Contacts of the strand formed by residues 355 - 359 (chain A) in PDB entry 3BMW
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 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.5 44.4 - - + +
13A SER* 3.9 0.9 - - - +
15A ASP 4.8 1.8 - - - +
17A ILE* 3.6 30.3 - - + -
254A PHE* 4.1 16.2 - - + -
319A ASN 3.7 12.3 - - - +
320A ASP* 4.2 4.5 - - - +
321A MET 2.8 10.5 + - - +
322A VAL* 3.3 15.0 - - + +
323A THR* 2.9 23.6 + - - -
353A ARG 4.3 1.2 + - - -
354A GLY* 1.3 78.4 - - - +
356A PRO* 1.3 66.0 - - + +
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Residues in contact with PRO 356 (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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15A ASP 3.4 20.9 - - - +
16A VAL* 4.5 4.9 - - + -
17A ILE* 2.8 28.9 + - - +
323A THR* 3.4 10.1 - - - +
349A THR* 3.7 25.6 - - + +
350A LEU* 4.2 18.4 - - + -
352A SER 5.0 0.7 - - - +
355A VAL* 1.3 86.3 - - - +
357A ALA* 1.3 58.7 + - - +
358A ILE* 5.5 1.3 - - + -
398A ARG* 3.5 39.7 - - - +
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Residues in contact with ALA 357 (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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17A ILE* 3.3 22.7 - - + -
19A GLN* 5.4 1.6 - - + -
75A TRP* 4.7 15.7 - - + -
282A LEU* 5.6 0.2 - - + -
322A VAL* 4.1 15.7 - - + -
323A THR 2.8 22.6 + - - +
324A PHE* 3.5 23.1 - - + +
325A ILE* 4.6 1.7 + - - +
349A THR* 5.0 2.4 - - - +
356A PRO* 1.3 74.1 - - - +
358A ILE* 1.3 65.0 + - - +
359A TYR 4.2 0.6 + - - -
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Residues in contact with ILE 358 (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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16A VAL* 3.9 17.5 - - + -
17A ILE 2.8 13.1 + - - +
18A TYR* 3.4 19.1 - - + -
19A GLN* 2.7 31.0 + - - -
69A MET* 5.8 0.2 - - - -
71A VAL* 6.2 0.9 - - + -
346A LEU* 4.1 19.7 - - + -
349A THR* 6.1 2.2 - - + -
350A LEU* 4.0 12.1 - - + -
356A PRO* 5.4 1.8 - - + -
357A ALA* 1.3 78.9 - - - +
359A TYR* 1.3 70.3 + - - +
360A TYR 3.5 0.3 + - - -
362A THR* 3.9 16.8 - - - +
363A GLU* 4.8 1.3 - - - +
391A ILE* 3.8 46.4 - - + -
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Residues in contact with TYR 359 (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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19A GLN* 3.4 27.5 + - - +
21A VAL* 3.8 11.7 - - + +
326A ASP* 3.1 38.8 + - - +
327A ASN* 3.7 17.0 - - - -
328A HIS* 3.3 30.3 - - + +
332A ARG* 3.3 36.8 - - - -
357A ALA 4.2 0.8 + - - -
358A ILE* 1.3 75.0 - - - +
360A TYR* 1.3 95.6 + + - +
361A GLY 3.3 0.2 + - - -
362A THR* 2.6 28.4 + - - +
374A ASN* 2.8 22.1 + - + -
375A ARG* 3.5 8.7 - - - +
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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