Contacts of the helix formed by residues 301 - 313 (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 GLY 301 (chain A).
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Specific contacts
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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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Residues in contact with GLU 302 (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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232A ARG* 3.2 56.0 + - - +
233A ASP* 5.6 1.2 - - - +
235A ARG* 6.3 1.8 - - - +
300A VAL 3.4 7.5 + - - +
301A GLY* 1.3 69.6 - - - -
303A GLU* 1.3 68.8 + - + +
305A ARG* 3.3 18.3 - - - +
306A ASN* 3.0 32.5 + - - +
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Residues in contact with GLU 303 (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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58A TYR* 3.6 26.1 + - + +
59A LYS* 5.5 7.7 - - + +
62A LYS* 5.6 3.5 + - - -
229A LYS* 5.2 6.7 - - - +
233A ASP* 4.1 16.8 - - - +
301A GLY* 5.4 0.7 - - - -
302A GLU* 1.3 76.2 - - + +
304A PHE* 1.3 70.0 + - + +
306A ASN* 3.1 7.4 + - - +
307A TYR* 2.9 27.2 + - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 4.5 15.9 - - + -
54A ILE* 4.0 32.1 - - + -
55A LEU* 4.0 27.4 - - + -
58A TYR* 5.2 3.6 - + - -
59A LYS* 5.4 7.0 - - + -
69A LEU* 4.9 13.5 - - + -
236A LEU* 5.5 4.5 - - + -
297A TYR* 3.4 59.2 - + + +
298A ALA* 4.6 4.5 - - - +
301A GLY* 4.1 6.7 - - - +
302A GLU 3.5 0.2 - - - -
303A GLU* 1.3 90.4 - - + +
305A ARG* 1.4 59.8 + - - +
307A TYR* 3.8 8.5 + - - +
308A LEU* 3.6 18.7 + - - +
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Residues in contact with ARG 305 (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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298A ALA* 3.6 22.8 + - - +
299A PHE 5.4 4.9 - - - +
301A GLY 3.2 17.8 + - - +
302A GLU* 3.3 24.4 + - - +
304A PHE* 1.4 76.2 - - - +
306A ASN* 1.3 72.1 + - - +
307A TYR 3.4 0.2 - - - -
308A LEU* 3.7 7.5 + - - +
309A LEU* 3.3 35.8 + - - +
144B PHE* 6.6 0.7 - - + -
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Residues in contact with ASN 306 (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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58A TYR* 5.7 0.9 - - - +
302A GLU* 3.0 26.8 + - - +
303A GLU* 3.1 8.8 + - - +
305A ARG* 1.3 86.1 + - - +
307A TYR* 1.4 63.4 + - - +
309A LEU* 3.4 26.5 + - - +
310A VAL* 3.5 18.7 + - - +
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Residues in contact with TYR 307 (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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54A ILE* 4.2 29.6 - - + -
58A TYR* 3.5 60.1 + + + +
303A GLU 2.9 16.3 + - - +
304A PHE* 4.0 6.7 - - - +
305A ARG 3.4 0.2 - - - -
306A ASN* 1.4 75.1 - - - +
308A LEU* 1.4 60.2 + - - +
310A VAL* 3.2 8.8 + - + +
311A PHE* 2.9 52.6 + + + +
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Residues in contact with LEU 308 (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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304A PHE 3.6 10.8 + - - +
305A ARG* 3.8 11.4 - - - +
306A ASN 3.4 0.2 - - - -
307A TYR* 1.4 80.6 - - + +
309A LEU* 1.4 60.5 + - - +
311A PHE* 3.9 10.9 - - + +
312A PHE* 3.2 38.6 + - + +
143B THR* 3.9 9.1 - - + +
147B VAL* 5.7 8.5 - - + -
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Residues in contact with LEU 309 (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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305A ARG* 3.3 30.0 + - - +
306A ASN* 3.4 26.0 + - - +
307A TYR 3.3 0.8 - - - -
308A LEU* 1.4 76.4 - - - +
310A VAL* 1.4 62.1 + - + +
312A PHE* 4.4 0.9 - - - +
313A GLN* 3.4 24.4 + - - +
141B THR* 3.4 24.5 - - + +
143B THR* 3.0 33.0 - - + +
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Residues in contact with VAL 310 (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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306A ASN* 3.6 15.7 - - - +
307A TYR* 3.2 10.6 + - + +
309A LEU* 1.4 76.0 - - + +
311A PHE* 1.4 63.0 + - - +
312A PHE 3.3 0.4 + - - -
313A GLN* 2.9 27.8 - - - +
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Residues in contact with PHE 311 (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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307A TYR* 2.9 42.1 + + + +
308A LEU* 3.9 10.1 - - + +
310A VAL* 1.4 76.7 - - - +
312A PHE* 1.4 81.8 + + - +
313A GLN 5.0 0.5 - - - +
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Residues in contact with PHE 312 (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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308A LEU* 3.2 29.4 + - + +
309A LEU 4.4 0.7 - - - +
311A PHE* 1.4 96.0 - + - +
313A GLN* 1.4 62.8 + - - +
142B VAL* 6.3 2.9 - - + -
143B THR* 3.7 26.2 - - + -
146B VAL* 4.3 28.0 - - + -
147B VAL* 6.3 3.6 - - + -
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Residues in contact with GLN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU 3.4 18.5 + - - +
310A VAL* 2.9 20.7 + - - +
311A PHE 5.1 0.4 - - - -
312A PHE* 1.4 82.1 - - - +
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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