 24.2 - - + -
148B THR* 3.6 23.8 - - + -
151B ILE* 3.4 31.2 - - + -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 4.0 40.6 + - + +
236A LEU* 4.0 21.3 + - + +
239A THR* 3.7 29.4 - - + +
296A ILE* 2.7 40.4 + - + +
299A PHE* 1.3 79.3 - - + +
301A GLY* 1.3 61.3 + - - +
302A GLU* 3.4 8.3 + - - +
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Residues in contact with GLY 301 (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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236A LEU* 4.0 22.2 - - - +
296A ILE 3.7 2.0 + - - -
297A TYR* 3.1 25.1 + - - +
298A ALA 4.6 0.7 - - - +
300A VAL* 1.3 76.0 - - - +
302A GLU* 1.3 63.8 + - - -
303A GLU* 3.5 3.4 - - - -
304A PHE* 4.2 7.2 - - - -
305A ARG* 3.2 21.4 + - - +
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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